Starting phenix.real_space_refine
on Fri Aug 22 23:01:50 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8kae_37008/08_2025/8kae_37008.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8kae_37008/08_2025/8kae_37008.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.18
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8kae_37008/08_2025/8kae_37008.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8kae_37008/08_2025/8kae_37008.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8kae_37008/08_2025/8kae_37008.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8kae_37008/08_2025/8kae_37008.cif"
  }
  resolution = 3.18
  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=  -0.002 sd=   0.108
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      41      5.16       5
     C    5393      2.51       5
     N    1412      2.21       5
     O    1594      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 55 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8440
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "H"
      Number of atoms: 1732
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 229, 1732
          Classifications: {'peptide': 229}
          Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 217}
    Chain: "K"
      Number of atoms: 922
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 120, 922
          Classifications: {'peptide': 120}
          Link IDs: {'PTRANS': 3, 'TRANS': 116}
    Chain: "L"
      Number of atoms: 1619
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 213, 1619
          Classifications: {'peptide': 213}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 202}
    Chain: "N"
      Number of atoms: 959
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 126, 959
          Classifications: {'peptide': 126}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 119}
    Chain: "R"
      Number of atoms: 3183
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 417, 3183
          Classifications: {'peptide': 417}
          Link IDs: {'PTRANS': 12, 'TRANS': 404}
          Chain breaks: 2
    Chain: "R"
      Number of atoms: 25
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 25
          Unusual residues: {'YUX': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.30, per 1000 atoms: 0.27
  Number of scatterers: 8440
  At special positions: 0
  Unit cell: (78.1, 89.1, 163.9, 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      41     16.00
     O    1594      8.00
     N    1412      7.00
     C    5393      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  26 " - pdb=" SG  CYS H 100 " distance=2.05
    Simple disulfide: pdb=" SG  CYS H 159 " - pdb=" SG  CYS H 215 " distance=2.03
    Simple disulfide: pdb=" SG  CYS K  22 " - pdb=" SG  CYS K  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  25 " - pdb=" SG  CYS L  90 " distance=2.05
    Simple disulfide: pdb=" SG  CYS L 136 " - pdb=" SG  CYS L 196 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  97 " distance=2.05

  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: 0.75
  Conformation dependent library (CDL) restraints added in 474.7 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2010

