Starting phenix.real_space_refine
on Wed Sep 17 06:59:01 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9mqy_48544/09_2025/9mqy_48544.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9mqy_48544/09_2025/9mqy_48544.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9mqy_48544/09_2025/9mqy_48544.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9mqy_48544/09_2025/9mqy_48544.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9mqy_48544/09_2025/9mqy_48544.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9mqy_48544/09_2025/9mqy_48544.map"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.008
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       4      5.49       5
     S      16      5.16       5
     C    4101      2.51       5
     N    1153      2.21       5
     O    1174      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6448
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3153
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 447, 3153
          Classifications: {'peptide': 447}
          Incomplete info: {'truncation_to_alanine': 56}
          Link IDs: {'PTRANS': 19, 'TRANS': 427}
          Unresolved non-hydrogen bonds: 225
          Unresolved non-hydrogen angles: 265
          Unresolved non-hydrogen dihedrals: 189
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'HIS:plan': 1, 'ASP:plan': 9, 'ARG:plan': 6, 'GLU:plan': 19, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 144
    Chain: "B"
      Number of atoms: 3189
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 447, 3189
          Classifications: {'peptide': 447}
          Incomplete info: {'truncation_to_alanine': 48}
          Link IDs: {'PTRANS': 19, 'TRANS': 427}
          Unresolved non-hydrogen bonds: 189
          Unresolved non-hydrogen angles: 223
          Unresolved non-hydrogen dihedrals: 159
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'HIS:plan': 1, 'ASP:plan': 7, 'ARG:plan': 3, 'GLU:plan': 18, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 119
    Chain: "A"
      Number of atoms: 53
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 53
          Unusual residues: {'FAD': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 53
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 53
          Unusual residues: {'FAD': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.91, per 1000 atoms: 0.30
  Number of scatterers: 6448
  At special positions: 0
  Unit cell: (109.44, 81.92, 69.12, 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)
     S      16     16.00
     P       4     15.00
     O    1174      8.00
     N    1153      7.00
     C    4101      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.59
  Conformation dependent library (CDL) restraints added in 407.0 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1612

