Starting phenix.real_space_refine
on Wed Mar 12 07:48:17 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8hc6_34653/03_2025/8hc6_34653.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8hc6_34653/03_2025/8hc6_34653.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.69
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8hc6_34653/03_2025/8hc6_34653.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8hc6_34653/03_2025/8hc6_34653.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8hc6_34653/03_2025/8hc6_34653.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8hc6_34653/03_2025/8hc6_34653.cif"
  }
  resolution = 4.69
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.058
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      27      5.16       5
     C    4704      2.51       5
     N    1226      2.21       5
     O    1420      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 7377
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "C"
      Number of atoms: 2134
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 267, 2134
          Classifications: {'peptide': 267}
          Link IDs: {'PTRANS': 15, 'TRANS': 251}
    Chain: "H"
      Number of atoms: 1588
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 214, 1588
          Classifications: {'peptide': 214}
          Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 202}
          Chain breaks: 1
    Chain: "L"
      Number of atoms: 1628
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 215, 1628
          Classifications: {'peptide': 215}
          Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 203}
    Chain: "B"
      Number of atoms: 1929
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 237, 1929
          Classifications: {'peptide': 237}
          Link IDs: {'PTRANS': 13, 'TRANS': 223}
          Chain breaks: 5
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "B"
      Number of atoms: 70
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 70
          Unusual residues: {'NAG': 5}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 5
  Time building chain proxies: 4.79, per 1000 atoms: 0.65
  Number of scatterers: 7377
  At special positions: 0
  Unit cell: (112.2, 84.15, 158.4, 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      27     16.00
     O    1420      8.00
     N    1226      7.00
     C    4704      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=10, symmetry=0
    Simple disulfide: pdb=" SG  CYS C 336 " - pdb=" SG  CYS C 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 379 " - pdb=" SG  CYS C 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 391 " - pdb=" SG  CYS C 525 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C 480 " - pdb=" SG  CYS C 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  95 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 143 " - pdb=" SG  CYS H 199 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  88 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L 135 " - pdb=" SG  CYS L 195 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  15 " - pdb=" SG  CYS B 136 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 131 " - pdb=" SG  CYS B 166 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG B1301 " - " ASN B  61 "
      " NAG B1302 " - " ASN B 122 "
      " NAG B1303 " - " ASN B 165 "
      " NAG B1304 " - " ASN B 234 "
      " NAG B1305 " - " ASN B 282 "
      " NAG C 601 " - " ASN C 331 "
      " NAG C 602 " - " ASN C 343 "
  Time building additional restraints: 1.66
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1740