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 16 sheets defined
      37.1% alpha, 29.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.38
  Creating SS restraints...
    Processing helix  chain 'H' and resid 32 through 36
      removed outlier: 3.841A  pdb=" N   TYR H  36 " --> pdb=" O   PHE H  33 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 91 through 95
      removed outlier: 3.569A  pdb=" N   ASP H  94 " --> pdb=" O   ARG H  91 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   THR H  95 " --> pdb=" O   ALA H  92 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 91 through 95'
    Processing helix  chain 'H' and resid 175 through 177
      No H-bonds generated for 'chain 'H' and resid 175 through 177'
    Processing helix  chain 'H' and resid 206 through 211
      removed outlier: 4.211A  pdb=" N   THR H 210 " --> pdb=" O   SER H 206 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 62 through 65
    Processing helix  chain 'K' and resid 87 through 91
    Processing helix  chain 'L' and resid 123 through 130
      removed outlier: 3.730A  pdb=" N   SER L 129 " --> pdb=" O   SER L 125 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 185 through 189
    Processing helix  chain 'N' and resid 88 through 92
      removed outlier: 3.793A  pdb=" N   THR N  92 " --> pdb=" O   PRO N  89 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 101 through 118
    Processing helix  chain 'R' and resid 122 through 124
      No H-bonds generated for 'chain 'R' and resid 122 through 124'
    Processing helix  chain 'R' and resid 125 through 134
      removed outlier: 3.575A  pdb=" N   GLN R 130 " --> pdb=" O   LEU R 126 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   GLN R 131 " --> pdb=" O   LEU R 127 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 136 through 165
      removed outlier: 3.989A  pdb=" N   LEU R 142 " --> pdb=" O   ARG R 138 " (cutoff:3.500A)
      removed outlier: 4.653A  pdb=" N   LEU R 143 " --> pdb=" O   GLY R 139 " (cutoff:3.500A)
      removed outlier: 5.313A  pdb=" N   GLN R 144 " --> pdb=" O   ALA R 140 " (cutoff:3.500A)
      removed outlier: 4.248A  pdb=" N   PHE R 147 " --> pdb=" O   LEU R 143 " (cutoff:3.500A)
      Proline residue:  R 156  - end of helix
      removed outlier: 3.526A  pdb=" N   GLY R 162 " --> pdb=" O   PHE R 158 " (cutoff:3.500A)
      removed outlier: 4.322A  pdb=" N   ASP R 163 " --> pdb=" O   GLY R 159 " (cutoff:3.500A)
      removed outlier: 3.946A  pdb=" N   ARG R 164 " --> pdb=" O   TYR R 160 " (cutoff:3.500A)
      removed outlier: 4.157A  pdb=" N   PHE R 165 " --> pdb=" O   LEU R 161 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 167 through 185
    Processing helix  chain 'R' and resid 186 through 188
      No H-bonds generated for 'chain 'R' and resid 186 through 188'
    Processing helix  chain 'R' and resid 193 through 220
      removed outlier: 3.557A  pdb=" N   VAL R 197 " --> pdb=" O   PHE R 193 " (cutoff:3.500A)
      Proline residue:  R 215  - end of helix
    Processing helix  chain 'R' and resid 226 through 236
    Processing helix  chain 'R' and resid 237 through 257
      removed outlier: 3.627A  pdb=" N   GLY R 241 " --> pdb=" O   ALA R 237 " (cutoff:3.500A)
      removed outlier: 3.922A  pdb=" N   TYR R 246 " --> pdb=" O   SER R 242 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 258 through 264
      removed outlier: 3.625A  pdb=" N   ARG R 264 " --> pdb=" O   TRP R 261 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 265 through 277
      removed outlier: 4.221A  pdb=" N   LEU R 269 " --> pdb=" O   VAL R 265 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 302 through 310
      removed outlier: 3.606A  pdb=" N   LYS R 307 " --> pdb=" O   LEU R 303 " (cutoff:3.500A)
      removed outlier: 3.913A  pdb=" N   ALA R 308 " --> pdb=" O   ARG R 304 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 312 through 347
      removed outlier: 3.968A  pdb=" N   VAL R 325 " --> pdb=" O   ALA R 321 " (cutoff:3.500A)
      Proline residue:  R 337  - end of helix
    Processing helix  chain 'R' and resid 362 through 389
      removed outlier: 3.936A  pdb=" N   PHE R 372 " --> pdb=" O   ALA R 368 " (cutoff:3.500A)
      removed outlier: 4.996A  pdb=" N   PHE R 375 " --> pdb=" O   CYS R 371 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   VAL R 378 " --> pdb=" O   GLY R 374 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 394 through 412
      removed outlier: 3.791A  pdb=" N   LEU R 398 " --> pdb=" O   ARG R 394 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 413 through 418
    Processing helix  chain 'R' and resid 422 through 438
      removed outlier: 3.886A  pdb=" N   PHE R 437 " --> pdb=" O   GLU R 433 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   SER R 438 " --> pdb=" O   THR R 434 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 442 through 448
    Processing helix  chain 'R' and resid 456 through 470
    Processing helix  chain 'R' and resid 474 through 488
      removed outlier: 3.615A  pdb=" N   LEU R 478 " --> pdb=" O   GLY R 474 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 493 through 505
    Processing helix  chain 'R' and resid 506 through 541
      removed outlier: 4.221A  pdb=" N   PHE R 510 " --> pdb=" O   MET R 506 " (cutoff:3.500A)
      removed outlier: 4.001A  pdb=" N   PHE R 525 " --> pdb=" O   ALA R 521 " (cutoff:3.500A)
      removed outlier: 5.610A  pdb=" N   VAL R 527 " --> pdb=" O   ALA R 523 " (cutoff:3.500A)
      removed outlier: 5.681A  pdb=" N   SER R 528 " --> pdb=" O   LEU R 524 " (cutoff:3.500A)
      removed outlier: 4.310A  pdb=" N   ALA R 541 " --> pdb=" O   VAL R 537 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'H' and resid 7 through 11
    Processing sheet with id=AA2, first strand: chain 'H' and resid 14 through 16
      removed outlier: 6.130A  pdb=" N   GLY H  14 " --> pdb=" O   THR H 129 " (cutoff:3.500A)
      removed outlier: 6.767A  pdb=" N   ILE H  38 " --> pdb=" O   TYR H  54 " (cutoff:3.500A)
      removed outlier: 4.453A  pdb=" N   TYR H  54 " --> pdb=" O   ILE H  38 " (cutoff:3.500A)
      removed outlier: 6.566A  pdb=" N   TRP H  40 " --> pdb=" O   VAL H  52 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'H' and resid 139 through 143
      removed outlier: 5.955A  pdb=" N   TYR H 195 " --> pdb=" O   ASP H 163 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'H' and resid 139 through 143
      removed outlier: 5.955A  pdb=" N   TYR H 195 " --> pdb=" O   ASP H 163 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'H' and resid 169 through 173
    Processing sheet with id=AA6, first strand: chain 'K' and resid 3 through 7
    Processing sheet with id=AA7, first strand: chain 'K' and resid 10 through 12
      removed outlier: 6.577A  pdb=" N   GLY K  10 " --> pdb=" O   THR K 118 " (cutoff:3.500A)
      removed outlier: 6.751A  pdb=" N   MET K  34 " --> pdb=" O   VAL K  50 " (cutoff:3.500A)
      removed outlier: 4.731A  pdb=" N   VAL K  50 " --> pdb=" O   MET K  34 " (cutoff:3.500A)
      removed outlier: 6.758A  pdb=" N   TRP K  36 " --> pdb=" O   VAL K  48 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'K' and resid 10 through 12
      removed outlier: 6.577A  pdb=" N   GLY K  10 " --> pdb=" O   THR K 118 " (cutoff:3.500A)
      removed outlier: 4.346A  pdb=" N   TYR K 110 " --> pdb=" O   ILE K  98 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'L' and resid 7 through 9
    Processing sheet with id=AB1, first strand: chain 'L' and resid 12 through 14
      removed outlier: 6.084A  pdb=" N   GLN L  39 " --> pdb=" O   LEU L  48 " (cutoff:3.500A)
      removed outlier: 5.777A  pdb=" N   LEU L  48 " --> pdb=" O   GLN L  39 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'L' and resid 12 through 14
    Processing sheet with id=AB3, first strand: chain 'L' and resid 116 through 120
      removed outlier: 6.128A  pdb=" N   TYR L 175 " --> pdb=" O   ASN L 140 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'L' and resid 155 through 156
    Processing sheet with id=AB5, first strand: chain 'N' and resid 5 through 7
    Processing sheet with id=AB6, first strand: chain 'N' and resid 10 through 12
      removed outlier: 6.147A  pdb=" N   GLY N  10 " --> pdb=" O   THR N 125 " (cutoff:3.500A)
      removed outlier: 6.615A  pdb=" N   TRP N  37 " --> pdb=" O   VAL N  49 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'N' and resid 10 through 12
      removed outlier: 6.147A  pdb=" N   GLY N  10 " --> pdb=" O   THR N 125 " (cutoff:3.500A)

    473 hydrogen bonds defined for protein.
    1281 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: 1.55