  Finding SS restraints...
    Secondary structure from input PDB file:
      37 helices and 12 sheets defined
      44.5% alpha, 18.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.29
  Creating SS restraints...
    Processing helix  chain 'A' and resid 20 through 30
    Processing helix  chain 'A' and resid 31 through 33
      No H-bonds generated for 'chain 'A' and resid 31 through 33'
    Processing helix  chain 'A' and resid 48 through 50
      No H-bonds generated for 'chain 'A' and resid 48 through 50'
    Processing helix  chain 'A' and resid 51 through 57
      removed outlier: 3.578A  pdb=" N   VAL A  55 " --> pdb=" O   LEU A  51 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 61 through 65
    Processing helix  chain 'A' and resid 68 through 73
    Processing helix  chain 'A' and resid 125 through 131
    Processing helix  chain 'A' and resid 137 through 156
      removed outlier: 3.587A  pdb=" N   PHE A 152 " --> pdb=" O   ILE A 148 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 160 through 168
    Processing helix  chain 'A' and resid 176 through 192
    Processing helix  chain 'A' and resid 202 through 206
    Processing helix  chain 'A' and resid 218 through 220
      No H-bonds generated for 'chain 'A' and resid 218 through 220'
    Processing helix  chain 'A' and resid 221 through 236
      removed outlier: 4.378A  pdb=" N   LEU A 225 " --> pdb=" O   MET A 221 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 281 through 290
      removed outlier: 4.079A  pdb=" N   ASP A 285 " --> pdb=" O   PRO A 281 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 318 through 321
    Processing helix  chain 'A' and resid 329 through 349
    Processing helix  chain 'A' and resid 386 through 401
      removed outlier: 3.751A  pdb=" N   TYR A 400 " --> pdb=" O   LEU A 396 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   LEU A 401 " --> pdb=" O   HIS A 397 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 403 through 420
    Processing helix  chain 'A' and resid 429 through 447
      removed outlier: 5.710A  pdb=" N   ARG A 436 " --> pdb=" O   GLN A 432 " (cutoff:3.500A)
      removed outlier: 6.008A  pdb=" N   THR A 437 " --> pdb=" O   ALA A 433 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 20 through 30
    Processing helix  chain 'B' and resid 48 through 50
      No H-bonds generated for 'chain 'B' and resid 48 through 50'
    Processing helix  chain 'B' and resid 51 through 57
      removed outlier: 3.572A  pdb=" N   VAL B  55 " --> pdb=" O   LEU B  51 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 61 through 66
      removed outlier: 4.001A  pdb=" N   ILE B  65 " --> pdb=" O   SER B  61 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 68 through 73
    Processing helix  chain 'B' and resid 125 through 131
    Processing helix  chain 'B' and resid 137 through 156
      removed outlier: 3.648A  pdb=" N   PHE B 152 " --> pdb=" O   ILE B 148 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 160 through 168
    Processing helix  chain 'B' and resid 176 through 192
    Processing helix  chain 'B' and resid 202 through 206
    Processing helix  chain 'B' and resid 218 through 221
    Processing helix  chain 'B' and resid 222 through 236
    Processing helix  chain 'B' and resid 281 through 291
      removed outlier: 4.060A  pdb=" N   ASP B 285 " --> pdb=" O   PRO B 281 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 318 through 321
    Processing helix  chain 'B' and resid 329 through 349
    Processing helix  chain 'B' and resid 387 through 401
      removed outlier: 3.870A  pdb=" N   TYR B 400 " --> pdb=" O   LEU B 396 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   LEU B 401 " --> pdb=" O   HIS B 397 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 403 through 420
    Processing helix  chain 'B' and resid 429 through 447
      removed outlier: 5.808A  pdb=" N   ARG B 436 " --> pdb=" O   GLN B 432 " (cutoff:3.500A)
      removed outlier: 5.964A  pdb=" N   THR B 437 " --> pdb=" O   ALA B 433 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 79 through 83
      removed outlier: 8.288A  pdb=" N   GLN A  80 " --> pdb=" O   VAL A  35 " (cutoff:3.500A)
      removed outlier: 6.611A  pdb=" N   VAL A  37 " --> pdb=" O   GLN A  80 " (cutoff:3.500A)
      removed outlier: 7.479A  pdb=" N   LEU A  82 " --> pdb=" O   VAL A  37 " (cutoff:3.500A)
      removed outlier: 6.072A  pdb=" N   LEU A  39 " --> pdb=" O   LEU A  82 " (cutoff:3.500A)
      removed outlier: 6.550A  pdb=" N   HIS A  12 " --> pdb=" O   ASP A  36 " (cutoff:3.500A)
      removed outlier: 7.760A  pdb=" N   LYS A  38 " --> pdb=" O   HIS A  12 " (cutoff:3.500A)
      removed outlier: 6.497A  pdb=" N   VAL A  14 " --> pdb=" O   LYS A  38 " (cutoff:3.500A)
      removed outlier: 7.652A  pdb=" N   ILE A  40 " --> pdb=" O   VAL A  14 " (cutoff:3.500A)
      removed outlier: 6.373A  pdb=" N   ILE A  16 " --> pdb=" O   ILE A  40 " (cutoff:3.500A)
      removed outlier: 4.143A  pdb=" N   LEU A 308 " --> pdb=" O   HIS A 311 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 85 through 90
      removed outlier: 5.435A  pdb=" N   VAL A  86 " --> pdb=" O   VAL A  99 " (cutoff:3.500A)
      removed outlier: 6.422A  pdb=" N   VAL A  99 " --> pdb=" O   VAL A  86 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 118 through 119
    Processing sheet with id=AA4, first strand: chain 'A' and resid 238 through 242
      removed outlier: 6.818A  pdb=" N   VAL A 208 " --> pdb=" O   GLU A 239 " (cutoff:3.500A)
      removed outlier: 7.352A  pdb=" N   GLN A 241 " --> pdb=" O   VAL A 208 " (cutoff:3.500A)
      removed outlier: 6.139A  pdb=" N   LEU A 210 " --> pdb=" O   GLN A 241 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 244 through 250
      removed outlier: 6.573A  pdb=" N   THR A 255 " --> pdb=" O   THR A 247 " (cutoff:3.500A)
      removed outlier: 4.658A  pdb=" N   VAL A 249 " --> pdb=" O   GLY A 253 " (cutoff:3.500A)
      removed outlier: 6.521A  pdb=" N   GLY A 253 " --> pdb=" O   VAL A 249 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 366 through 371
      removed outlier: 6.690A  pdb=" N   SER A 374 " --> pdb=" O   VAL A 370 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 79 through 83
      removed outlier: 6.677A  pdb=" N   VAL B  37 " --> pdb=" O   GLN B  80 " (cutoff:3.500A)
      removed outlier: 7.449A  pdb=" N   LEU B  82 " --> pdb=" O   VAL B  37 " (cutoff:3.500A)
      removed outlier: 6.098A  pdb=" N   LEU B  39 " --> pdb=" O   LEU B  82 " (cutoff:3.500A)
      removed outlier: 4.121A  pdb=" N   LEU B 308 " --> pdb=" O   HIS B 311 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 85 through 90
      removed outlier: 5.416A  pdb=" N   VAL B  86 " --> pdb=" O   VAL B  99 " (cutoff:3.500A)
      removed outlier: 6.470A  pdb=" N   VAL B  99 " --> pdb=" O   VAL B  86 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 118 through 119
    Processing sheet with id=AB1, first strand: chain 'B' and resid 239 through 242
      removed outlier: 6.870A  pdb=" N   VAL B 208 " --> pdb=" O   GLU B 239 " (cutoff:3.500A)
      removed outlier: 7.398A  pdb=" N   GLN B 241 " --> pdb=" O   VAL B 208 " (cutoff:3.500A)
      removed outlier: 5.926A  pdb=" N   LEU B 210 " --> pdb=" O   GLN B 241 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 245 through 250
      removed outlier: 6.523A  pdb=" N   THR B 255 " --> pdb=" O   THR B 247 " (cutoff:3.500A)
      removed outlier: 4.587A  pdb=" N   VAL B 249 " --> pdb=" O   GLY B 253 " (cutoff:3.500A)
      removed outlier: 6.522A  pdb=" N   GLY B 253 " --> pdb=" O   VAL B 249 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 366 through 371
      removed outlier: 6.719A  pdb=" N   SER B 374 " --> pdb=" O   VAL B 370 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   ALA B 375 " --> pdb=" O   GLY B 386 " (cutoff:3.500A)

    335 hydrogen bonds defined for protein.
    909 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: 1.16

