Starting phenix.real_space_refine
on Tue Jan 14 03:16:03 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8s7d_19766/01_2025/8s7d_19766.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8s7d_19766/01_2025/8s7d_19766.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8s7d_19766/01_2025/8s7d_19766.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8s7d_19766/01_2025/8s7d_19766.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8s7d_19766/01_2025/8s7d_19766.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8s7d_19766/01_2025/8s7d_19766.cif"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.122
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      31      5.16       5
     C    3507      2.51       5
     N     931      2.21       5
     O    1019      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 5488
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 904
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 113, 904
          Classifications: {'peptide': 113}
          Link IDs: {'PTRANS': 2, 'TRANS': 110}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 914
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 114, 914
          Classifications: {'peptide': 114}
          Link IDs: {'PTRANS': 2, 'TRANS': 111}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 1005
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 123, 1005
          Classifications: {'peptide': 123}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 119}
          Chain breaks: 2
    Chain: "D"
      Number of atoms: 2665
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 341, 2665
          Classifications: {'peptide': 341}
          Link IDs: {'PTRANS': 13, 'TRANS': 327}
          Chain breaks: 5
  Time building chain proxies: 3.77, per 1000 atoms: 0.69
  Number of scatterers: 5488
  At special positions: 0
  Unit cell: (92.105, 104.78, 95.485, 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      31     16.00
     O    1019      8.00
     N     931      7.00
     C    3507      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: 1.29
  Conformation dependent library (CDL) restraints added in 605.1 milliseconds
  

  1330 Ramachandran restraints generated.
    665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1318

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 8 sheets defined
      48.3% alpha, 14.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.58
  Creating SS restraints...
    Processing helix  chain 'A' and resid 11 through 26
    Processing helix  chain 'A' and resid 44 through 51
    Processing helix  chain 'A' and resid 53 through 60
    Processing helix  chain 'A' and resid 76 through 90
      Proline residue:  A  82  - end of helix
    Processing helix  chain 'A' and resid 98 through 110
    Processing helix  chain 'A' and resid 116 through 121
      removed outlier: 3.803A  pdb=" N   GLN A 120 " --> pdb=" O   GLU A 116 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 11 through 27
    Processing helix  chain 'B' and resid 44 through 52
    Processing helix  chain 'B' and resid 52 through 60
    Processing helix  chain 'B' and resid 76 through 90
      Proline residue:  B  82  - end of helix
      removed outlier: 3.578A  pdb=" N   GLN B  85 " --> pdb=" O   GLU B  81 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 98 through 110
    Processing helix  chain 'B' and resid 115 through 123
      removed outlier: 4.009A  pdb=" N   PHE B 119 " --> pdb=" O   GLU B 115 " (cutoff:3.500A)
      removed outlier: 4.024A  pdb=" N   LEU B 122 " --> pdb=" O   CYS B 118 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 18 through 23
      removed outlier: 4.618A  pdb=" N   GLN C  23 " --> pdb=" O   GLU C  19 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 26 through 32
      removed outlier: 4.173A  pdb=" N   MET C  30 " --> pdb=" O   THR C  26 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   GLU C  32 " --> pdb=" O   LYS C  28 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 53 through 64