  Time building geometry restraints manager: 1.02 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2227
        1.33 -     1.45: 2073
        1.45 -     1.58: 4278
        1.58 -     1.70: 0
        1.70 -     1.83: 59
  Bond restraints: 8637
  Sorted by residual:
  bond pdb=" C07 YUX R 601 "
       pdb=" N06 YUX R 601 "
    ideal  model  delta    sigma   weight residual
    1.367  1.440 -0.073 2.00e-02 2.50e+03 1.32e+01
  bond pdb=" C07 YUX R 601 "
       pdb=" C08 YUX R 601 "
    ideal  model  delta    sigma   weight residual
    1.460  1.520 -0.060 2.00e-02 2.50e+03 9.14e+00
  bond pdb=" C04 YUX R 601 "
       pdb=" C05 YUX R 601 "
    ideal  model  delta    sigma   weight residual
    1.481  1.536 -0.055 2.00e-02 2.50e+03 7.61e+00
  bond pdb=" CB  VAL N  94 "
       pdb=" CG1 VAL N  94 "
    ideal  model  delta    sigma   weight residual
    1.521  1.431  0.090 3.30e-02 9.18e+02 7.43e+00
  bond pdb=" C07 YUX R 601 "
       pdb=" N24 YUX R 601 "
    ideal  model  delta    sigma   weight residual
    1.300  1.354 -0.054 2.00e-02 2.50e+03 7.37e+00
  ... (remaining 8632 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.38: 11267
        2.38 -     4.77: 386
        4.77 -     7.15: 67
        7.15 -     9.53: 6
        9.53 -    11.92: 4
  Bond angle restraints: 11730
  Sorted by residual:
  angle pdb=" CA  TRP R 178 "
        pdb=" CB  TRP R 178 "
        pdb=" CG  TRP R 178 "
      ideal   model   delta    sigma   weight residual
     113.60  123.37   -9.77 1.90e+00 2.77e-01 2.65e+01
  angle pdb=" C   SER L  95 "
        pdb=" N   SER L  96 "
        pdb=" CA  SER L  96 "
      ideal   model   delta    sigma   weight residual
     121.54  112.30    9.24 1.91e+00 2.74e-01 2.34e+01
  angle pdb=" C   TYR H 104 "
        pdb=" N   GLN H 105 "
        pdb=" CA  GLN H 105 "
      ideal   model   delta    sigma   weight residual
     121.54  130.40   -8.86 1.91e+00 2.74e-01 2.15e+01
  angle pdb=" CA  TYR N  32 "
        pdb=" CB  TYR N  32 "
        pdb=" CG  TYR N  32 "
      ideal   model   delta    sigma   weight residual
     113.90  122.23   -8.33 1.80e+00 3.09e-01 2.14e+01
  angle pdb=" C   THR N  34 "
        pdb=" CA  THR N  34 "
        pdb=" CB  THR N  34 "
      ideal   model   delta    sigma   weight residual
     109.34  103.07    6.27 1.55e+00 4.16e-01 1.63e+01
  ... (remaining 11725 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    26.56: 4875
       26.56 -    53.13: 162
       53.13 -    79.69: 11
       79.69 -   106.26: 2
      106.26 -   132.82: 3
  Dihedral angle restraints: 5053
    sinusoidal: 1890
      harmonic: 3163
  Sorted by residual:
  dihedral pdb=" CA  THR N  34 "
           pdb=" C   THR N  34 "
           pdb=" N   LEU N  35 "
           pdb=" CA  LEU N  35 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -143.57  -36.43     0      5.00e+00 4.00e-02 5.31e+01
  dihedral pdb=" CB  CYS L 136 "
           pdb=" SG  CYS L 136 "
           pdb=" SG  CYS L 196 "
           pdb=" CB  CYS L 196 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  152.59  -59.59     1      1.00e+01 1.00e-02 4.74e+01
  dihedral pdb=" CA  LEU N  35 "
           pdb=" C   LEU N  35 "
           pdb=" N   GLY N  36 "
           pdb=" CA  GLY N  36 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.00   26.00     0      5.00e+00 4.00e-02 2.70e+01
  ... (remaining 5050 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.056: 915
       0.056 -    0.113: 315
       0.113 -    0.169: 74
       0.169 -    0.226: 10
       0.226 -    0.282: 3
  Chirality restraints: 1317
  Sorted by residual:
  chirality pdb=" CB  THR N  34 "
            pdb=" CA  THR N  34 "
            pdb=" OG1 THR N  34 "
            pdb=" CG2 THR N  34 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.27    0.28 2.00e-01 2.50e+01 1.99e+00
  chirality pdb=" CA  HIS H 110 "
            pdb=" N   HIS H 110 "
            pdb=" C   HIS H 110 "
            pdb=" CB  HIS H 110 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.24 2.00e-01 2.50e+01 1.38e+00
  chirality pdb=" CA  PHE R 519 "
            pdb=" N   PHE R 519 "
            pdb=" C   PHE R 519 "
            pdb=" CB  PHE R 519 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.33e+00
  ... (remaining 1314 not shown)

  Planarity restraints: 1478
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA R 214 "   -0.073 5.00e-02 4.00e+02   1.08e-01 1.87e+01
        pdb=" N   PRO R 215 "    0.187 5.00e-02 4.00e+02
        pdb=" CA  PRO R 215 "   -0.056 5.00e-02 4.00e+02
        pdb=" CD  PRO R 215 "   -0.059 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE R 526 "   -0.033 2.00e-02 2.50e+03   2.70e-02 1.28e+01
        pdb=" CG  PHE R 526 "    0.062 2.00e-02 2.50e+03
        pdb=" CD1 PHE R 526 "   -0.007 2.00e-02 2.50e+03
        pdb=" CD2 PHE R 526 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE1 PHE R 526 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 PHE R 526 "   -0.007 2.00e-02 2.50e+03
        pdb=" CZ  PHE R 526 "   -0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR N  32 "   -0.034 2.00e-02 2.50e+03   2.20e-02 9.70e+00
        pdb=" CG  TYR N  32 "    0.049 2.00e-02 2.50e+03
        pdb=" CD1 TYR N  32 "    0.006 2.00e-02 2.50e+03
        pdb=" CD2 TYR N  32 "    0.005 2.00e-02 2.50e+03
        pdb=" CE1 TYR N  32 "   -0.010 2.00e-02 2.50e+03
        pdb=" CE2 TYR N  32 "   -0.008 2.00e-02 2.50e+03
        pdb=" CZ  TYR N  32 "   -0.006 2.00e-02 2.50e+03
        pdb=" OH  TYR N  32 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 1475 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 358
        2.70 -     3.25: 7885
        3.25 -     3.80: 12282
        3.80 -     4.35: 15294
        4.35 -     4.90: 27145
  Nonbonded interactions: 62964
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP N  74 "
            pdb=" NZ  LYS N  77 "
     model   vdw
     2.147 3.120
  nonbonded pdb=" OD1 ASP K  62 "
            pdb=" OG1 THR L 111 "
     model   vdw
     2.302 3.040
  nonbonded pdb=" O   THR R 284 "
            pdb=" OG1 THR R 284 "
     model   vdw
     2.313 3.040
  nonbonded pdb=" OG  SER H  21 "
            pdb=" O   MET H  87 "
     model   vdw
     2.314 3.040
  nonbonded pdb=" OD2 ASP H  77 "
            pdb=" NZ  LYS H  80 "
     model   vdw
     2.315 3.120
  ... (remaining 62959 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.170
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     10.270
  Find NCS groups from input model:        0.050
  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:1.390
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.140
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7828
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      :  0.013   0.105   8643  Z= 0.532
  Angle     :  1.059  11.918  11742  Z= 0.586
  Chirality :  0.060   0.282   1317
  Planarity :  0.007   0.108   1478
  Dihedral  : 13.537 132.821   3025
  Min Nonbonded Distance : 2.147

Molprobity Statistics.
  All-atom Clashscore : 7.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.24 %
    Favored  : 92.76 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.55 %
    Favored  : 99.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: 1091
  helix: -0.39 (0.26), residues: 370
  sheet:  0.20 (0.30), residues: 309
  loop : -1.79 (0.29), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG L  63 
 TYR   0.049   0.004   TYR N  32 
 PHE   0.062   0.004   PHE R 526 
 TRP   0.039   0.003   TRP R 178 
 HIS   0.009   0.002   HIS H 110 