  Time building geometry restraints manager: 0.77 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2145
        1.34 -     1.45: 795
        1.45 -     1.57: 3604
        1.57 -     1.68: 4
        1.68 -     1.80: 28
  Bond restraints: 6576
  Sorted by residual:
  bond pdb=" O5B FAD A 501 "
       pdb=" PA  FAD A 501 "
    ideal  model  delta    sigma   weight residual
    1.634  1.539  0.095 2.00e-02 2.50e+03 2.24e+01
  bond pdb=" O3P FAD A 501 "
       pdb=" P   FAD A 501 "
    ideal  model  delta    sigma   weight residual
    1.660  1.568  0.092 2.00e-02 2.50e+03 2.10e+01
  bond pdb=" O3P FAD B 501 "
       pdb=" P   FAD B 501 "
    ideal  model  delta    sigma   weight residual
    1.660  1.575  0.085 2.00e-02 2.50e+03 1.81e+01
  bond pdb=" O5B FAD B 501 "
       pdb=" PA  FAD B 501 "
    ideal  model  delta    sigma   weight residual
    1.634  1.561  0.073 2.00e-02 2.50e+03 1.35e+01
  bond pdb=" O5' FAD B 501 "
       pdb=" P   FAD B 501 "
    ideal  model  delta    sigma   weight residual
    1.637  1.567  0.070 2.00e-02 2.50e+03 1.21e+01
  ... (remaining 6571 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.82: 8731
        1.82 -     3.63: 241
        3.63 -     5.45: 22
        5.45 -     7.26: 6
        7.26 -     9.08: 2
  Bond angle restraints: 9002
  Sorted by residual:
  angle pdb=" N   GLN A  49 "
        pdb=" CA  GLN A  49 "
        pdb=" C   GLN A  49 "
      ideal   model   delta    sigma   weight residual
     109.81  116.55   -6.74 2.21e+00 2.05e-01 9.30e+00
  angle pdb=" O1P FAD A 501 "
        pdb=" P   FAD A 501 "
        pdb=" O2P FAD A 501 "
      ideal   model   delta    sigma   weight residual
     122.50  113.42    9.08 3.00e+00 1.11e-01 9.16e+00
  angle pdb=" C   ASN A 252 "
        pdb=" N   GLY A 253 "
        pdb=" CA  GLY A 253 "
      ideal   model   delta    sigma   weight residual
     120.72  116.96    3.76 1.33e+00 5.65e-01 8.01e+00
  angle pdb=" O1A FAD B 501 "
        pdb=" PA  FAD B 501 "
        pdb=" O5B FAD B 501 "
      ideal   model   delta    sigma   weight residual
     104.10  112.44   -8.34 3.00e+00 1.11e-01 7.73e+00
  angle pdb=" C   ASN B 252 "
        pdb=" N   GLY B 253 "
        pdb=" CA  GLY B 253 "
      ideal   model   delta    sigma   weight residual
     120.91  117.11    3.80 1.38e+00 5.25e-01 7.56e+00
  ... (remaining 8997 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.41: 3767
       22.41 -    44.81: 91
       44.81 -    67.22: 22
       67.22 -    89.63: 9
       89.63 -   112.04: 1
  Dihedral angle restraints: 3890
    sinusoidal: 1370
      harmonic: 2520
  Sorted by residual:
  dihedral pdb=" CA  ARG B 296 "
           pdb=" C   ARG B 296 "
           pdb=" N   ALA B 297 "
           pdb=" CA  ALA B 297 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -157.43  -22.57     0      5.00e+00 4.00e-02 2.04e+01
  dihedral pdb=" CA  ILE A 201 "
           pdb=" C   ILE A 201 "
           pdb=" N   ASP A 202 "
           pdb=" CA  ASP A 202 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.64   22.36     0      5.00e+00 4.00e-02 2.00e+01
  dihedral pdb=" CA  ASP B 295 "
           pdb=" C   ASP B 295 "
           pdb=" N   ARG B 296 "
           pdb=" CA  ARG B 296 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.02   20.98     0      5.00e+00 4.00e-02 1.76e+01
  ... (remaining 3887 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 570
       0.034 -    0.069: 348
       0.069 -    0.103: 116
       0.103 -    0.137: 51
       0.137 -    0.171: 9
  Chirality restraints: 1094
  Sorted by residual:
  chirality pdb=" CA  ILE B 254 "
            pdb=" N   ILE B 254 "
            pdb=" C   ILE B 254 "
            pdb=" CB  ILE B 254 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.17 2.00e-01 2.50e+01 7.34e-01
  chirality pdb=" C2B FAD B 501 "
            pdb=" C1B FAD B 501 "
            pdb=" C3B FAD B 501 "
            pdb=" O2B FAD B 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.53   -2.71    0.17 2.00e-01 2.50e+01 7.34e-01
  chirality pdb=" CA  PRO B  50 "
            pdb=" N   PRO B  50 "
            pdb=" C   PRO B  50 "
            pdb=" CB  PRO B  50 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.56    0.15 2.00e-01 2.50e+01 6.00e-01
  ... (remaining 1091 not shown)

  Planarity restraints: 1138
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY B 283 "    0.017 2.00e-02 2.50e+03   3.45e-02 1.19e+01
        pdb=" C   GLY B 283 "   -0.060 2.00e-02 2.50e+03
        pdb=" O   GLY B 283 "    0.022 2.00e-02 2.50e+03
        pdb=" N   LYS B 284 "    0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG A 147 "    0.017 2.00e-02 2.50e+03   3.34e-02 1.11e+01
        pdb=" C   ARG A 147 "   -0.058 2.00e-02 2.50e+03
        pdb=" O   ARG A 147 "    0.021 2.00e-02 2.50e+03
        pdb=" N   ILE A 148 "    0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A 283 "   -0.017 2.00e-02 2.50e+03   3.33e-02 1.11e+01
        pdb=" C   GLY A 283 "    0.058 2.00e-02 2.50e+03
        pdb=" O   GLY A 283 "   -0.021 2.00e-02 2.50e+03
        pdb=" N   LYS A 284 "   -0.019 2.00e-02 2.50e+03
  ... (remaining 1135 not shown)

  Histogram of nonbonded interaction distances:
        2.38 -     2.88: 2494
        2.88 -     3.39: 6197
        3.39 -     3.89: 10917
        3.89 -     4.40: 12627
        4.40 -     4.90: 21665
  Nonbonded interactions: 53900
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A 305 "
            pdb=" OG1 THR A 307 "
     model   vdw
     2.375 3.040
  nonbonded pdb=" OD1 ASP B 305 "
            pdb=" OG1 THR B 307 "
     model   vdw
     2.403 3.040
  nonbonded pdb=" NH2 ARG B  11 "
            pdb=" OD1 ASP B  34 "
     model   vdw
     2.412 3.120
  nonbonded pdb=" O   PHE B  21 "
            pdb=" OG1 THR B  25 "
     model   vdw
     2.444 3.040
  nonbonded pdb=" OH  TYR B 339 "
            pdb=" O   THR B 357 "
     model   vdw
     2.455 3.040
  ... (remaining 53895 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
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'B' and (resid 2 through 27 or (resid 28 and (name N or name CA or name C \ 
 or name O or name CB )) or resid 29 through 31 or (resid 32 through 33 and (nam \ 
e N or name CA or name C or name O or name CB )) or resid 34 through 37 or (resi \ 
d 38 and (name N or name CA or name C or name O or name CB )) or resid 39 throug \ 
h 63 or (resid 64 and (name N or name CA or name C or name O or name CB )) or re \ 
sid 65 through 190 or (resid 191 and (name N or name CA or name C or name O or n \ 
ame CB )) or resid 192 through 250 or (resid 251 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 252 through 257 or (resid 258 and (name N or  \ 
name CA or name C or name O or name CB )) or resid 259 through 437 or (resid 438 \ 
 and (name N or name CA or name C or name O or name CB )) or resid 439 through 5 \ 
01))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.860
  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:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.730
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:8.370
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.280
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8464
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      :  0.007   0.095   6576  Z= 0.310
  Angle     :  0.749   9.079   9002  Z= 0.426
  Chirality :  0.051   0.171   1094
  Planarity :  0.009   0.098   1138
  Dihedral  : 12.524 112.035   2278
  Min Nonbonded Distance : 2.375