    Processing helix  chain 'C' and resid 86 through 93
    Processing helix  chain 'C' and resid 96 through 111
    Processing helix  chain 'C' and resid 112 through 128
    Processing helix  chain 'C' and resid 131 through 140
    Processing helix  chain 'C' and resid 146 through 157
    Processing helix  chain 'D' and resid 19 through 26
      removed outlier: 3.842A  pdb=" N   LEU D  23 " --> pdb=" O   SER D  19 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 26 through 36
      removed outlier: 4.059A  pdb=" N   PHE D  36 " --> pdb=" O   ARG D  32 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 38 through 46
    Processing helix  chain 'D' and resid 49 through 62
    Processing helix  chain 'D' and resid 83 through 92
    Processing helix  chain 'D' and resid 108 through 112
    Processing helix  chain 'D' and resid 129 through 138
    Processing helix  chain 'D' and resid 202 through 209
      removed outlier: 3.596A  pdb=" N   LEU D 206 " --> pdb=" O   GLU D 202 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   VAL D 209 " --> pdb=" O   GLN D 205 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 236 through 244
      removed outlier: 3.770A  pdb=" N   PHE D 243 " --> pdb=" O   VAL D 239 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 298 through 311
    Processing helix  chain 'D' and resid 340 through 349
    Processing sheet with id=AA1, first strand: chain 'A' and resid 7 through 8
    Processing sheet with id=AA2, first strand: chain 'A' and resid 32 through 36
    Processing sheet with id=AA3, first strand: chain 'A' and resid 91 through 94
      removed outlier: 4.696A  pdb=" N   VAL B   4 " --> pdb=" O   CYS D 378 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   ARG D 376 " --> pdb=" O   ALA B   6 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 39 through 43
    Processing sheet with id=AA5, first strand: chain 'D' and resid 174 through 180
      removed outlier: 5.938A  pdb=" N   HIS D 100 " --> pdb=" O   GLN D 144 " (cutoff:3.500A)
      removed outlier: 7.556A  pdb=" N   LEU D 146 " --> pdb=" O   HIS D 100 " (cutoff:3.500A)
      removed outlier: 6.294A  pdb=" N   VAL D 102 " --> pdb=" O   LEU D 146 " (cutoff:3.500A)
      removed outlier: 8.139A  pdb=" N   ILE D 148 " --> pdb=" O   VAL D 102 " (cutoff:3.500A)
      removed outlier: 6.804A  pdb=" N   TYR D 104 " --> pdb=" O   ILE D 148 " (cutoff:3.500A)
      removed outlier: 7.933A  pdb=" N   THR D 150 " --> pdb=" O   TYR D 104 " (cutoff:3.500A)
      removed outlier: 6.059A  pdb=" N   ALA D 106 " --> pdb=" O   THR D 150 " (cutoff:3.500A)
      removed outlier: 6.871A  pdb=" N   VAL D 145 " --> pdb=" O   LEU D 261 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   LEU D 261 " --> pdb=" O   VAL D 145 " (cutoff:3.500A)
      removed outlier: 6.315A  pdb=" N   GLY D 147 " --> pdb=" O   SER D 259 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 153 through 155
    Processing sheet with id=AA7, first strand: chain 'D' and resid 191 through 193
      removed outlier: 3.751A  pdb=" N   GLY D 274 " --> pdb=" O   TYR D 225 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   TYR D 225 " --> pdb=" O   GLY D 274 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   VAL D 219 " --> pdb=" O   PHE D 280 " (cutoff:3.500A)
      removed outlier: 6.071A  pdb=" N   VAL D 220 " --> pdb=" O   ALA D 251 " (cutoff:3.500A)
      removed outlier: 7.987A  pdb=" N   GLY D 253 " --> pdb=" O   VAL D 220 " (cutoff:3.500A)
      removed outlier: 6.517A  pdb=" N   VAL D 222 " --> pdb=" O   GLY D 253 " (cutoff:3.500A)
      removed outlier: 7.356A  pdb=" N   VAL D 255 " --> pdb=" O   VAL D 222 " (cutoff:3.500A)
      removed outlier: 5.755A  pdb=" N   GLY D 224 " --> pdb=" O   VAL D 255 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   ILE D 363 " --> pdb=" O   GLY D 252 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 354 through 359