Details of bonding type rmsd
  covalent geometry    : bond        0.01292 ( 8637)
  covalent geometry    : angle       1.05797 (11730)
  SS BOND              : bond        0.01261 (    6)
  SS BOND              : angle       1.95503 (   12)
  hydrogen bonds       : bond        0.14339 (  446)
  hydrogen bonds       : angle       6.84287 ( 1281)

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

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

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 0.320 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  163 ASP cc_start: 0.7809 (m-30) cc_final: 0.7579 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 96
  average time/residue: 0.1124
  time to fit residues: 14.6938
Evaluate side-chains
  87 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 49 optimal weight:   20.0000
   chunk 97 optimal weight:    0.6980
   chunk 53 optimal weight:   10.0000
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:   40.0000
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    6.9990
   chunk 100 optimal weight:    0.9980
   chunk 106 optimal weight:    0.7980
   chunk 38 optimal weight:    1.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
H 108 GLN
** L   8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4161 r_free = 0.4161 target = 0.189902 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.135559 restraints weight = 10263.321|
|-----------------------------------------------------------------------------|
r_work (start): 0.3589 rms_B_bonded: 2.52
r_work: 0.3317 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.3179 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.3179
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7920
moved from start:          0.1398

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8643  Z= 0.142
  Angle     :  0.592   6.121  11742  Z= 0.318
  Chirality :  0.043   0.146   1317
  Planarity :  0.005   0.073   1478
  Dihedral  :  6.930  93.894   1218
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 4.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  0.55 %
    Allowed  :  6.49 %
    Favored  : 92.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -0.13 (0.26), residues: 1091
  helix:  0.87 (0.28), residues: 374
  sheet:  0.76 (0.31), residues: 299
  loop : -1.63 (0.29), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG N  28 
 TYR   0.021   0.001   TYR N  32 
 PHE   0.019   0.001   PHE R 526 
 TRP   0.028   0.002   TRP R 178 
 HIS   0.003   0.001   HIS H 110 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 ( 8637)
  covalent geometry    : angle       0.59197 (11730)
  SS BOND              : bond        0.00640 (    6)
  SS BOND              : angle       0.96109 (   12)
  hydrogen bonds       : bond        0.06013 (  446)
  hydrogen bonds       : angle       5.12557 ( 1281)

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

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

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 100
  time to evaluate  : 0.332 
Fit side-chains
   revert: symmetry clash
REVERT: H   75 SER cc_start: 0.8495 (t) cc_final: 0.8238 (m)
REVERT: L    8 GLN cc_start: 0.6923 (mt0) cc_final: 0.6620 (mt0)
REVERT: L  190 LYS cc_start: 0.8331 (mmmm) cc_final: 0.7908 (mmtm)
  outliers start: 5
  outliers final: 3
  residues processed: 102
  average time/residue: 0.1071
  time to fit residues: 15.1567
Evaluate side-chains
  96 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 93
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   82 THR
Chi-restraints excluded: chain L residue  119 ILE
Chi-restraints excluded: chain R residue  423 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 6 optimal weight:    3.9990
   chunk 38 optimal weight:    3.9990
   chunk 75 optimal weight:    3.9990
   chunk 99 optimal weight:    0.4980
   chunk 33 optimal weight:   30.0000
   chunk 103 optimal weight:    2.9990
   chunk 76 optimal weight:    0.7980
   chunk 102 optimal weight:    0.5980
   chunk 93 optimal weight:    0.9980
   chunk 106 optimal weight:    0.9990
   chunk 28 optimal weight:   20.0000
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
H 108 GLN
** L   8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 140 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4176 r_free = 0.4176 target = 0.191500 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.135979 restraints weight = 10302.087|
|-----------------------------------------------------------------------------|
r_work (start): 0.3582 rms_B_bonded: 2.63
r_work: 0.3326 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3185 rms_B_bonded: 4.62 restraints_weight: 0.2500
r_work (final): 0.3185
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7900
moved from start:          0.1813

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8643  Z= 0.129
  Angle     :  0.557   7.054  11742  Z= 0.296
  Chirality :  0.042   0.138   1317
  Planarity :  0.004   0.060   1478
  Dihedral  :  6.305  83.927   1218
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 4.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  :  9.02 %
    Favored  : 89.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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:  0.38 (0.26), residues: 1091
  helix:  1.40 (0.29), residues: 366
  sheet:  1.17 (0.32), residues: 280
  loop : -1.38 (0.28), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG N  28 
 TYR   0.021   0.001   TYR N  32 
 PHE   0.017   0.001   PHE K  68 
 TRP   0.026   0.001   TRP R 178 
 HIS   0.003   0.001   HIS H 110 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 8637)
  covalent geometry    : angle       0.55677 (11730)
  SS BOND              : bond        0.00575 (    6)
  SS BOND              : angle       0.88545 (   12)
  hydrogen bonds       : bond        0.05393 (  446)
  hydrogen bonds       : angle       4.74807 ( 1281)

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

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

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 100
  time to evaluate  : 0.230 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   21 SER cc_start: 0.8279 (t) cc_final: 0.7998 (t)
REVERT: H   75 SER cc_start: 0.8441 (t) cc_final: 0.8195 (m)
REVERT: H  104 TYR cc_start: 0.8902 (OUTLIER) cc_final: 0.6352 (t80)
REVERT: L    8 GLN cc_start: 0.6858 (mt0) cc_final: 0.6519 (mt0)
REVERT: L  190 LYS cc_start: 0.8523 (mmmm) cc_final: 0.8127 (mmtm)
REVERT: N   91 ASP cc_start: 0.8789 (m-30) cc_final: 0.8302 (m-30)
  outliers start: 11
  outliers final: 9
  residues processed: 105
  average time/residue: 0.0967
  time to fit residues: 13.8261
Evaluate side-chains
  104 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 94
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   17 GLN
Chi-restraints excluded: chain H residue   82 THR
Chi-restraints excluded: chain H residue   87 MET
Chi-restraints excluded: chain H residue  104 TYR
Chi-restraints excluded: chain K residue   86 LEU
Chi-restraints excluded: chain L residue    6 MET
Chi-restraints excluded: chain L residue  119 ILE
Chi-restraints excluded: chain R residue  212 THR
Chi-restraints excluded: chain R residue  345 VAL
Chi-restraints excluded: chain R residue  423 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 69 optimal weight:    2.9990
   chunk 68 optimal weight:    0.6980
   chunk 56 optimal weight:    0.9980
   chunk 95 optimal weight:    2.9990
   chunk 92 optimal weight:    3.9990
   chunk 18 optimal weight:    3.9990
   chunk 67 optimal weight:    2.9990
   chunk 105 optimal weight:    2.9990
   chunk 91 optimal weight:    0.9980
   chunk 47 optimal weight:    8.9990
   chunk 97 optimal weight:    0.8980
   overall best weight:    1.3182