Molprobity Statistics.
  All-atom Clashscore : 0.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  0.67 %
    Allowed  :  3.83 %
    Favored  : 95.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.16 (0.25), residues: 890
  helix: -0.80 (0.24), residues: 340
  sheet:  0.27 (0.38), residues: 182
  loop : -1.13 (0.30), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.020   0.003   ARG A 423 
 TYR   0.024   0.005   TYR B  53 
 PHE   0.017   0.003   PHE A 384 
 TRP   0.029   0.009   TRP A 393 
 HIS   0.006   0.002   HIS A 127 

Details of bonding type rmsd
  covalent geometry    : bond        0.00682 ( 6576)
  covalent geometry    : angle       0.74880 ( 9002)
  hydrogen bonds       : bond        0.10335 (  335)
  hydrogen bonds       : angle       6.79368 (  909)

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

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

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 76
  time to evaluate  : 0.296 
Fit side-chains
REVERT: B  153 GLU cc_start: 0.8990 (mm-30) cc_final: 0.8726 (mm-30)
REVERT: B  438 ARG cc_start: 0.7966 (mmm160) cc_final: 0.7521 (ttm170)
  outliers start: 4
  outliers final: 1
  residues processed: 79
  average time/residue: 0.6244
  time to fit residues: 51.8356
Evaluate side-chains
  51 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 50
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  370 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    0.5980
   chunk 33 optimal weight:    0.6980
   chunk 65 optimal weight:    0.0570
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9980
   chunk 45 optimal weight:    0.7980
   chunk 74 optimal weight:    3.9990
   overall best weight:    0.5898

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

Flipped N/Q/H residues before XYZ refinement:
A  93 ASN
B  93 ASN
B 432 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.083526 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2773 r_free = 0.2773 target = 0.069366 restraints weight = 11251.524|
|-----------------------------------------------------------------------------|
r_work (start): 0.2766 rms_B_bonded: 2.56
r_work: 0.2641 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.2502 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.2502
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8347
moved from start:          0.1271

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6576  Z= 0.119
  Angle     :  0.513   6.254   9002  Z= 0.270
  Chirality :  0.045   0.146   1094
  Planarity :  0.004   0.039   1138
  Dihedral  :  8.240 104.002   1048
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 1.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.12 %
    Favored  : 98.88 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  :  7.83 %
    Favored  : 90.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.56 (0.28), residues: 890
  helix:  1.20 (0.27), residues: 348
  sheet:  0.31 (0.39), residues: 172
  loop : -0.29 (0.33), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  70 
 TYR   0.011   0.001   TYR B 109 
 PHE   0.012   0.001   PHE A 315 
 TRP   0.018   0.002   TRP B 390 
 HIS   0.003   0.001   HIS B 397 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 6576)
  covalent geometry    : angle       0.51272 ( 9002)
  hydrogen bonds       : bond        0.03270 (  335)
  hydrogen bonds       : angle       4.82396 (  909)

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

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

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 60
  time to evaluate  : 0.260 
Fit side-chains
REVERT: A  250 ASP cc_start: 0.8541 (m-30) cc_final: 0.8205 (m-30)
REVERT: B   64 GLU cc_start: 0.8997 (OUTLIER) cc_final: 0.8457 (mp0)
REVERT: B   78 ASN cc_start: 0.8747 (m-40) cc_final: 0.8473 (t0)
REVERT: B  153 GLU cc_start: 0.9124 (mm-30) cc_final: 0.8856 (mm-30)
REVERT: B  156 GLU cc_start: 0.9242 (mm-30) cc_final: 0.8879 (mm-30)
REVERT: B  250 ASP cc_start: 0.8442 (m-30) cc_final: 0.8180 (m-30)
REVERT: B  438 ARG cc_start: 0.8244 (mmm160) cc_final: 0.7684 (ttm170)
  outliers start: 12
  outliers final: 4
  residues processed: 67
  average time/residue: 0.5740
  time to fit residues: 40.6832
Evaluate side-chains
  53 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 48
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 SER
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain B residue   64 GLU
Chi-restraints excluded: chain B residue  262 THR
Chi-restraints excluded: chain B residue  263 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 30 optimal weight:    0.0370
   chunk 21 optimal weight:    0.0070
   chunk 42 optimal weight:    0.5980
   chunk 54 optimal weight:    2.9990
   chunk 17 optimal weight:    0.6980
   chunk 64 optimal weight:    2.9990
   chunk 37 optimal weight:    5.9990
   chunk 62 optimal weight:    0.5980
   chunk 31 optimal weight:    1.9990
   chunk 81 optimal weight:    7.9990
   chunk 9 optimal weight:    4.9990
   overall best weight:    0.3876

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

Flipped N/Q/H residues before XYZ refinement:
A  93 ASN
B  93 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.085645 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2807 r_free = 0.2807 target = 0.071756 restraints weight = 11248.098|
|-----------------------------------------------------------------------------|
r_work (start): 0.2781 rms_B_bonded: 2.54
r_work: 0.2655 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.2511 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.2511
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8330
moved from start:          0.1629

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   6576  Z= 0.092
  Angle     :  0.441   5.553   9002  Z= 0.233
  Chirality :  0.043   0.138   1094
  Planarity :  0.004   0.042   1138
  Dihedral  :  7.805  96.163   1047
  Min Nonbonded Distance : 2.621

Molprobity Statistics.
  All-atom Clashscore : 1.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  :  9.00 %
    Favored  : 89.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.86 (0.28), residues: 890
  helix:  1.66 (0.28), residues: 350
  sheet:  0.20 (0.41), residues: 148
  loop : -0.19 (0.31), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  70 
 TYR   0.007   0.001   TYR B  53 
 PHE   0.008   0.001   PHE A 384 
 TRP   0.011   0.001   TRP B 390 
 HIS   0.004   0.001   HIS A 397 