  Finding SS restraints...
    Secondary structure from input PDB file:
      7 helices and 20 sheets defined
      4.3% alpha, 27.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.88
  Creating SS restraints...
    Processing helix  chain 'C' and resid 337 through 343
      removed outlier: 3.666A  pdb=" N   VAL C 341 " --> pdb=" O   PRO C 337 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 365 through 372
      removed outlier: 3.769A  pdb=" N   LEU C 371 " --> pdb=" O   VAL C 367 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 404 through 408
    Processing helix  chain 'C' and resid 416 through 422
    Processing helix  chain 'H' and resid 159 through 161
      No H-bonds generated for 'chain 'H' and resid 159 through 161'
    Processing helix  chain 'H' and resid 188 through 192
      removed outlier: 3.531A  pdb=" N   SER H 191 " --> pdb=" O   PRO H 188 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   LEU H 192 " --> pdb=" O   SER H 189 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 188 through 192'
    Processing helix  chain 'L' and resid 184 through 188
      removed outlier: 4.126A  pdb=" N   GLU L 188 " --> pdb=" O   LYS L 184 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'L' and resid 184 through 188'
    Processing sheet with id=AA1, first strand: chain 'C' and resid 356 through 358
      removed outlier: 3.619A  pdb=" N   ASN C 394 " --> pdb=" O   GLU C 516 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   GLU C 516 " --> pdb=" O   ASN C 394 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   VAL C 510 " --> pdb=" O   PHE C 400 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   CYS C 432 " --> pdb=" O   LEU C 513 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 452 through 454
    Processing sheet with id=AA3, first strand: chain 'C' and resid 473 through 474
    Processing sheet with id=AA4, first strand: chain 'C' and resid 541 through 543
      removed outlier: 3.667A  pdb=" N   GLY C 548 " --> pdb=" O   PHE C 541 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'H' and resid 4 through 7
      removed outlier: 3.538A  pdb=" N   SER H   7 " --> pdb=" O   SER H  21 " (cutoff:3.500A)
      removed outlier: 3.991A  pdb=" N   LEU H  20 " --> pdb=" O   LEU H  80 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   THR H  77 " --> pdb=" O   ASN H  72 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   ASN H  72 " --> pdb=" O   THR H  77 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'H' and resid 11 through 12
    Processing sheet with id=AA7, first strand: chain 'H' and resid 57 through 59
      removed outlier: 4.979A  pdb=" N   TRP H  47 " --> pdb=" O   ARG H  38 " (cutoff:3.500A)
      removed outlier: 6.242A  pdb=" N   ARG H  38 " --> pdb=" O   TRP H  47 " (cutoff:3.500A)
      removed outlier: 4.298A  pdb=" N   SER H  49 " --> pdb=" O   TRP H  36 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'H' and resid 57 through 59
      removed outlier: 4.979A  pdb=" N   TRP H  47 " --> pdb=" O   ARG H  38 " (cutoff:3.500A)
      removed outlier: 6.242A  pdb=" N   ARG H  38 " --> pdb=" O   TRP H  47 " (cutoff:3.500A)
      removed outlier: 4.298A  pdb=" N   SER H  49 " --> pdb=" O   TRP H  36 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'H' and resid 123 through 126
      removed outlier: 3.538A  pdb=" N   LYS H 146 " --> pdb=" O   SER H 123 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'H' and resid 123 through 126
      removed outlier: 3.538A  pdb=" N   LYS H 146 " --> pdb=" O   SER H 123 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'H' and resid 154 through 157
      removed outlier: 3.755A  pdb=" N   THR H 154 " --> pdb=" O   ASN H 202 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   ASN H 202 " --> pdb=" O   THR H 154 " (cutoff:3.500A)
      removed outlier: 4.249A  pdb=" N   VAL H 201 " --> pdb=" O   VAL H 210 " (cutoff:3.500A)
      removed outlier: 4.616A  pdb=" N   VAL H 210 " --> pdb=" O   VAL H 201 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'L' and resid 4 through 5
      removed outlier: 3.790A  pdb=" N   CYS L  23 " --> pdb=" O   PHE L  71 " (cutoff:3.500A)
      removed outlier: 4.230A  pdb=" N   PHE L  71 " --> pdb=" O   CYS L  23 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'L' and resid 10 through 12
      removed outlier: 6.548A  pdb=" N   VAL L  11 " --> pdb=" O   GLU L 106 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB4
    Processing sheet with id=AB5, first strand: chain 'L' and resid 53 through 54
      removed outlier: 3.949A  pdb=" N   TYR L  49 " --> pdb=" O   THR L  53 " (cutoff:3.500A)
      removed outlier: 6.828A  pdb=" N   TRP L  35 " --> pdb=" O   LEU L  47 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   GLN L  38 " --> pdb=" O   SER L  85 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   SER L  85 " --> pdb=" O   GLN L  38 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   GLN L  90 " --> pdb=" O   THR L  98 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'L' and resid 117 through 119
      removed outlier: 3.761A  pdb=" N   PHE L 117 " --> pdb=" O   LEU L 136 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   LEU L 136 " --> pdb=" O   PHE L 117 " (cutoff:3.500A)
      removed outlier: 4.370A  pdb=" N   VAL L 134 " --> pdb=" O   PHE L 119 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   ALA L 131 " --> pdb=" O   LEU L 182 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   VAL L 133 " --> pdb=" O   LEU L 180 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   CYS L 135 " --> pdb=" O   SER L 178 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   SER L 178 " --> pdb=" O   CYS L 135 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   THR L 179 " --> pdb=" O   GLN L 161 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   GLN L 161 " --> pdb=" O   THR L 179 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'L' and resid 149 through 151
      removed outlier: 4.273A  pdb=" N   TRP L 149 " --> pdb=" O   GLN L 156 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'L' and resid 192 through 193
      removed outlier: 3.622A  pdb=" N   PHE L 210 " --> pdb=" O   TYR L 193 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'B' and resid 27 through 30
      removed outlier: 3.628A  pdb=" N   ALA B  27 " --> pdb=" O   TRP B  64 " (cutoff:3.500A)
      removed outlier: 8.073A  pdb=" N   ASN B  61 " --> pdb=" O   TYR B 269 " (cutoff:3.500A)
      removed outlier: 6.009A  pdb=" N   TYR B 269 " --> pdb=" O   ASN B  61 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   VAL B 267 " --> pdb=" O   THR B  63 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   PHE B  65 " --> pdb=" O   TYR B 265 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   ALA B 264 " --> pdb=" O   ILE B  95 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   VAL B  90 " --> pdb=" O   PHE B 194 " (cutoff:3.500A)
      removed outlier: 3.962A  pdb=" N   VAL B 227 " --> pdb=" O   ILE B 203 " (cutoff:3.500A)
      removed outlier: 6.713A  pdb=" N   SER B 205 " --> pdb=" O   PRO B 225 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'B' and resid 48 through 52
      removed outlier: 3.843A  pdb=" N   HIS B  49 " --> pdb=" O   LEU B 277 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   LEU B 277 " --> pdb=" O   HIS B  49 " (cutoff:3.500A)
      removed outlier: 4.026A  pdb=" N   THR B  51 " --> pdb=" O   PHE B 275 " (cutoff:3.500A)
      removed outlier: 4.458A  pdb=" N   PHE B 275 " --> pdb=" O   THR B  51 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AC1
    Processing sheet with id=AC2, first strand: chain 'B' and resid 140 through 141
      removed outlier: 4.519A  pdb=" N   GLY B 103 " --> pdb=" O   LEU B 241 " (cutoff:3.500A)
      removed outlier: 6.578A  pdb=" N   ALA B 243 " --> pdb=" O   ILE B 101 " (cutoff:3.500A)
      removed outlier: 6.011A  pdb=" N   ILE B 101 " --> pdb=" O   ALA B 243 " (cutoff:3.500A)
      removed outlier: 5.647A  pdb=" N   ARG B 102 " --> pdb=" O   ASN B 121 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   ASN B 121 " --> pdb=" O   ARG B 102 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   TRP B 104 " --> pdb=" O   ILE B 119 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   LEU B 118 " --> pdb=" O   LYS B 129 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   LYS B 129 " --> pdb=" O   LEU B 118 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   VAL B 120 " --> pdb=" O   VAL B 127 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   VAL B 127 " --> pdb=" O   VAL B 120 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   VAL B 126 " --> pdb=" O   SER B 172 " (cutoff:3.500A)
      removed outlier: 4.095A  pdb=" N   VAL B 130 " --> pdb=" O   PHE B 168 " (cutoff:3.500A)
      removed outlier: 5.663A  pdb=" N   PHE B 168 " --> pdb=" O   VAL B 130 " (cutoff:3.500A)