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

Flipped N/Q/H residues before XYZ refinement:
H 108 GLN
** L   8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4153 r_free = 0.4153 target = 0.188867 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.133220 restraints weight = 10622.544|
|-----------------------------------------------------------------------------|
r_work (start): 0.3570 rms_B_bonded: 3.32
r_work: 0.3277 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.3133 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.3133
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7924
moved from start:          0.1756

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   8643  Z= 0.163
  Angle     :  0.588   6.834  11742  Z= 0.311
  Chirality :  0.043   0.143   1317
  Planarity :  0.004   0.056   1478
  Dihedral  :  6.170  77.886   1218
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 4.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 10.23 %
    Favored  : 88.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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:  0.42 (0.26), residues: 1091
  helix:  1.34 (0.29), residues: 368
  sheet:  1.17 (0.31), residues: 294
  loop : -1.34 (0.29), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG N  28 
 TYR   0.028   0.001   TYR N  32 
 PHE   0.017   0.001   PHE R 526 
 TRP   0.027   0.001   TRP R 178 
 HIS   0.003   0.001   HIS H 110 

Details of bonding type rmsd
  covalent geometry    : bond        0.00376 ( 8637)
  covalent geometry    : angle       0.58664 (11730)
  SS BOND              : bond        0.00687 (    6)
  SS BOND              : angle       1.56105 (   12)
  hydrogen bonds       : bond        0.06249 (  446)
  hydrogen bonds       : angle       4.76867 ( 1281)

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

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

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 96
  time to evaluate  : 0.399 
Fit side-chains
   revert: symmetry clash
REVERT: H   75 SER cc_start: 0.8476 (t) cc_final: 0.8209 (m)
REVERT: H  104 TYR cc_start: 0.9007 (OUTLIER) cc_final: 0.6536 (t80)
REVERT: H  105 GLN cc_start: 0.8226 (OUTLIER) cc_final: 0.7685 (tp40)
REVERT: L    8 GLN cc_start: 0.6831 (mt0) cc_final: 0.6498 (mt0)
REVERT: L  190 LYS cc_start: 0.8481 (mmmm) cc_final: 0.8085 (mmtm)
REVERT: N   91 ASP cc_start: 0.8815 (m-30) cc_final: 0.8303 (m-30)
REVERT: R  192 TYR cc_start: 0.8188 (m-80) cc_final: 0.7850 (m-80)
  outliers start: 15
  outliers final: 9
  residues processed: 104
  average time/residue: 0.1065
  time to fit residues: 15.1994
Evaluate side-chains
  104 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 93
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   54 TYR
Chi-restraints excluded: chain H residue   82 THR
Chi-restraints excluded: chain H residue   87 MET
Chi-restraints excluded: chain H residue  104 TYR
Chi-restraints excluded: chain H residue  105 GLN
Chi-restraints excluded: chain H residue  160 LEU
Chi-restraints excluded: chain L residue    6 MET
Chi-restraints excluded: chain L residue  163 GLU
Chi-restraints excluded: chain R residue  212 THR
Chi-restraints excluded: chain R residue  345 VAL
Chi-restraints excluded: chain R residue  423 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 35 optimal weight:    9.9990
   chunk 52 optimal weight:    0.9990
   chunk 55 optimal weight:    0.7980
   chunk 49 optimal weight:   10.0000
   chunk 103 optimal weight:    0.3980
   chunk 50 optimal weight:    0.5980
   chunk 59 optimal weight:    0.8980
   chunk 64 optimal weight:    0.7980
   chunk 85 optimal weight:    0.6980
   chunk 62 optimal weight:    0.3980
   chunk 93 optimal weight:    0.7980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
H 108 GLN
** L   8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4193 r_free = 0.4193 target = 0.193252 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.138198 restraints weight = 10496.439|
|-----------------------------------------------------------------------------|
r_work (start): 0.3605 rms_B_bonded: 2.67
r_work: 0.3349 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.3207 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.3207
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7857
moved from start:          0.2171

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   8643  Z= 0.111
  Angle     :  0.521   6.310  11742  Z= 0.275
  Chirality :  0.041   0.140   1317
  Planarity :  0.004   0.052   1478
  Dihedral  :  5.605  63.733   1218
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 4.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 10.01 %
    Favored  : 88.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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 (0.27), residues: 1091
  helix:  1.85 (0.30), residues: 354
  sheet:  1.29 (0.32), residues: 282
  loop : -0.97 (0.30), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG N  28 
 TYR   0.015   0.001   TYR N  32 
 PHE   0.014   0.001   PHE R 176 
 TRP   0.022   0.001   TRP R 178 
 HIS   0.002   0.001   HIS H  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00231 ( 8637)
  covalent geometry    : angle       0.52065 (11730)
  SS BOND              : bond        0.00495 (    6)
  SS BOND              : angle       0.98970 (   12)
  hydrogen bonds       : bond        0.04727 (  446)
  hydrogen bonds       : angle       4.47064 ( 1281)

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

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

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 96
  time to evaluate  : 0.352 
Fit side-chains
   revert: symmetry clash
REVERT: H   75 SER cc_start: 0.8397 (t) cc_final: 0.8133 (m)
REVERT: H  104 TYR cc_start: 0.8929 (OUTLIER) cc_final: 0.6596 (t80)
REVERT: H  105 GLN cc_start: 0.8245 (OUTLIER) cc_final: 0.7489 (tp40)
REVERT: K   68 PHE cc_start: 0.7240 (OUTLIER) cc_final: 0.6988 (t80)
REVERT: L    8 GLN cc_start: 0.6833 (mt0) cc_final: 0.6433 (mt0)
REVERT: N   91 ASP cc_start: 0.8788 (m-30) cc_final: 0.8241 (m-30)
  outliers start: 18
  outliers final: 9
  residues processed: 105
  average time/residue: 0.1125
  time to fit residues: 16.0115
Evaluate side-chains
  102 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 90
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   54 TYR
Chi-restraints excluded: chain H residue   82 THR
Chi-restraints excluded: chain H residue   87 MET
Chi-restraints excluded: chain H residue  104 TYR
Chi-restraints excluded: chain H residue  105 GLN
Chi-restraints excluded: chain K residue   68 PHE
Chi-restraints excluded: chain L residue    6 MET
Chi-restraints excluded: chain L residue   50 ILE
Chi-restraints excluded: chain L residue  119 ILE
Chi-restraints excluded: chain L residue  163 GLU
Chi-restraints excluded: chain R residue  345 VAL
Chi-restraints excluded: chain R residue  423 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 85 optimal weight:    0.9990
   chunk 95 optimal weight:    0.1980
   chunk 44 optimal weight:    4.9990
   chunk 78 optimal weight:    1.9990
   chunk 107 optimal weight:    0.9990
   chunk 14 optimal weight:   50.0000
   chunk 105 optimal weight:    0.9980
   chunk 35 optimal weight:    2.9990
   chunk 23 optimal weight:    0.0870
   chunk 16 optimal weight:    2.9990
   chunk 82 optimal weight:    6.9990
   overall best weight:    0.6562