Details of bonding type rmsd
  covalent geometry    : bond        0.00205 ( 6576)
  covalent geometry    : angle       0.44058 ( 9002)
  hydrogen bonds       : bond        0.02847 (  335)
  hydrogen bonds       : angle       4.38587 (  909)

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

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

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 52
  time to evaluate  : 0.233 
Fit side-chains
REVERT: A  250 ASP cc_start: 0.8513 (m-30) cc_final: 0.8223 (m-30)
REVERT: A  405 LYS cc_start: 0.8667 (tmtp) cc_final: 0.8431 (tmtp)
REVERT: B   64 GLU cc_start: 0.8968 (OUTLIER) cc_final: 0.8455 (mp0)
REVERT: B   78 ASN cc_start: 0.8735 (m-40) cc_final: 0.8309 (t0)
REVERT: B  156 GLU cc_start: 0.9258 (mm-30) cc_final: 0.8911 (mm-30)
REVERT: B  250 ASP cc_start: 0.8430 (m-30) cc_final: 0.8201 (m-30)
REVERT: B  438 ARG cc_start: 0.8247 (mmm160) cc_final: 0.7567 (ttm170)
  outliers start: 12
  outliers final: 3
  residues processed: 60
  average time/residue: 0.5755
  time to fit residues: 36.4956
Evaluate side-chains
  50 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 46
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   64 GLU
Chi-restraints excluded: chain B residue  259 SER
Chi-restraints excluded: chain B residue  262 THR
Chi-restraints excluded: chain B residue  263 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 36 optimal weight:    5.9990
   chunk 24 optimal weight:    5.9990
   chunk 42 optimal weight:    1.9990
   chunk 59 optimal weight:    1.9990
   chunk 50 optimal weight:    2.9990
   chunk 63 optimal weight:    3.9990
   chunk 1 optimal weight:    3.9990
   chunk 32 optimal weight:    4.9990
   chunk 46 optimal weight:    3.9990
   chunk 15 optimal weight:    3.9990
   chunk 61 optimal weight:    4.9990
   overall best weight:    2.9990

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

Flipped N/Q/H residues before XYZ refinement:
A  93 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2923 r_free = 0.2923 target = 0.078158 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2671 r_free = 0.2671 target = 0.064216 restraints weight = 11677.819|
|-----------------------------------------------------------------------------|
r_work (start): 0.2666 rms_B_bonded: 2.47
r_work: 0.2541 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.2399 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.2399
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8477
moved from start:          0.1791

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.047   6576  Z= 0.382
  Angle     :  0.630   8.891   9002  Z= 0.320
  Chirality :  0.050   0.155   1094
  Planarity :  0.005   0.043   1138
  Dihedral  :  7.867  86.336   1047
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 2.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  3.50 %
    Allowed  :  9.00 %
    Favored  : 87.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.46 (0.28), residues: 890
  helix:  1.30 (0.27), residues: 348
  sheet: -0.27 (0.37), residues: 182
  loop : -0.25 (0.33), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 265 
 TYR   0.012   0.002   TYR A 109 
 PHE   0.013   0.002   PHE A 152 
 TRP   0.012   0.001   TRP B 390 
 HIS   0.004   0.001   HIS B  12 

Details of bonding type rmsd
  covalent geometry    : bond        0.00904 ( 6576)
  covalent geometry    : angle       0.62953 ( 9002)
  hydrogen bonds       : bond        0.03784 (  335)
  hydrogen bonds       : angle       4.55257 (  909)

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

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

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 47
  time to evaluate  : 0.275 
Fit side-chains
REVERT: A  136 LYS cc_start: 0.8832 (tptt) cc_final: 0.8588 (tptt)
REVERT: A  250 ASP cc_start: 0.8713 (m-30) cc_final: 0.8422 (m-30)
REVERT: B   78 ASN cc_start: 0.9068 (m-40) cc_final: 0.8820 (t0)
REVERT: B  156 GLU cc_start: 0.9408 (mm-30) cc_final: 0.9128 (mm-30)
REVERT: B  438 ARG cc_start: 0.8272 (mmm160) cc_final: 0.7671 (ttm170)
  outliers start: 21
  outliers final: 6
  residues processed: 63
  average time/residue: 0.6015
  time to fit residues: 39.9871
Evaluate side-chains
  52 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 46
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  259 SER
Chi-restraints excluded: chain A residue  329 VAL
Chi-restraints excluded: chain B residue  259 SER
Chi-restraints excluded: chain B residue  262 THR
Chi-restraints excluded: chain B residue  263 ILE
Chi-restraints excluded: chain B residue  329 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 57 optimal weight:    0.9990
   chunk 1 optimal weight:    0.6980
   chunk 12 optimal weight:    0.7980
   chunk 17 optimal weight:    0.9980
   chunk 8 optimal weight:    0.7980
   chunk 72 optimal weight:    0.6980
   chunk 26 optimal weight:    0.9980
   chunk 10 optimal weight:    0.9990
   chunk 4 optimal weight:    0.5980
   chunk 7 optimal weight:    0.7980
   chunk 13 optimal weight:    0.3980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A  93 ASN
B  93 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2989 r_free = 0.2989 target = 0.081882 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2743 r_free = 0.2743 target = 0.067734 restraints weight = 11333.480|
|-----------------------------------------------------------------------------|
r_work (start): 0.2732 rms_B_bonded: 2.53
r_work: 0.2606 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.2464 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.2464
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8385
moved from start:          0.1984

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6576  Z= 0.111
  Angle     :  0.467   7.954   9002  Z= 0.240
  Chirality :  0.044   0.151   1094
  Planarity :  0.004   0.044   1138
  Dihedral  :  7.156  87.172   1047
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 2.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 10.50 %
    Favored  : 87.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.79 (0.28), residues: 890
  helix:  1.74 (0.28), residues: 350
  sheet: -0.36 (0.36), residues: 182
  loop : -0.11 (0.34), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  70 
 TYR   0.007   0.001   TYR A 109 
 PHE   0.008   0.001   PHE B 384 
 TRP   0.006   0.001   TRP A 393 
 HIS   0.004   0.001   HIS A 397 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 6576)
  covalent geometry    : angle       0.46693 ( 9002)
  hydrogen bonds       : bond        0.02855 (  335)
  hydrogen bonds       : angle       4.24635 (  909)