    254 hydrogen bonds defined for protein.
    723 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: 1.40

  Time building geometry restraints manager: 1.50 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: 1796
        1.34 -     1.46: 1137
        1.46 -     1.58: 2608
        1.58 -     1.70: 0
        1.70 -     1.82: 40
  Bond restraints: 5581
  Sorted by residual:
  bond pdb=" CB  GLN A 120 "
       pdb=" CG  GLN A 120 "
    ideal  model  delta    sigma   weight residual
    1.520  1.558 -0.038 3.00e-02 1.11e+03 1.58e+00
  bond pdb=" CB  LYS D 141 "
       pdb=" CG  LYS D 141 "
    ideal  model  delta    sigma   weight residual
    1.520  1.552 -0.032 3.00e-02 1.11e+03 1.17e+00
  bond pdb=" CB  PHE A 108 "
       pdb=" CG  PHE A 108 "
    ideal  model  delta    sigma   weight residual
    1.502  1.526 -0.024 2.30e-02 1.89e+03 1.07e+00
  bond pdb=" CB  ARG D  86 "
       pdb=" CG  ARG D  86 "
    ideal  model  delta    sigma   weight residual
    1.520  1.551 -0.031 3.00e-02 1.11e+03 1.05e+00
  bond pdb=" CB  LYS D 347 "
       pdb=" CG  LYS D 347 "
    ideal  model  delta    sigma   weight residual
    1.520  1.549 -0.029 3.00e-02 1.11e+03 9.60e-01
  ... (remaining 5576 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.08: 7454
        2.08 -     4.15: 61
        4.15 -     6.23: 17
        6.23 -     8.30: 1
        8.30 -    10.38: 3
  Bond angle restraints: 7536
  Sorted by residual:
  angle pdb=" CA  GLN A 120 "
        pdb=" CB  GLN A 120 "
        pdb=" CG  GLN A 120 "
      ideal   model   delta    sigma   weight residual
     114.10  123.44   -9.34 2.00e+00 2.50e-01 2.18e+01
  angle pdb=" CB  MET D 306 "
        pdb=" CG  MET D 306 "
        pdb=" SD  MET D 306 "
      ideal   model   delta    sigma   weight residual
     112.70  122.86  -10.16 3.00e+00 1.11e-01 1.15e+01
  angle pdb=" CB  LYS D 141 "
        pdb=" CG  LYS D 141 "
        pdb=" CD  LYS D 141 "
      ideal   model   delta    sigma   weight residual
     111.30  118.36   -7.06 2.30e+00 1.89e-01 9.43e+00
  angle pdb=" CA  LEU C  55 "
        pdb=" CB  LEU C  55 "
        pdb=" CG  LEU C  55 "
      ideal   model   delta    sigma   weight residual
     116.30  126.68  -10.38 3.50e+00 8.16e-02 8.79e+00
  angle pdb=" CA  LYS D 347 "
        pdb=" CB  LYS D 347 "
        pdb=" CG  LYS D 347 "
      ideal   model   delta    sigma   weight residual
     114.10  119.90   -5.80 2.00e+00 2.50e-01 8.40e+00
  ... (remaining 7531 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.95: 2790
       17.95 -    35.90: 388
       35.90 -    53.85: 140
       53.85 -    71.80: 30
       71.80 -    89.75: 11
  Dihedral angle restraints: 3359
    sinusoidal: 1350
      harmonic: 2009
  Sorted by residual:
  dihedral pdb=" CA  ASP D 107 "
           pdb=" C   ASP D 107 "
           pdb=" N   SER D 108 "
           pdb=" CA  SER D 108 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.27  -17.73     0      5.00e+00 4.00e-02 1.26e+01
  dihedral pdb=" CA  ASP B  22 "
           pdb=" CB  ASP B  22 "
           pdb=" CG  ASP B  22 "
           pdb=" OD1 ASP B  22 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -89.15   59.15     1      2.00e+01 2.50e-03 1.17e+01
  dihedral pdb=" CA  ASP C  17 "
           pdb=" CB  ASP C  17 "
           pdb=" CG  ASP C  17 "
           pdb=" OD1 ASP C  17 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -87.66   57.66     1      2.00e+01 2.50e-03 1.12e+01
  ... (remaining 3356 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 498
       0.027 -    0.054: 228
       0.054 -    0.081: 81
       0.081 -    0.108: 59
       0.108 -    0.136: 16
  Chirality restraints: 882
  Sorted by residual:
  chirality pdb=" CA  ILE D 374 "
            pdb=" N   ILE D 374 "
            pdb=" C   ILE D 374 "
            pdb=" CB  ILE D 374 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.59e-01
  chirality pdb=" CA  VAL D 276 "
            pdb=" N   VAL D 276 "
            pdb=" C   VAL D 276 "
            pdb=" CB  VAL D 276 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 3.98e-01
  chirality pdb=" CG  LEU C  55 "
            pdb=" CB  LEU C  55 "
            pdb=" CD1 LEU C  55 "
            pdb=" CD2 LEU C  55 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.47   -0.12 2.00e-01 2.50e+01 3.88e-01
  ... (remaining 879 not shown)

  Planarity restraints: 957
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR D 156 "    0.040 5.00e-02 4.00e+02   6.05e-02 5.86e+00
        pdb=" N   PRO D 157 "   -0.105 5.00e-02 4.00e+02
        pdb=" CA  PRO D 157 "    0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO D 157 "    0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN A 120 "   -0.010 2.00e-02 2.50e+03   1.94e-02 3.76e+00
        pdb=" C   GLN A 120 "    0.034 2.00e-02 2.50e+03
        pdb=" O   GLN A 120 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   PHE A 121 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 108 "   -0.010 2.00e-02 2.50e+03   1.28e-02 2.86e+00
        pdb=" CG  PHE B 108 "    0.029 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 108 "   -0.010 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 108 "   -0.009 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 108 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 108 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 108 "   -0.000 2.00e-02 2.50e+03
  ... (remaining 954 not shown)