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

Flipped N/Q/H residues before XYZ refinement:
H 108 GLN
** L   8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4194 r_free = 0.4194 target = 0.193206 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.131972 restraints weight = 10415.937|
|-----------------------------------------------------------------------------|
r_work (start): 0.3555 rms_B_bonded: 3.37
r_work: 0.3322 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.3322
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7805
moved from start:          0.2287

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   8643  Z= 0.114
  Angle     :  0.521   7.041  11742  Z= 0.273
  Chirality :  0.042   0.141   1317
  Planarity :  0.004   0.050   1478
  Dihedral  :  4.852  59.105   1218
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 4.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 10.45 %
    Favored  : 87.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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 (0.27), residues: 1091
  helix:  1.86 (0.30), residues: 356
  sheet:  1.40 (0.31), residues: 282
  loop : -0.95 (0.30), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG N  28 
 TYR   0.019   0.001   TYR N  32 
 PHE   0.012   0.001   PHE R 176 
 TRP   0.023   0.001   TRP R 178 
 HIS   0.003   0.001   HIS H 110 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 ( 8637)
  covalent geometry    : angle       0.52023 (11730)
  SS BOND              : bond        0.00499 (    6)
  SS BOND              : angle       0.87350 (   12)
  hydrogen bonds       : bond        0.04806 (  446)
  hydrogen bonds       : angle       4.37237 ( 1281)

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

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

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 91
  time to evaluate  : 0.334 
Fit side-chains
   revert: symmetry clash
REVERT: H    5 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7785 (mm-30)
REVERT: H   75 SER cc_start: 0.8425 (t) cc_final: 0.8134 (m)
REVERT: H  104 TYR cc_start: 0.8858 (OUTLIER) cc_final: 0.6566 (t80)
REVERT: H  105 GLN cc_start: 0.8199 (OUTLIER) cc_final: 0.7486 (tp40)
REVERT: K   68 PHE cc_start: 0.7117 (OUTLIER) cc_final: 0.6896 (t80)
REVERT: N   91 ASP cc_start: 0.8730 (m-30) cc_final: 0.8148 (m-30)
  outliers start: 19
  outliers final: 14
  residues processed: 100
  average time/residue: 0.1072
  time to fit residues: 14.7242
Evaluate side-chains
  107 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 89
  time to evaluate  : 0.396 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    5 GLU
Chi-restraints excluded: chain H residue   17 GLN
Chi-restraints excluded: chain H residue   54 TYR
Chi-restraints excluded: chain H residue   82 THR
Chi-restraints excluded: chain H residue   87 MET
Chi-restraints excluded: chain H residue  104 TYR
Chi-restraints excluded: chain H residue  105 GLN
Chi-restraints excluded: chain H residue  160 LEU
Chi-restraints excluded: chain K residue   68 PHE
Chi-restraints excluded: chain L residue    6 MET
Chi-restraints excluded: chain L residue   50 ILE
Chi-restraints excluded: chain L residue  117 VAL
Chi-restraints excluded: chain L residue  119 ILE
Chi-restraints excluded: chain L residue  163 GLU
Chi-restraints excluded: chain R residue  213 ILE
Chi-restraints excluded: chain R residue  345 VAL
Chi-restraints excluded: chain R residue  423 VAL
Chi-restraints excluded: chain R residue  538 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 68 optimal weight:    0.6980
   chunk 23 optimal weight:    6.9990
   chunk 77 optimal weight:    2.9990
   chunk 89 optimal weight:    1.9990
   chunk 19 optimal weight:    8.9990
   chunk 79 optimal weight:    0.5980
   chunk 66 optimal weight:    3.9990
   chunk 57 optimal weight:    0.4980
   chunk 88 optimal weight:    0.7980
   chunk 12 optimal weight:    7.9990
   chunk 36 optimal weight:    6.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
L   8 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4177 r_free = 0.4177 target = 0.191348 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.135763 restraints weight = 10282.561|
|-----------------------------------------------------------------------------|
r_work (start): 0.3589 rms_B_bonded: 2.65
r_work: 0.3317 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.3176 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.3176
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7872
moved from start:          0.2243

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8643  Z= 0.129
  Angle     :  0.534   6.751  11742  Z= 0.280
  Chirality :  0.042   0.142   1317
  Planarity :  0.004   0.049   1478
  Dihedral  :  4.597  46.723   1218
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 4.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 10.78 %
    Favored  : 87.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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 (0.27), residues: 1091
  helix:  1.82 (0.30), residues: 356
  sheet:  1.29 (0.31), residues: 299
  loop : -0.91 (0.31), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG N  28 
 TYR   0.023   0.001   TYR N  32 
 PHE   0.013   0.001   PHE R 327 
 TRP   0.024   0.001   TRP R 178 
 HIS   0.004   0.001   HIS H 110 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 8637)
  covalent geometry    : angle       0.53380 (11730)
  SS BOND              : bond        0.00576 (    6)
  SS BOND              : angle       0.90885 (   12)
  hydrogen bonds       : bond        0.05325 (  446)
  hydrogen bonds       : angle       4.38317 ( 1281)