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

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

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 53
  time to evaluate  : 0.276 
Fit side-chains
REVERT: A  250 ASP cc_start: 0.8662 (m-30) cc_final: 0.8377 (m-30)
REVERT: B   78 ASN cc_start: 0.8985 (m-40) cc_final: 0.8745 (t0)
REVERT: B  156 GLU cc_start: 0.9348 (mm-30) cc_final: 0.8932 (mm-30)
REVERT: B  250 ASP cc_start: 0.8623 (m-30) cc_final: 0.8393 (m-30)
REVERT: B  438 ARG cc_start: 0.8307 (mmm160) cc_final: 0.7735 (ttm170)
  outliers start: 11
  outliers final: 3
  residues processed: 61
  average time/residue: 0.5707
  time to fit residues: 36.9089
Evaluate side-chains
  52 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 49
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  262 THR
Chi-restraints excluded: chain B residue  263 ILE
Chi-restraints excluded: chain B residue  329 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 52 optimal weight:    0.2980
   chunk 87 optimal weight:    2.9990
   chunk 3 optimal weight:    3.9990
   chunk 54 optimal weight:    3.9990
   chunk 25 optimal weight:    0.2980
   chunk 66 optimal weight:    0.9990
   chunk 22 optimal weight:    0.9980
   chunk 74 optimal weight:    1.9990
   chunk 56 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 63 optimal weight:    2.9990
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
A  93 ASN
B  93 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2982 r_free = 0.2982 target = 0.081635 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2733 r_free = 0.2733 target = 0.067430 restraints weight = 11336.805|
|-----------------------------------------------------------------------------|
r_work (start): 0.2724 rms_B_bonded: 2.54
r_work: 0.2599 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.2456 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.2456
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8390
moved from start:          0.2114

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6576  Z= 0.138
  Angle     :  0.466   7.524   9002  Z= 0.238
  Chirality :  0.044   0.146   1094
  Planarity :  0.004   0.043   1138
  Dihedral  :  6.897  84.444   1047
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 2.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 10.33 %
    Favored  : 87.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.89 (0.29), residues: 890
  helix:  1.89 (0.28), residues: 350
  sheet: -0.46 (0.36), residues: 182
  loop : -0.03 (0.34), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 264 
 TYR   0.006   0.001   TYR B 109 
 PHE   0.007   0.001   PHE A 152 
 TRP   0.006   0.001   TRP B 390 
 HIS   0.003   0.001   HIS A 397 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 6576)
  covalent geometry    : angle       0.46553 ( 9002)
  hydrogen bonds       : bond        0.02855 (  335)
  hydrogen bonds       : angle       4.20935 (  909)

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

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

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 60
  time to evaluate  : 0.288 
Fit side-chains
REVERT: A  250 ASP cc_start: 0.8671 (m-30) cc_final: 0.8402 (m-30)
REVERT: A  405 LYS cc_start: 0.8917 (tmmt) cc_final: 0.8657 (tmtm)
REVERT: B   78 ASN cc_start: 0.8984 (m-40) cc_final: 0.8755 (t0)
REVERT: B  250 ASP cc_start: 0.8622 (m-30) cc_final: 0.8407 (m-30)
REVERT: B  438 ARG cc_start: 0.8304 (mmm160) cc_final: 0.7727 (ttm170)
  outliers start: 14
  outliers final: 7
  residues processed: 71
  average time/residue: 0.6283
  time to fit residues: 46.9107
Evaluate side-chains
  55 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 48
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  367 MET
Chi-restraints excluded: chain A residue  396 LEU
Chi-restraints excluded: chain B residue  259 SER
Chi-restraints excluded: chain B residue  262 THR
Chi-restraints excluded: chain B residue  263 ILE
Chi-restraints excluded: chain B residue  329 VAL
Chi-restraints excluded: chain B residue  396 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 78 optimal weight:    0.9980
   chunk 66 optimal weight:    0.0970
   chunk 0 optimal weight:   10.0000
   chunk 23 optimal weight:    2.9990
   chunk 52 optimal weight:    0.9990
   chunk 50 optimal weight:    0.9990
   chunk 10 optimal weight:    1.9990
   chunk 61 optimal weight:    3.9990
   chunk 49 optimal weight:    1.9990
   chunk 6 optimal weight:    2.9990
   chunk 87 optimal weight:    2.9990
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
A  93 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.081580 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2731 r_free = 0.2731 target = 0.067375 restraints weight = 11220.710|
|-----------------------------------------------------------------------------|
r_work (start): 0.2724 rms_B_bonded: 2.53
r_work: 0.2598 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.2456 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.2456
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8392
moved from start:          0.2197

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6576  Z= 0.146
  Angle     :  0.471   7.002   9002  Z= 0.240
  Chirality :  0.044   0.162   1094
  Planarity :  0.004   0.043   1138
  Dihedral  :  6.901  88.797   1047
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 2.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 12.33 %
    Favored  : 85.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.93 (0.29), residues: 890
  helix:  1.97 (0.28), residues: 350
  sheet: -0.49 (0.36), residues: 182
  loop : -0.02 (0.34), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 264 
 TYR   0.007   0.001   TYR A 109 
 PHE   0.007   0.001   PHE A 152 
 TRP   0.006   0.001   TRP B 390 
 HIS   0.002   0.001   HIS A 397 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 ( 6576)
  covalent geometry    : angle       0.47114 ( 9002)
  hydrogen bonds       : bond        0.02857 (  335)
  hydrogen bonds       : angle       4.17652 (  909)