    147 hydrogen bonds defined for protein.
    375 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.21

  Time building geometry restraints manager: 2.01 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 2336
        1.35 -     1.46: 1912
        1.46 -     1.58: 3276
        1.58 -     1.70: 0
        1.70 -     1.82: 31
  Bond restraints: 7555
  Sorted by residual:
  bond pdb=" C1  NAG B1303 "
       pdb=" O5  NAG B1303 "
    ideal  model  delta    sigma   weight residual
    1.406  1.449 -0.043 2.00e-02 2.50e+03 4.60e+00
  bond pdb=" C1  NAG B1305 "
       pdb=" O5  NAG B1305 "
    ideal  model  delta    sigma   weight residual
    1.406  1.440 -0.034 2.00e-02 2.50e+03 2.93e+00
  bond pdb=" C1  NAG B1304 "
       pdb=" O5  NAG B1304 "
    ideal  model  delta    sigma   weight residual
    1.406  1.439 -0.033 2.00e-02 2.50e+03 2.78e+00
  bond pdb=" C1  NAG C 601 "
       pdb=" O5  NAG C 601 "
    ideal  model  delta    sigma   weight residual
    1.406  1.438 -0.032 2.00e-02 2.50e+03 2.53e+00
  bond pdb=" C1  NAG C 602 "
       pdb=" O5  NAG C 602 "
    ideal  model  delta    sigma   weight residual
    1.406  1.438 -0.032 2.00e-02 2.50e+03 2.50e+00
  ... (remaining 7550 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.40: 9927
        1.40 -     2.80: 282
        2.80 -     4.20: 47
        4.20 -     5.60: 10
        5.60 -     7.00: 6
  Bond angle restraints: 10272
  Sorted by residual:
  angle pdb=" C   ARG L 109 "
        pdb=" N   THR L 110 "
        pdb=" CA  THR L 110 "
      ideal   model   delta    sigma   weight residual
     121.54  128.05   -6.51 1.91e+00 2.74e-01 1.16e+01
  angle pdb=" C   SER H 206 "
        pdb=" N   ASN H 207 "
        pdb=" CA  ASN H 207 "
      ideal   model   delta    sigma   weight residual
     121.54  127.10   -5.56 1.91e+00 2.74e-01 8.49e+00
  angle pdb=" N   VAL B 159 "
        pdb=" CA  VAL B 159 "
        pdb=" C   VAL B 159 "
      ideal   model   delta    sigma   weight residual
     113.53  110.68    2.85 9.80e-01 1.04e+00 8.47e+00
  angle pdb=" C   GLY H 100 "
        pdb=" N   ASP H 101 "
        pdb=" CA  ASP H 101 "
      ideal   model   delta    sigma   weight residual
     121.54  126.94   -5.40 1.91e+00 2.74e-01 8.00e+00
  angle pdb=" N   CYS H 219 "
        pdb=" CA  CYS H 219 "
        pdb=" C   CYS H 219 "
      ideal   model   delta    sigma   weight residual
     114.04  110.59    3.45 1.24e+00 6.50e-01 7.75e+00
  ... (remaining 10267 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.92: 4057
       15.92 -    31.83: 407
       31.83 -    47.75: 81
       47.75 -    63.67: 16
       63.67 -    79.58: 15
  Dihedral angle restraints: 4576
    sinusoidal: 1868
      harmonic: 2708
  Sorted by residual:
  dihedral pdb=" CB  CYS H 143 "
           pdb=" SG  CYS H 143 "
           pdb=" SG  CYS H 199 "
           pdb=" CB  CYS H 199 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  168.38  -75.38     1      1.00e+01 1.00e-02 7.18e+01
  dihedral pdb=" CB  CYS C 480 "
           pdb=" SG  CYS C 480 "
           pdb=" SG  CYS C 488 "
           pdb=" CB  CYS C 488 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  141.82  -48.82     1      1.00e+01 1.00e-02 3.28e+01
  dihedral pdb=" CB  CYS B  15 "
           pdb=" SG  CYS B  15 "
           pdb=" SG  CYS B 136 "
           pdb=" CB  CYS B 136 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  138.26  -45.26     1      1.00e+01 1.00e-02 2.84e+01
  ... (remaining 4573 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.065: 1009
       0.065 -    0.130: 150
       0.130 -    0.196: 5
       0.196 -    0.261: 2
       0.261 -    0.326: 1
  Chirality restraints: 1167
  Sorted by residual:
  chirality pdb=" C1  NAG B1303 "
            pdb=" ND2 ASN B 165 "
            pdb=" C2  NAG B1303 "
            pdb=" O5  NAG B1303 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.07   -0.33 2.00e-01 2.50e+01 2.66e+00
  chirality pdb=" C1  NAG B1304 "
            pdb=" ND2 ASN B 234 "
            pdb=" C2  NAG B1304 "
            pdb=" O5  NAG B1304 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.16   -0.24 2.00e-01 2.50e+01 1.41e+00
  chirality pdb=" CB  VAL L 147 "
            pdb=" CA  VAL L 147 "
            pdb=" CG1 VAL L 147 "
            pdb=" CG2 VAL L 147 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.41   -0.22 2.00e-01 2.50e+01 1.17e+00
  ... (remaining 1164 not shown)