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

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

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 87
  time to evaluate  : 0.236 
Fit side-chains
   revert: symmetry clash
REVERT: H    5 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7824 (mm-30)
REVERT: H   75 SER cc_start: 0.8295 (t) cc_final: 0.8033 (m)
REVERT: H  104 TYR cc_start: 0.8939 (OUTLIER) cc_final: 0.6643 (t80)
REVERT: H  105 GLN cc_start: 0.8280 (OUTLIER) cc_final: 0.7492 (tp40)
REVERT: K   68 PHE cc_start: 0.7186 (OUTLIER) cc_final: 0.6934 (t80)
REVERT: N   91 ASP cc_start: 0.8756 (m-30) cc_final: 0.8177 (m-30)
  outliers start: 17
  outliers final: 12
  residues processed: 95
  average time/residue: 0.1090
  time to fit residues: 14.1299
Evaluate side-chains
  102 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 86
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    5 GLU
Chi-restraints excluded: chain H residue   54 TYR
Chi-restraints excluded: chain H residue   82 THR
Chi-restraints excluded: chain H residue   87 MET
Chi-restraints excluded: chain H residue  104 TYR
Chi-restraints excluded: chain H residue  105 GLN
Chi-restraints excluded: chain K residue   68 PHE
Chi-restraints excluded: chain L residue    6 MET
Chi-restraints excluded: chain L residue   50 ILE
Chi-restraints excluded: chain L residue  117 VAL
Chi-restraints excluded: chain L residue  119 ILE
Chi-restraints excluded: chain L residue  163 GLU
Chi-restraints excluded: chain R residue  213 ILE
Chi-restraints excluded: chain R residue  345 VAL
Chi-restraints excluded: chain R residue  423 VAL
Chi-restraints excluded: chain R residue  538 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 77 optimal weight:    0.5980
   chunk 17 optimal weight:    9.9990
   chunk 104 optimal weight:    3.9990
   chunk 6 optimal weight:    0.7980
   chunk 51 optimal weight:    9.9990
   chunk 8 optimal weight:    3.9990
   chunk 83 optimal weight:    3.9990
   chunk 59 optimal weight:    0.2980
   chunk 19 optimal weight:    3.9990
   chunk 23 optimal weight:   20.0000
   chunk 9 optimal weight:    3.9990
   overall best weight:    1.9384

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

Flipped N/Q/H residues before XYZ refinement:
H 108 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4139 r_free = 0.4139 target = 0.187106 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.130172 restraints weight = 10396.183|
|-----------------------------------------------------------------------------|
r_work (start): 0.3527 rms_B_bonded: 2.83
r_work: 0.3245 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.3103 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.3103
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7986
moved from start:          0.1911

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   8643  Z= 0.207
  Angle     :  0.618   7.763  11742  Z= 0.326
  Chirality :  0.045   0.152   1317
  Planarity :  0.004   0.051   1478
  Dihedral  :  4.818  34.363   1218
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 4.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.67 %
    Favored  : 95.33 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 10.89 %
    Favored  : 86.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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:  0.62 (0.27), residues: 1091
  helix:  1.27 (0.29), residues: 367
  sheet:  1.23 (0.30), residues: 314
  loop : -1.04 (0.31), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG N  28 
 TYR   0.030   0.002   TYR N  32 
 PHE   0.019   0.002   PHE R 526 
 TRP   0.024   0.002   TRP R 178 
 HIS   0.006   0.001   HIS H 110 

Details of bonding type rmsd
  covalent geometry    : bond        0.00498 ( 8637)
  covalent geometry    : angle       0.61750 (11730)
  SS BOND              : bond        0.00731 (    6)
  SS BOND              : angle       1.19957 (   12)
  hydrogen bonds       : bond        0.07037 (  446)
  hydrogen bonds       : angle       4.67773 ( 1281)

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

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

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 87
  time to evaluate  : 0.324 
Fit side-chains
   revert: symmetry clash
REVERT: H    5 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7897 (mm-30)
REVERT: H   75 SER cc_start: 0.8538 (t) cc_final: 0.8273 (m)
REVERT: H  104 TYR cc_start: 0.9035 (OUTLIER) cc_final: 0.6629 (t80)
REVERT: H  105 GLN cc_start: 0.8354 (OUTLIER) cc_final: 0.7961 (tp40)
REVERT: K   68 PHE cc_start: 0.7243 (OUTLIER) cc_final: 0.7008 (t80)
REVERT: N   91 ASP cc_start: 0.8810 (m-30) cc_final: 0.8301 (m-30)
  outliers start: 22
  outliers final: 14
  residues processed: 99
  average time/residue: 0.1031
  time to fit residues: 14.1475
Evaluate side-chains
  104 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 86
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    5 GLU
Chi-restraints excluded: chain H residue   17 GLN
Chi-restraints excluded: chain H residue   54 TYR
Chi-restraints excluded: chain H residue   82 THR
Chi-restraints excluded: chain H residue   87 MET
Chi-restraints excluded: chain H residue  104 TYR
Chi-restraints excluded: chain H residue  105 GLN
Chi-restraints excluded: chain H residue  160 LEU
Chi-restraints excluded: chain K residue   68 PHE
Chi-restraints excluded: chain L residue    6 MET
Chi-restraints excluded: chain L residue  117 VAL
Chi-restraints excluded: chain L residue  119 ILE
Chi-restraints excluded: chain L residue  148 VAL
Chi-restraints excluded: chain L residue  166 THR
Chi-restraints excluded: chain R residue  212 THR
Chi-restraints excluded: chain R residue  213 ILE
Chi-restraints excluded: chain R residue  345 VAL
Chi-restraints excluded: chain R residue  423 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 29 optimal weight:    8.9990
   chunk 85 optimal weight:    0.9980
   chunk 59 optimal weight:    0.6980
   chunk 3 optimal weight:    2.9990
   chunk 13 optimal weight:    5.9990
   chunk 54 optimal weight:    4.9990
   chunk 34 optimal weight:   10.0000
   chunk 84 optimal weight:    0.1980
   chunk 65 optimal weight:    0.9990
   chunk 76 optimal weight:    0.7980
   chunk 18 optimal weight:    0.0670
   overall best weight:    0.5518

-------------------------------------------------------------------------------
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 = 0.4197 r_free = 0.4197 target = 0.193709 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.138302 restraints weight = 10494.022|
|-----------------------------------------------------------------------------|
r_work (start): 0.3627 rms_B_bonded: 3.12
r_work: 0.3352 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.3208 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.3208
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7839
moved from start:          0.2421

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   8643  Z= 0.109
  Angle     :  0.514   7.392  11742  Z= 0.270
  Chirality :  0.041   0.137   1317
  Planarity :  0.004   0.049   1478
  Dihedral  :  4.408  31.750   1218
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 4.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 11.44 %
    Favored  : 86.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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:  1.00 (0.27), residues: 1091
  helix:  1.87 (0.30), residues: 354
  sheet:  1.36 (0.32), residues: 283
  loop : -0.79 (0.30), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG N  28 
 TYR   0.014   0.001   TYR N  32 
 PHE   0.015   0.001   PHE R 176 
 TRP   0.021   0.001   TRP R 178 
 HIS   0.002   0.001   HIS H  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00227 ( 8637)
  covalent geometry    : angle       0.51385 (11730)
  SS BOND              : bond        0.00457 (    6)
  SS BOND              : angle       0.74071 (   12)
  hydrogen bonds       : bond        0.04599 (  446)
  hydrogen bonds       : angle       4.32668 ( 1281)