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

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

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 50
  time to evaluate  : 0.250 
Fit side-chains
REVERT: A  250 ASP cc_start: 0.8680 (m-30) cc_final: 0.8414 (m-30)
REVERT: A  405 LYS cc_start: 0.8901 (tmmt) cc_final: 0.8647 (tmtm)
REVERT: B   78 ASN cc_start: 0.9009 (m-40) cc_final: 0.8789 (t0)
REVERT: B  250 ASP cc_start: 0.8624 (m-30) cc_final: 0.8415 (m-30)
REVERT: B  438 ARG cc_start: 0.8302 (mmm160) cc_final: 0.7771 (ttm170)
  outliers start: 14
  outliers final: 7
  residues processed: 61
  average time/residue: 0.5654
  time to fit residues: 36.5241
Evaluate side-chains
  53 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 46
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  367 MET
Chi-restraints excluded: chain A residue  396 LEU
Chi-restraints excluded: chain B residue  259 SER
Chi-restraints excluded: chain B residue  262 THR
Chi-restraints excluded: chain B residue  263 ILE
Chi-restraints excluded: chain B residue  329 VAL
Chi-restraints excluded: chain B residue  396 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 60 optimal weight:    4.9990
   chunk 33 optimal weight:    1.9990
   chunk 43 optimal weight:    3.9990
   chunk 4 optimal weight:    0.9980
   chunk 56 optimal weight:    0.9980
   chunk 30 optimal weight:    6.9990
   chunk 37 optimal weight:    6.9990
   chunk 31 optimal weight:    0.6980
   chunk 61 optimal weight:    1.9990
   chunk 34 optimal weight:    2.9990
   chunk 25 optimal weight:    2.9990
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
** A  49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  93 ASN
B  93 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2962 r_free = 0.2962 target = 0.080426 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2707 r_free = 0.2707 target = 0.066096 restraints weight = 11401.191|
|-----------------------------------------------------------------------------|
r_work (start): 0.2703 rms_B_bonded: 2.54
r_work: 0.2580 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.2439 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.2439
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8410
moved from start:          0.2254

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   6576  Z= 0.181
  Angle     :  0.491   6.797   9002  Z= 0.249
  Chirality :  0.044   0.156   1094
  Planarity :  0.004   0.043   1138
  Dihedral  :  6.753  82.857   1047
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 2.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 12.00 %
    Favored  : 85.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.92 (0.29), residues: 890
  helix:  1.97 (0.28), residues: 350
  sheet: -0.53 (0.36), residues: 182
  loop : -0.03 (0.34), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 265 
 TYR   0.007   0.001   TYR A 109 
 PHE   0.008   0.001   PHE A 152 
 TRP   0.006   0.001   TRP B 390 
 HIS   0.002   0.001   HIS B  12 

Details of bonding type rmsd
  covalent geometry    : bond        0.00426 ( 6576)
  covalent geometry    : angle       0.49103 ( 9002)
  hydrogen bonds       : bond        0.02980 (  335)
  hydrogen bonds       : angle       4.20399 (  909)

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

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

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 47
  time to evaluate  : 0.249 
Fit side-chains
REVERT: A  250 ASP cc_start: 0.8707 (m-30) cc_final: 0.8445 (m-30)
REVERT: B   78 ASN cc_start: 0.9047 (m-40) cc_final: 0.8816 (t0)
REVERT: B  120 GLN cc_start: 0.8634 (OUTLIER) cc_final: 0.7182 (pp30)
REVERT: B  156 GLU cc_start: 0.9332 (mm-30) cc_final: 0.9050 (mm-30)
REVERT: B  438 ARG cc_start: 0.8322 (mmm160) cc_final: 0.7793 (ttm170)
  outliers start: 14
  outliers final: 10
  residues processed: 57
  average time/residue: 0.5617
  time to fit residues: 33.8653
Evaluate side-chains
  58 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 47
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 LEU
Chi-restraints excluded: chain A residue  329 VAL
Chi-restraints excluded: chain A residue  367 MET
Chi-restraints excluded: chain A residue  396 LEU
Chi-restraints excluded: chain B residue   62 GLU
Chi-restraints excluded: chain B residue  120 GLN
Chi-restraints excluded: chain B residue  259 SER
Chi-restraints excluded: chain B residue  262 THR
Chi-restraints excluded: chain B residue  263 ILE
Chi-restraints excluded: chain B residue  329 VAL
Chi-restraints excluded: chain B residue  396 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 3 optimal weight:    1.9990
   chunk 35 optimal weight:    5.9990
   chunk 21 optimal weight:    0.7980
   chunk 71 optimal weight:    3.9990
   chunk 32 optimal weight:    0.9980
   chunk 38 optimal weight:    1.9990
   chunk 4 optimal weight:    0.0670
   chunk 16 optimal weight:    0.9980
   chunk 87 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9980
   overall best weight:    0.7718

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

Flipped N/Q/H residues before XYZ refinement:
** A  49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  93 ASN
A 311 HIS
B  93 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2989 r_free = 0.2989 target = 0.082093 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2736 r_free = 0.2736 target = 0.067700 restraints weight = 11362.297|
|-----------------------------------------------------------------------------|
r_work (start): 0.2730 rms_B_bonded: 2.57
r_work: 0.2602 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.2460 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.2460
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8386
moved from start:          0.2343

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6576  Z= 0.119
  Angle     :  0.461   6.579   9002  Z= 0.234
  Chirality :  0.043   0.159   1094
  Planarity :  0.004   0.043   1138
  Dihedral  :  6.067  83.428   1047
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 2.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.46 %
    Favored  : 98.54 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 12.50 %
    Favored  : 85.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.03 (0.29), residues: 890
  helix:  2.07 (0.28), residues: 350
  sheet: -0.45 (0.36), residues: 182
  loop :  0.00 (0.34), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  70 
 TYR   0.007   0.001   TYR B 109 
 PHE   0.007   0.001   PHE A 384 
 TRP   0.006   0.001   TRP A 393 
 HIS   0.002   0.000   HIS A 397 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 6576)
  covalent geometry    : angle       0.46059 ( 9002)
  hydrogen bonds       : bond        0.02740 (  335)
  hydrogen bonds       : angle       4.14297 (  909)