  Planarity restraints: 1317
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL C 524 "   -0.008 2.00e-02 2.50e+03   1.70e-02 2.88e+00
        pdb=" C   VAL C 524 "    0.029 2.00e-02 2.50e+03
        pdb=" O   VAL C 524 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   CYS C 525 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE B 235 "    0.007 2.00e-02 2.50e+03   1.44e-02 2.07e+00
        pdb=" C   ILE B 235 "   -0.025 2.00e-02 2.50e+03
        pdb=" O   ILE B 235 "    0.009 2.00e-02 2.50e+03
        pdb=" N   THR B 236 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE C 329 "   -0.022 5.00e-02 4.00e+02   3.36e-02 1.81e+00
        pdb=" N   PRO C 330 "    0.058 5.00e-02 4.00e+02
        pdb=" CA  PRO C 330 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO C 330 "   -0.019 5.00e-02 4.00e+02
  ... (remaining 1314 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 2188
        2.82 -     3.34: 5884
        3.34 -     3.86: 11654
        3.86 -     4.38: 12475
        4.38 -     4.90: 21939
  Nonbonded interactions: 54140
  Sorted by model distance:
  nonbonded pdb=" OH  TYR B  37 "
            pdb=" O   LEU B  54 "
     model   vdw
     2.296 3.040
  nonbonded pdb=" O   PRO H 126 "
            pdb=" OG  SER L 122 "
     model   vdw
     2.339 3.040
  nonbonded pdb=" OH  TYR C 501 "
            pdb=" O   GLY L  30 "
     model   vdw
     2.346 3.040
  nonbonded pdb=" O   LYS B 278 "
            pdb=" OG1 THR B 286 "
     model   vdw
     2.352 3.040
  nonbonded pdb=" O   LEU C 455 "
            pdb=" OH  TYR H  33 "
     model   vdw
     2.353 3.040
  ... (remaining 54135 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.460
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.290
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     20.520
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.060
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.610
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6996
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7555  Z= 0.178
  Angle     :  0.566   7.001  10272  Z= 0.284
  Chirality :  0.045   0.326   1167
  Planarity :  0.004   0.034   1310
  Dihedral  : 13.451  79.582   2806
  Min Nonbonded Distance : 2.296

Molprobity Statistics.
  All-atom Clashscore : 4.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  0.49 %
    Favored  : 99.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.00 %
    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: -0.78 (0.27), residues: 913
  helix: -3.66 (0.60), residues: 24
  sheet:  0.99 (0.34), residues: 235
  loop : -1.05 (0.23), residues: 654

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP L  32 
 HIS   0.003   0.000   HIS H 203 
 PHE   0.014   0.001   PHE L 140 
 TYR   0.008   0.001   TYR H  93 
 ARG   0.003   0.000   ARG L 212 

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

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

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 60
  time to evaluate  : 0.931 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   34 MET cc_start: 0.8591 (tpt) cc_final: 0.8215 (tpp)
REVERT: H   35 HIS cc_start: 0.8593 (m90) cc_final: 0.8238 (m170)
REVERT: H   82 MET cc_start: 0.6132 (tmm) cc_final: 0.5096 (tmm)
REVERT: H  101 ASP cc_start: 0.7600 (t0) cc_final: 0.7335 (t0)
REVERT: L   62 PHE cc_start: 0.8011 (m-80) cc_final: 0.7776 (m-80)
REVERT: B   42 VAL cc_start: 0.8923 (t) cc_final: 0.8481 (t)
REVERT: B   55 PHE cc_start: 0.7434 (m-80) cc_final: 0.6410 (m-10)
REVERT: B   80 ASP cc_start: 0.7432 (m-30) cc_final: 0.7149 (m-30)
  outliers start: 1
  outliers final: 0
  residues processed: 61
  average time/residue: 0.1880
  time to fit residues: 16.4940
Evaluate side-chains
  37 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 37
  time to evaluate  : 0.908 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 76 optimal weight:    4.9990
   chunk 68 optimal weight:    9.9990
   chunk 38 optimal weight:    0.7980
   chunk 23 optimal weight:    1.9990
   chunk 46 optimal weight:    2.9990
   chunk 36 optimal weight:    9.9990
   chunk 71 optimal weight:    3.9990
   chunk 27 optimal weight:   10.0000
   chunk 43 optimal weight:    6.9990
   chunk 53 optimal weight:    0.0370
   chunk 82 optimal weight:    0.9990
   overall best weight:    1.3664

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

Flipped N/Q/H residues before XYZ refinement:
C 409 GLN
C 422 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.080077 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.063606 restraints weight = 47143.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.064311 restraints weight = 25423.667|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.064953 restraints weight = 20604.375|
|-----------------------------------------------------------------------------|
r_work (final): 0.3471
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7273
moved from start:          0.1773

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7555  Z= 0.209
  Angle     :  0.560   6.156  10272  Z= 0.293
  Chirality :  0.044   0.355   1167
  Planarity :  0.004   0.029   1310
  Dihedral  :  5.041  49.437   1151
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 9.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.78 %
    Favored  : 94.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.00 %
    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: -0.77 (0.27), residues: 913
  helix: -2.93 (0.69), residues: 20
  sheet:  0.55 (0.34), residues: 256
  loop : -0.93 (0.24), residues: 637

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP L  35 
 HIS   0.005   0.001   HIS H 203 
 PHE   0.013   0.001   PHE B 220 
 TYR   0.015   0.001   TYR L  49 
 ARG   0.005   0.001   ARG B 190 