  Histogram of nonbonded interaction distances:
        2.09 -     2.65: 81
        2.65 -     3.21: 5018
        3.21 -     3.78: 8590
        3.78 -     4.34: 11768
        4.34 -     4.90: 19382
  Nonbonded interactions: 44839
  Sorted by model distance:
  nonbonded pdb=" O   GLN B  85 "
            pdb=" OG1 THR B  89 "
     model   vdw
     2.090 3.040
  nonbonded pdb=" OD1 ASP D 107 "
            pdb=" OG1 THR D 110 "
     model   vdw
     2.194 3.040
  nonbonded pdb=" O   THR C  26 "
            pdb=" OG1 THR C  29 "
     model   vdw
     2.198 3.040
  nonbonded pdb=" OG  SER D 173 "
            pdb=" N   GLY D 174 "
     model   vdw
     2.291 3.120
  nonbonded pdb=" ND2 ASN A  15 "
            pdb=" OD1 ASN B 113 "
     model   vdw
     2.295 3.120
  ... (remaining 44834 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' and (resid 4 through 60 or resid 69 through 122))
  selection = (chain 'B' and (resid 4 through 60 or resid 69 through 122))
}

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:             0.450
  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:          0.230
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     16.230
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.810
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.940
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6883
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5581  Z= 0.166
  Angle     :  0.569  10.379   7536  Z= 0.297
  Chirality :  0.042   0.136    882
  Planarity :  0.004   0.061    957
  Dihedral  : 19.447  89.753   2041
  Min Nonbonded Distance : 2.090

Molprobity Statistics.
  All-atom Clashscore : 13.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.46 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  4.70 %
    Allowed  : 33.23 %
    Favored  : 62.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.33 (0.34), residues: 665
  helix:  0.72 (0.31), residues: 296
  sheet: -2.22 (0.53), residues: 98
  loop : -0.29 (0.40), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP D  68 
 HIS   0.003   0.001   HIS D 398 
 PHE   0.029   0.001   PHE B 108 
 TYR   0.009   0.001   TYR A  88 
 ARG   0.008   0.000   ARG D  58 

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

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

  1330 Ramachandran restraints generated.
    665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1330 Ramachandran restraints generated.
    665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 66
  time to evaluate  : 0.649 
Fit side-chains
REVERT: A  116 GLU cc_start: 0.3903 (mm-30) cc_final: 0.3150 (mt-10)
  outliers start: 29
  outliers final: 27
  residues processed: 92
  average time/residue: 0.2075
  time to fit residues: 24.2001
Evaluate side-chains
  91 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 64
  time to evaluate  : 0.567 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 ASP
Chi-restraints excluded: chain A residue   46 SER
Chi-restraints excluded: chain A residue   74 GLU
Chi-restraints excluded: chain B residue   13 SER
Chi-restraints excluded: chain B residue   53 SER
Chi-restraints excluded: chain B residue  105 CYS
Chi-restraints excluded: chain C residue   17 ASP
Chi-restraints excluded: chain C residue  110 LEU
Chi-restraints excluded: chain C residue  157 ASN
Chi-restraints excluded: chain D residue   84 LEU
Chi-restraints excluded: chain D residue   97 ILE
Chi-restraints excluded: chain D residue  105 MET
Chi-restraints excluded: chain D residue  131 THR
Chi-restraints excluded: chain D residue  144 GLN
Chi-restraints excluded: chain D residue  146 LEU
Chi-restraints excluded: chain D residue  182 ILE
Chi-restraints excluded: chain D residue  188 GLN
Chi-restraints excluded: chain D residue  222 VAL
Chi-restraints excluded: chain D residue  244 SER
Chi-restraints excluded: chain D residue  250 LEU
Chi-restraints excluded: chain D residue  261 LEU
Chi-restraints excluded: chain D residue  262 THR
Chi-restraints excluded: chain D residue  276 VAL
Chi-restraints excluded: chain D residue  287 SER
Chi-restraints excluded: chain D residue  366 ASP
Chi-restraints excluded: chain D residue  370 THR
Chi-restraints excluded: chain D residue  383 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 57 optimal weight:    3.9990
   chunk 51 optimal weight:    1.9990
   chunk 28 optimal weight:    8.9990
   chunk 17 optimal weight:   10.0000
   chunk 34 optimal weight:    0.3980
   chunk 27 optimal weight:   10.0000
   chunk 53 optimal weight:    0.9990
   chunk 20 optimal weight:    3.9990
   chunk 32 optimal weight:   20.0000
   chunk 39 optimal weight:    3.9990
   chunk 61 optimal weight:    0.9990
   overall best weight:    1.6788