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

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

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 50
  time to evaluate  : 0.263 
Fit side-chains
REVERT: A  250 ASP cc_start: 0.8694 (m-30) cc_final: 0.8423 (m-30)
REVERT: A  405 LYS cc_start: 0.8918 (tmmt) cc_final: 0.8660 (tmtm)
REVERT: B   78 ASN cc_start: 0.9015 (m-40) cc_final: 0.8770 (t0)
REVERT: B  120 GLN cc_start: 0.8591 (OUTLIER) cc_final: 0.7136 (pp30)
REVERT: B  156 GLU cc_start: 0.9336 (mm-30) cc_final: 0.9049 (mm-30)
REVERT: B  250 ASP cc_start: 0.8635 (m-30) cc_final: 0.8425 (m-30)
REVERT: B  438 ARG cc_start: 0.8294 (mmm160) cc_final: 0.7780 (ttm170)
  outliers start: 12
  outliers final: 6
  residues processed: 61
  average time/residue: 0.5260
  time to fit residues: 34.0289
Evaluate side-chains
  56 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 49
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 LEU
Chi-restraints excluded: chain A residue  329 VAL
Chi-restraints excluded: chain B residue  120 GLN
Chi-restraints excluded: chain B residue  262 THR
Chi-restraints excluded: chain B residue  263 ILE
Chi-restraints excluded: chain B residue  329 VAL
Chi-restraints excluded: chain B residue  396 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 57 optimal weight:    2.9990
   chunk 17 optimal weight:    3.9990
   chunk 65 optimal weight:    0.0470
   chunk 64 optimal weight:    0.9980
   chunk 47 optimal weight:    1.9990
   chunk 58 optimal weight:    0.6980
   chunk 22 optimal weight:    6.9990
   chunk 41 optimal weight:    0.8980
   chunk 80 optimal weight:    0.0670
   chunk 14 optimal weight:    0.8980
   chunk 21 optimal weight:    0.0370
   overall best weight:    0.3494

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

Flipped N/Q/H residues before XYZ refinement:
** A  49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  93 ASN
B  93 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3030 r_free = 0.3030 target = 0.084443 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2784 r_free = 0.2784 target = 0.070141 restraints weight = 11037.285|
|-----------------------------------------------------------------------------|
r_work (start): 0.2776 rms_B_bonded: 2.51
r_work: 0.2652 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.2509 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.2509
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8353
moved from start:          0.2521

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   6576  Z= 0.086
  Angle     :  0.443   6.139   9002  Z= 0.225
  Chirality :  0.043   0.155   1094
  Planarity :  0.004   0.044   1138
  Dihedral  :  5.835  73.745   1047
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 3.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.35 %
    Favored  : 98.65 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 13.50 %
    Favored  : 85.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.37 (0.29), residues: 890
  helix:  2.47 (0.29), residues: 338
  sheet: -0.31 (0.37), residues: 182
  loop :  0.18 (0.34), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 264 
 TYR   0.006   0.001   TYR B  53 
 PHE   0.007   0.001   PHE A 152 
 TRP   0.008   0.001   TRP A 393 
 HIS   0.003   0.000   HIS A 397 

Details of bonding type rmsd
  covalent geometry    : bond        0.00190 ( 6576)
  covalent geometry    : angle       0.44306 ( 9002)
  hydrogen bonds       : bond        0.02465 (  335)
  hydrogen bonds       : angle       4.04058 (  909)

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

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

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 58
  time to evaluate  : 0.262 
Fit side-chains
REVERT: A  250 ASP cc_start: 0.8679 (m-30) cc_final: 0.8436 (m-30)
REVERT: B   78 ASN cc_start: 0.8901 (m-40) cc_final: 0.8689 (t0)
REVERT: B  156 GLU cc_start: 0.9324 (mm-30) cc_final: 0.9048 (mm-30)
REVERT: B  438 ARG cc_start: 0.8283 (mmm160) cc_final: 0.7648 (ttm170)
REVERT: B  442 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.8113 (mm)
  outliers start: 9
  outliers final: 6
  residues processed: 67
  average time/residue: 0.5320
  time to fit residues: 37.8348
Evaluate side-chains
  54 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 47
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 LEU
Chi-restraints excluded: chain A residue  329 VAL
Chi-restraints excluded: chain B residue  259 SER
Chi-restraints excluded: chain B residue  262 THR
Chi-restraints excluded: chain B residue  263 ILE
Chi-restraints excluded: chain B residue  396 LEU
Chi-restraints excluded: chain B residue  442 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 28 optimal weight:    0.8980
   chunk 39 optimal weight:    0.7980
   chunk 26 optimal weight:    0.7980
   chunk 38 optimal weight:    0.8980
   chunk 68 optimal weight:    0.0970
   chunk 37 optimal weight:    1.9990
   chunk 54 optimal weight:    2.9990
   chunk 42 optimal weight:    0.6980
   chunk 64 optimal weight:    0.8980
   chunk 55 optimal weight:    2.9990
   chunk 57 optimal weight:    0.0040
   overall best weight:    0.4790

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

Flipped N/Q/H residues before XYZ refinement:
** A  49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  93 ASN
B  93 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3032 r_free = 0.3032 target = 0.085139 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2788 r_free = 0.2788 target = 0.071237 restraints weight = 11308.206|
|-----------------------------------------------------------------------------|
r_work (start): 0.2770 rms_B_bonded: 2.51
r_work: 0.2646 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.2503 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.2503
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8360
moved from start:          0.2589

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   6576  Z= 0.098
  Angle     :  0.454   6.129   9002  Z= 0.233
  Chirality :  0.043   0.133   1094
  Planarity :  0.004   0.044   1138
  Dihedral  :  5.835  68.730   1047
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 3.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.35 %
    Favored  : 98.65 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 14.17 %
    Favored  : 84.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.39 (0.29), residues: 890
  helix:  2.43 (0.28), residues: 338
  sheet: -0.25 (0.37), residues: 182
  loop :  0.22 (0.34), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 264 
 TYR   0.006   0.001   TYR B 109 
 PHE   0.005   0.001   PHE A 152 
 TRP   0.005   0.001   TRP A 393 
 HIS   0.003   0.000   HIS A 397 

Details of bonding type rmsd
  covalent geometry    : bond        0.00222 ( 6576)
  covalent geometry    : angle       0.45367 ( 9002)
  hydrogen bonds       : bond        0.02546 (  335)
  hydrogen bonds       : angle       4.07182 (  909)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2250.47 seconds
wall clock time: 39 minutes 12.95 seconds (2352.95 seconds total)