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

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

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 53
  time to evaluate  : 0.769 
Fit side-chains
   revert: symmetry clash
REVERT: C  434 ILE cc_start: 0.8401 (mm) cc_final: 0.8185 (mm)
REVERT: H   35 HIS cc_start: 0.9027 (m90) cc_final: 0.8109 (m90)
REVERT: H   82 MET cc_start: 0.6691 (tmm) cc_final: 0.5897 (tmm)
REVERT: L  118 ILE cc_start: 0.7318 (pt) cc_final: 0.7038 (mp)
REVERT: B   42 VAL cc_start: 0.8938 (t) cc_final: 0.8511 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 53
  average time/residue: 0.1556
  time to fit residues: 12.4973
Evaluate side-chains
  31 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 31
  time to evaluate  : 0.908 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 43 optimal weight:    9.9990
   chunk 67 optimal weight:    4.9990
   chunk 2 optimal weight:    3.9990
   chunk 6 optimal weight:    0.0020
   chunk 59 optimal weight:    7.9990
   chunk 90 optimal weight:    0.6980
   chunk 10 optimal weight:    6.9990
   chunk 22 optimal weight:    0.9980
   chunk 4 optimal weight:   20.0000
   chunk 74 optimal weight:    0.9980
   chunk 9 optimal weight:    4.9990
   overall best weight:    1.3390

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

Flipped N/Q/H residues before XYZ refinement:
H 200 ASN
** L  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 161 GLN
** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 196 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.077847 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.060091 restraints weight = 47067.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.061753 restraints weight = 29242.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.062791 restraints weight = 17783.138|
|-----------------------------------------------------------------------------|
r_work (final): 0.3406
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7360
moved from start:          0.2596

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7555  Z= 0.198
  Angle     :  0.519   8.990  10272  Z= 0.271
  Chirality :  0.044   0.317   1167
  Planarity :  0.004   0.064   1310
  Dihedral  :  4.579  50.163   1151
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 10.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.41 %
    Favored  : 94.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.97 (0.27), residues: 913
  helix: -2.59 (0.73), residues: 31
  sheet:  0.48 (0.33), residues: 254
  loop : -1.08 (0.24), residues: 628

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP L  35 
 HIS   0.004   0.001   HIS H 203 
 PHE   0.014   0.002   PHE B 133 
 TYR   0.011   0.001   TYR H  33 
 ARG   0.004   0.001   ARG B  44 

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

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

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 0.846 
Fit side-chains
   revert: symmetry clash
REVERT: H   34 MET cc_start: 0.8579 (mmp) cc_final: 0.7969 (mmm)
REVERT: H   35 HIS cc_start: 0.9148 (m90) cc_final: 0.8562 (m90)
REVERT: H   82 MET cc_start: 0.6920 (tmm) cc_final: 0.6188 (tmm)
REVERT: L  118 ILE cc_start: 0.7386 (pt) cc_final: 0.7045 (mp)
REVERT: B   40 ASP cc_start: 0.9258 (p0) cc_final: 0.9054 (p0)
REVERT: B   42 VAL cc_start: 0.9063 (t) cc_final: 0.8661 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 54
  average time/residue: 0.1485
  time to fit residues: 12.4694
Evaluate side-chains
  25 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 25
  time to evaluate  : 0.826 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 72 optimal weight:    0.5980
   chunk 66 optimal weight:    8.9990
   chunk 36 optimal weight:    5.9990
   chunk 62 optimal weight:    2.9990
   chunk 68 optimal weight:   10.0000
   chunk 29 optimal weight:    0.8980
   chunk 45 optimal weight:    0.1980
   chunk 86 optimal weight:    5.9990
   chunk 77 optimal weight:    4.9990
   chunk 65 optimal weight:    4.9990
   chunk 54 optimal weight:    5.9990
   overall best weight:    1.9384

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

Flipped N/Q/H residues before XYZ refinement:
C 409 GLN
H  35 HIS
** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 239 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.075324 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.059483 restraints weight = 47045.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.060607 restraints weight = 38062.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.061238 restraints weight = 27978.131|
|-----------------------------------------------------------------------------|
r_work (final): 0.3382
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7335
moved from start:          0.3572

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   7555  Z= 0.277
  Angle     :  0.596  10.372  10272  Z= 0.310
  Chirality :  0.045   0.323   1167
  Planarity :  0.004   0.049   1310
  Dihedral  :  4.895  41.409   1151
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 12.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.81 %
    Favored  : 94.19 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.30 (0.27), residues: 913
  helix: -2.64 (0.75), residues: 30
  sheet: -0.03 (0.34), residues: 241
  loop : -1.17 (0.24), residues: 642

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP C 436 
 HIS   0.007   0.002   HIS H 203 
 PHE   0.015   0.002   PHE B 220 
 TYR   0.021   0.002   TYR B 279 
 ARG   0.007   0.001   ARG B  44 