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

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

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 91
  time to evaluate  : 0.630 
Fit side-chains
REVERT: H   75 SER cc_start: 0.8332 (t) cc_final: 0.8064 (m)
REVERT: H  104 TYR cc_start: 0.8965 (OUTLIER) cc_final: 0.6617 (t80)
REVERT: H  105 GLN cc_start: 0.8230 (OUTLIER) cc_final: 0.7410 (tp40)
REVERT: K   68 PHE cc_start: 0.7183 (OUTLIER) cc_final: 0.6917 (t80)
REVERT: N   91 ASP cc_start: 0.8738 (m-30) cc_final: 0.8176 (m-30)
  outliers start: 15
  outliers final: 11
  residues processed: 100
  average time/residue: 0.1065
  time to fit residues: 14.6566
Evaluate side-chains
  102 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 88
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   54 TYR
Chi-restraints excluded: chain H residue   82 THR
Chi-restraints excluded: chain H residue   87 MET
Chi-restraints excluded: chain H residue  104 TYR
Chi-restraints excluded: chain H residue  105 GLN
Chi-restraints excluded: chain K residue   68 PHE
Chi-restraints excluded: chain L residue    6 MET
Chi-restraints excluded: chain L residue   50 ILE
Chi-restraints excluded: chain L residue  117 VAL
Chi-restraints excluded: chain L residue  119 ILE
Chi-restraints excluded: chain L residue  148 VAL
Chi-restraints excluded: chain R residue  213 ILE
Chi-restraints excluded: chain R residue  423 VAL
Chi-restraints excluded: chain R residue  538 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 73 optimal weight:    3.9990
   chunk 1 optimal weight:    5.9990
   chunk 4 optimal weight:    2.9990
   chunk 87 optimal weight:    2.9990
   chunk 107 optimal weight:    0.6980
   chunk 92 optimal weight:    3.9990
   chunk 103 optimal weight:    5.9990
   chunk 76 optimal weight:    0.1980
   chunk 72 optimal weight:    0.9990
   chunk 83 optimal weight:    3.9990
   chunk 17 optimal weight:    0.9980
   overall best weight:    1.1784

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

Flipped N/Q/H residues before XYZ refinement:
H 108 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4166 r_free = 0.4166 target = 0.190214 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.134296 restraints weight = 10451.230|
|-----------------------------------------------------------------------------|
r_work (start): 0.3578 rms_B_bonded: 2.90
r_work: 0.3293 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3150 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.3150
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7932
moved from start:          0.2233

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8643  Z= 0.148
  Angle     :  0.560   7.101  11742  Z= 0.294
  Chirality :  0.043   0.142   1317
  Planarity :  0.004   0.048   1478
  Dihedral  :  4.460  32.327   1218
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 4.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 12.21 %
    Favored  : 86.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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:  0.88 (0.27), residues: 1091
  helix:  1.58 (0.29), residues: 362
  sheet:  1.33 (0.31), residues: 314
  loop : -0.92 (0.32), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG N  28 
 TYR   0.028   0.001   TYR N  32 
 PHE   0.022   0.001   PHE R 176 
 TRP   0.026   0.001   TRP R 178 
 HIS   0.005   0.001   HIS H 110 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 8637)
  covalent geometry    : angle       0.55953 (11730)
  SS BOND              : bond        0.00599 (    6)
  SS BOND              : angle       0.99047 (   12)
  hydrogen bonds       : bond        0.05817 (  446)
  hydrogen bonds       : angle       4.46849 ( 1281)

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

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

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 87
  time to evaluate  : 0.342 
Fit side-chains
REVERT: H   75 SER cc_start: 0.8353 (t) cc_final: 0.8105 (m)
REVERT: H  104 TYR cc_start: 0.8971 (OUTLIER) cc_final: 0.6698 (t80)
REVERT: H  105 GLN cc_start: 0.8235 (OUTLIER) cc_final: 0.7675 (tp40)
REVERT: N   91 ASP cc_start: 0.8791 (m-30) cc_final: 0.8272 (m-30)
  outliers start: 15
  outliers final: 12
  residues processed: 96
  average time/residue: 0.1153
  time to fit residues: 14.9943
Evaluate side-chains
  100 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 86
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   54 TYR
Chi-restraints excluded: chain H residue   82 THR
Chi-restraints excluded: chain H residue   87 MET
Chi-restraints excluded: chain H residue  104 TYR
Chi-restraints excluded: chain H residue  105 GLN
Chi-restraints excluded: chain L residue    6 MET
Chi-restraints excluded: chain L residue   50 ILE
Chi-restraints excluded: chain L residue  117 VAL
Chi-restraints excluded: chain L residue  119 ILE
Chi-restraints excluded: chain L residue  148 VAL
Chi-restraints excluded: chain L residue  163 GLU
Chi-restraints excluded: chain R residue  213 ILE
Chi-restraints excluded: chain R residue  423 VAL
Chi-restraints excluded: chain R residue  538 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 56 optimal weight:    0.8980
   chunk 11 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9990
   chunk 37 optimal weight:    2.9990
   chunk 13 optimal weight:    2.9990
   chunk 46 optimal weight:   20.0000
   chunk 50 optimal weight:    6.9990
   chunk 67 optimal weight:    2.9990
   chunk 68 optimal weight:    0.0980
   chunk 9 optimal weight:    0.7980
   chunk 38 optimal weight:    2.9990
   overall best weight:    0.9584

-------------------------------------------------------------------------------
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 = 0.4145 r_free = 0.4145 target = 0.192137 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.138279 restraints weight = 10008.736|
|-----------------------------------------------------------------------------|
r_work (start): 0.3524 rms_B_bonded: 2.83
r_work: 0.3246 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3107 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.3107
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7916
moved from start:          0.2353

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8643  Z= 0.135
  Angle     :  0.552   7.181  11742  Z= 0.291
  Chirality :  0.042   0.142   1317
  Planarity :  0.004   0.048   1478
  Dihedral  :  4.441  31.953   1218
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 5.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 12.32 %
    Favored  : 86.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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:  0.84 (0.27), residues: 1091
  helix:  1.62 (0.29), residues: 362
  sheet:  1.35 (0.32), residues: 273
  loop : -0.83 (0.30), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG R 386 
 TYR   0.021   0.001   TYR N  32 
 PHE   0.022   0.001   PHE R 176 
 TRP   0.038   0.002   TRP K  36 
 HIS   0.003   0.001   HIS H 110 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 8637)
  covalent geometry    : angle       0.55123 (11730)
  SS BOND              : bond        0.00567 (    6)
  SS BOND              : angle       1.21608 (   12)
  hydrogen bonds       : bond        0.05424 (  446)
  hydrogen bonds       : angle       4.48366 ( 1281)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2766.78 seconds
wall clock time: 48 minutes 2.21 seconds (2882.21 seconds total)