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

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

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 47
  time to evaluate  : 0.798 
Fit side-chains
   revert: symmetry clash
REVERT: H   34 MET cc_start: 0.8508 (mmp) cc_final: 0.7801 (mmm)
REVERT: H   82 MET cc_start: 0.7593 (tmm) cc_final: 0.6909 (tmm)
REVERT: L   83 PHE cc_start: 0.8434 (m-80) cc_final: 0.8112 (m-80)
REVERT: L  118 ILE cc_start: 0.7504 (pt) cc_final: 0.7285 (mt)
REVERT: B   40 ASP cc_start: 0.9315 (p0) cc_final: 0.9070 (p0)
REVERT: B   42 VAL cc_start: 0.9161 (t) cc_final: 0.8853 (t)
REVERT: B   49 HIS cc_start: 0.8301 (t70) cc_final: 0.7965 (t70)
REVERT: B  198 ASP cc_start: 0.9210 (t0) cc_final: 0.9001 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 47
  average time/residue: 0.1517
  time to fit residues: 11.1230
Evaluate side-chains
  24 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.793 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 23 optimal weight:    1.9990
   chunk 16 optimal weight:    7.9990
   chunk 85 optimal weight:    0.9990
   chunk 51 optimal weight:    6.9990
   chunk 32 optimal weight:    3.9990
   chunk 80 optimal weight:    2.9990
   chunk 50 optimal weight:    9.9990
   chunk 20 optimal weight:    0.0170
   chunk 66 optimal weight:   10.0000
   chunk 43 optimal weight:   20.0000
   chunk 42 optimal weight:    5.9990
   overall best weight:    2.0026

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

Flipped N/Q/H residues before XYZ refinement:
** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.074675 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.058864 restraints weight = 47095.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.058920 restraints weight = 39057.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.059528 restraints weight = 33218.386|
|-----------------------------------------------------------------------------|
r_work (final): 0.3323
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7436
moved from start:          0.4130

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   7555  Z= 0.251
  Angle     :  0.581  11.267  10272  Z= 0.298
  Chirality :  0.045   0.320   1167
  Planarity :  0.004   0.047   1310
  Dihedral  :  5.048  36.698   1151
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 12.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.91 %
    Favored  : 94.09 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.21 (0.27), residues: 913
  helix: -2.63 (0.76), residues: 30
  sheet:  0.07 (0.33), residues: 256
  loop : -1.14 (0.24), residues: 627

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP H 157 
 HIS   0.006   0.001   HIS H 203 
 PHE   0.012   0.002   PHE B  86 
 TYR   0.012   0.001   TYR C 421 
 ARG   0.003   0.001   ARG B  44 

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

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

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 40
  time to evaluate  : 0.886 
Fit side-chains
   revert: symmetry clash
REVERT: H   34 MET cc_start: 0.8559 (mmp) cc_final: 0.7875 (mmm)
REVERT: H   82 MET cc_start: 0.7596 (tmm) cc_final: 0.7008 (tmm)
REVERT: L   62 PHE cc_start: 0.8367 (m-80) cc_final: 0.8116 (m-80)
REVERT: L  118 ILE cc_start: 0.7626 (pt) cc_final: 0.7383 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 40
  average time/residue: 0.1604
  time to fit residues: 10.1703
Evaluate side-chains
  23 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 23
  time to evaluate  : 0.874 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 63 optimal weight:    6.9990
   chunk 52 optimal weight:   10.0000
   chunk 81 optimal weight:   10.0000
   chunk 30 optimal weight:    3.9990
   chunk 68 optimal weight:    0.7980
   chunk 57 optimal weight:    0.0370
   chunk 66 optimal weight:    0.8980
   chunk 23 optimal weight:    0.0470
   chunk 90 optimal weight:    1.9990
   chunk 64 optimal weight:    6.9990
   chunk 34 optimal weight:    3.9990
   overall best weight:    0.7558

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.075561 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.059953 restraints weight = 46720.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.061269 restraints weight = 34834.286|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.061832 restraints weight = 24389.887|
|-----------------------------------------------------------------------------|
r_work (final): 0.3389
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7324
moved from start:          0.4225

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   7555  Z= 0.151
  Angle     :  0.517   9.543  10272  Z= 0.266
  Chirality :  0.044   0.322   1167
  Planarity :  0.004   0.044   1310
  Dihedral  :  4.481  32.832   1151
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 10.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.37 %
    Favored  : 94.63 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.35 %
    Favored  : 98.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.23 (0.27), residues: 913
  helix: -2.82 (0.71), residues: 30
  sheet: -0.06 (0.33), residues: 251
  loop : -1.07 (0.24), residues: 632

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 258 
 HIS   0.004   0.001   HIS H 203 
 PHE   0.011   0.001   PHE B 133 
 TYR   0.012   0.001   TYR C 369 
 ARG   0.012   0.001   ARG B 246 

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

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

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 45
  time to evaluate  : 0.851 
Fit side-chains
   revert: symmetry clash
REVERT: H   34 MET cc_start: 0.8471 (mmp) cc_final: 0.7728 (mmm)
REVERT: H   82 MET cc_start: 0.7503 (tmm) cc_final: 0.6981 (tmm)
REVERT: L    4 MET cc_start: 0.8221 (mmp) cc_final: 0.7578 (ptp)
REVERT: B   49 HIS cc_start: 0.8297 (t70) cc_final: 0.8003 (t70)
REVERT: B  191 GLU cc_start: 0.9003 (mt-10) cc_final: 0.7934 (tt0)
REVERT: B  198 ASP cc_start: 0.9256 (t0) cc_final: 0.9026 (t0)
REVERT: B  223 LEU cc_start: 0.9222 (mm) cc_final: 0.8997 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 45
  average time/residue: 0.1415
  time to fit residues: 10.3531
Evaluate side-chains
  21 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 21
  time to evaluate  : 0.867 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 68 optimal weight:   10.0000
   chunk 17 optimal weight:    3.9990
   chunk 86 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9980
   chunk 38 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9980
   chunk 18 optimal weight:    3.9990
   chunk 36 optimal weight:   10.0000
   chunk 27 optimal weight:    0.4980
   chunk 11 optimal weight:    1.9990
   chunk 55 optimal weight:    4.9990
   overall best weight:    1.0982

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

Flipped N/Q/H residues before XYZ refinement:
** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.075713 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.059068 restraints weight = 48100.775|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.059615 restraints weight = 27352.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.059992 restraints weight = 21034.703|
|-----------------------------------------------------------------------------|
r_work (final): 0.3337
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7433
moved from start:          0.4470

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7555  Z= 0.174
  Angle     :  0.524   8.981  10272  Z= 0.270
  Chirality :  0.044   0.325   1167
  Planarity :  0.004   0.042   1310
  Dihedral  :  4.336  33.966   1151
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 11.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.15 %
    Favored  : 94.85 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.11 %
    Favored  : 98.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.21 (0.27), residues: 913
  helix: -2.96 (0.72), residues: 30
  sheet: -0.04 (0.34), residues: 236
  loop : -1.03 (0.24), residues: 647

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 258 
 HIS   0.007   0.001   HIS B  49 
 PHE   0.015   0.001   PHE B  43 
 TYR   0.014   0.001   TYR C 369 
 ARG   0.006   0.000   ARG B  44 

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

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

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 43
  time to evaluate  : 0.828 
Fit side-chains
   revert: symmetry clash
REVERT: H   34 MET cc_start: 0.8790 (mmp) cc_final: 0.8079 (mmm)
REVERT: H   82 MET cc_start: 0.7552 (tmm) cc_final: 0.7102 (tmm)
REVERT: L    4 MET cc_start: 0.8098 (mmp) cc_final: 0.7638 (ptp)
REVERT: L   62 PHE cc_start: 0.8113 (m-80) cc_final: 0.7892 (m-80)
REVERT: B   40 ASP cc_start: 0.9388 (p0) cc_final: 0.9179 (p0)
REVERT: B   42 VAL cc_start: 0.9355 (t) cc_final: 0.9074 (t)
REVERT: B   49 HIS cc_start: 0.8170 (t70) cc_final: 0.7769 (t70)
REVERT: B  191 GLU cc_start: 0.8787 (mt-10) cc_final: 0.7828 (mt-10)
REVERT: B  198 ASP cc_start: 0.9253 (t0) cc_final: 0.9001 (t0)
REVERT: B  223 LEU cc_start: 0.9144 (mm) cc_final: 0.8860 (mm)
REVERT: B  280 ASN cc_start: 0.9162 (t0) cc_final: 0.8917 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 43
  average time/residue: 0.1414
  time to fit residues: 10.0855
Evaluate side-chains
  24 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.918 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 0 optimal weight:    5.9990
   chunk 76 optimal weight:    4.9990
   chunk 23 optimal weight:    1.9990
   chunk 60 optimal weight:    0.9980
   chunk 53 optimal weight:   10.0000
   chunk 10 optimal weight:    8.9990
   chunk 74 optimal weight:    2.9990
   chunk 1 optimal weight:    2.9990
   chunk 12 optimal weight:   10.0000
   chunk 52 optimal weight:    6.9990
   chunk 62 optimal weight:    5.9990
   overall best weight:    2.7988

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

Flipped N/Q/H residues before XYZ refinement:
** H  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.070544 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.053468 restraints weight = 48928.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.054198 restraints weight = 27274.625|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.054882 restraints weight = 20521.736|
|-----------------------------------------------------------------------------|
r_work (final): 0.3171
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7553
moved from start:          0.5525

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.063   7555  Z= 0.364
  Angle     :  0.701  11.280  10272  Z= 0.364
  Chirality :  0.047   0.305   1167
  Planarity :  0.005   0.047   1310
  Dihedral  :  5.344  38.659   1151
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 20.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.11 %
    Favored  : 91.89 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.35 %
    Favored  : 98.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.52 (0.27), residues: 913
  helix: -3.06 (0.68), residues: 36
  sheet: -0.17 (0.32), residues: 258
  loop : -1.31 (0.25), residues: 619

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP H 157 
 HIS   0.021   0.003   HIS B  49 
 PHE   0.026   0.002   PHE B  43 
 TYR   0.021   0.002   TYR L 187 
 ARG   0.010   0.001   ARG B  44 

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

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

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  35 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 35
  time to evaluate  : 0.806 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   34 MET cc_start: 0.8917 (mmp) cc_final: 0.8260 (mmm)
REVERT: H   82 MET cc_start: 0.7565 (tmm) cc_final: 0.7026 (tmm)
REVERT: L    4 MET cc_start: 0.8043 (mmp) cc_final: 0.7600 (ptm)
REVERT: B  198 ASP cc_start: 0.9279 (t0) cc_final: 0.9031 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 35
  average time/residue: 0.1447
  time to fit residues: 8.3619
Evaluate side-chains
  18 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 18
  time to evaluate  : 0.819 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 74 optimal weight:    0.8980
   chunk 87 optimal weight:    2.9990
   chunk 29 optimal weight:    0.0970
   chunk 6 optimal weight:    0.0670
   chunk 31 optimal weight:    1.9990
   chunk 48 optimal weight:    0.0000
   chunk 58 optimal weight:    5.9990
   chunk 70 optimal weight:    0.9980
   chunk 83 optimal weight:    0.5980
   chunk 79 optimal weight:    0.2980
   chunk 72 optimal weight:    0.7980
   overall best weight:    0.2120

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

Flipped N/Q/H residues before XYZ refinement:
** H  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.075418 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.060127 restraints weight = 47398.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.061024 restraints weight = 37812.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.062021 restraints weight = 26740.925|
|-----------------------------------------------------------------------------|
r_work (final): 0.3395
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7328
moved from start:          0.5135

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   7555  Z= 0.145
  Angle     :  0.544   8.669  10272  Z= 0.278
  Chirality :  0.045   0.318   1167
  Planarity :  0.004   0.042   1310
  Dihedral  :  4.551  32.178   1151
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 10.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.91 %
    Favored  : 94.09 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.25 %
    Favored  : 99.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.34 (0.27), residues: 913
  helix: -3.08 (0.63), residues: 37
  sheet: -0.20 (0.33), residues: 240
  loop : -1.07 (0.24), residues: 636

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 258 
 HIS   0.006   0.001   HIS B  49 
 PHE   0.013   0.001   PHE B 238 
 TYR   0.011   0.001   TYR C 421 
 ARG   0.007   0.001   ARG B  44 

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

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

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 45
  time to evaluate  : 0.815 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   34 MET cc_start: 0.8566 (mmp) cc_final: 0.7934 (mmm)
REVERT: H   82 MET cc_start: 0.7440 (tmm) cc_final: 0.6886 (tmm)
REVERT: L    4 MET cc_start: 0.8099 (mmp) cc_final: 0.7755 (ptp)
REVERT: B  198 ASP cc_start: 0.9190 (t0) cc_final: 0.8947 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 45
  average time/residue: 0.1354
  time to fit residues: 9.9658
Evaluate side-chains
  22 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 22
  time to evaluate  : 0.813 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 71 optimal weight:    2.9990
   chunk 20 optimal weight:   20.0000
   chunk 69 optimal weight:    0.7980
   chunk 58 optimal weight:    5.9990
   chunk 48 optimal weight:    7.9990
   chunk 82 optimal weight:    0.0670
   chunk 12 optimal weight:   10.0000
   chunk 61 optimal weight:    0.9990
   chunk 40 optimal weight:    7.9990
   chunk 36 optimal weight:    7.9990
   chunk 80 optimal weight:    0.8980
   overall best weight:    1.1522

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

Flipped N/Q/H residues before XYZ refinement:
** H  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.073222 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.055286 restraints weight = 47957.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.056120 restraints weight = 26921.943|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.056980 restraints weight = 18929.620|
|-----------------------------------------------------------------------------|
r_work (final): 0.3214
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7523
moved from start:          0.5313

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7555  Z= 0.181
  Angle     :  0.538   8.915  10272  Z= 0.279
  Chirality :  0.044   0.311   1167
  Planarity :  0.004   0.041   1310
  Dihedral  :  4.560  34.370   1151
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 11.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.46 %
    Favored  : 93.54 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.34 (0.27), residues: 913
  helix: -3.09 (0.66), residues: 36
  sheet: -0.27 (0.33), residues: 241
  loop : -1.04 (0.25), residues: 636

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 258 
 HIS   0.013   0.002   HIS B  49 
 PHE   0.012   0.001   PHE B 133 
 TYR   0.009   0.001   TYR L 187 
 ARG   0.008   0.001   ARG B 190 

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

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

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 39
  time to evaluate  : 0.879 
Fit side-chains
   revert: symmetry clash
REVERT: H   34 MET cc_start: 0.8851 (mmp) cc_final: 0.8160 (mmm)
REVERT: H   82 MET cc_start: 0.7428 (tmm) cc_final: 0.6911 (tmm)
REVERT: L    4 MET cc_start: 0.8027 (mmp) cc_final: 0.7597 (ptp)
REVERT: L   78 LEU cc_start: 0.9225 (mt) cc_final: 0.8962 (mt)
REVERT: B  191 GLU cc_start: 0.8853 (mt-10) cc_final: 0.8170 (mt-10)
REVERT: B  198 ASP cc_start: 0.9146 (t0) cc_final: 0.8871 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 39
  average time/residue: 0.1439
  time to fit residues: 9.2728
Evaluate side-chains
  20 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 20
  time to evaluate  : 0.877 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 83 optimal weight:    0.4980
   chunk 21 optimal weight:    2.9990
   chunk 87 optimal weight:    4.9990
   chunk 47 optimal weight:   10.0000
   chunk 55 optimal weight:    1.9990
   chunk 56 optimal weight:    0.8980
   chunk 44 optimal weight:    7.9990
   chunk 73 optimal weight:    1.9990
   chunk 64 optimal weight:    6.9990
   chunk 40 optimal weight:    2.9990
   chunk 45 optimal weight:    0.8980
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
** H  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 185 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.072565 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.055188 restraints weight = 48339.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.055985 restraints weight = 25714.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.056522 restraints weight = 19917.179|
|-----------------------------------------------------------------------------|
r_work (final): 0.3191
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7525
moved from start:          0.5619

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7555  Z= 0.184
  Angle     :  0.543   9.439  10272  Z= 0.281
  Chirality :  0.044   0.324   1167
  Planarity :  0.004   0.042   1310
  Dihedral  :  4.661  36.978   1151
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 12.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.90 %
    Favored  : 93.10 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.49 %
    Favored  : 99.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.29 (0.27), residues: 913
  helix: -3.04 (0.67), residues: 36
  sheet: -0.11 (0.33), residues: 250
  loop : -1.07 (0.25), residues: 627

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 258 
 HIS   0.013   0.002   HIS B  49 
 PHE   0.012   0.001   PHE B  43 
 TYR   0.010   0.001   TYR L 187 
 ARG   0.008   0.001   ARG B  44 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2129.91 seconds
wall clock time: 38 minutes 5.13 seconds (2285.13 seconds total)