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

Flipped N/Q/H residues before XYZ refinement:
B  44 HIS
** D  63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  82 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5057 r_free = 0.5057 target = 0.274402 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4755 r_free = 0.4755 target = 0.233562 restraints weight = 4808.014|
|-----------------------------------------------------------------------------|
r_work (start): 0.4754 rms_B_bonded: 1.34
r_work: 0.4398 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work (final): 0.4398
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6985
moved from start:          0.1060

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   5581  Z= 0.281
  Angle     :  0.577   7.450   7536  Z= 0.304
  Chirality :  0.044   0.154    882
  Planarity :  0.004   0.063    957
  Dihedral  :  8.174  77.559    773
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 12.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  5.19 %
    Allowed  : 30.47 %
    Favored  : 64.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.58 (0.34), residues: 665
  helix:  0.55 (0.30), residues: 296
  sheet: -2.47 (0.52), residues: 97
  loop : -0.43 (0.40), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP D  68 
 HIS   0.006   0.001   HIS B  56 
 PHE   0.012   0.001   PHE A 121 
 TYR   0.016   0.002   TYR D 104 
 ARG   0.005   0.001   ARG C 136 

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

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

  1330 Ramachandran restraints generated.
    665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1330 Ramachandran restraints generated.
    665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 66
  time to evaluate  : 0.583 
Fit side-chains
   revert: symmetry clash
REVERT: A   93 ILE cc_start: 0.7935 (OUTLIER) cc_final: 0.7701 (mm)
REVERT: A  115 GLU cc_start: 0.6526 (OUTLIER) cc_final: 0.4550 (mp0)
REVERT: B   48 LEU cc_start: 0.7551 (OUTLIER) cc_final: 0.6863 (mp)
REVERT: B   93 ILE cc_start: 0.7574 (OUTLIER) cc_final: 0.7293 (mp)
REVERT: C   30 MET cc_start: 0.5665 (pmm) cc_final: 0.5168 (pmm)
REVERT: D   58 ARG cc_start: 0.8033 (ttp-110) cc_final: 0.7631 (ttp-110)
REVERT: D  105 MET cc_start: 0.7140 (OUTLIER) cc_final: 0.6850 (mtm)
REVERT: D  148 ILE cc_start: 0.7836 (OUTLIER) cc_final: 0.7582 (mm)
REVERT: D  213 ASP cc_start: 0.8359 (OUTLIER) cc_final: 0.7633 (t70)
REVERT: D  347 LYS cc_start: 0.6300 (tptp) cc_final: 0.5342 (ttpt)
  outliers start: 32
  outliers final: 20
  residues processed: 91
  average time/residue: 0.2499
  time to fit residues: 28.2479
Evaluate side-chains
  90 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 63
  time to evaluate  : 0.632 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 VAL
Chi-restraints excluded: chain A residue   28 VAL
Chi-restraints excluded: chain A residue   93 ILE
Chi-restraints excluded: chain A residue  115 GLU
Chi-restraints excluded: chain B residue   28 VAL
Chi-restraints excluded: chain B residue   30 CYS
Chi-restraints excluded: chain B residue   32 VAL
Chi-restraints excluded: chain B residue   48 LEU
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain C residue   17 ASP
Chi-restraints excluded: chain C residue   50 VAL
Chi-restraints excluded: chain C residue   83 ASP
Chi-restraints excluded: chain D residue   84 LEU
Chi-restraints excluded: chain D residue  105 MET
Chi-restraints excluded: chain D residue  131 THR
Chi-restraints excluded: chain D residue  146 LEU
Chi-restraints excluded: chain D residue  148 ILE
Chi-restraints excluded: chain D residue  188 GLN
Chi-restraints excluded: chain D residue  193 ILE
Chi-restraints excluded: chain D residue  213 ASP
Chi-restraints excluded: chain D residue  222 VAL
Chi-restraints excluded: chain D residue  250 LEU
Chi-restraints excluded: chain D residue  261 LEU
Chi-restraints excluded: chain D residue  276 VAL
Chi-restraints excluded: chain D residue  284 ARG
Chi-restraints excluded: chain D residue  287 SER
Chi-restraints excluded: chain D residue  329 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 59 optimal weight:    0.9990
   chunk 46 optimal weight:    6.9990
   chunk 63 optimal weight:    0.9990
   chunk 8 optimal weight:    0.8980
   chunk 14 optimal weight:    0.9980
   chunk 15 optimal weight:    0.8980
   chunk 10 optimal weight:    4.9990
   chunk 35 optimal weight:    0.8980
   chunk 20 optimal weight:    5.9990
   chunk 23 optimal weight:    5.9990
   chunk 9 optimal weight:    0.7980
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
A 112 HIS
** D  63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 163 ASN ** 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 = 0.5089 r_free = 0.5089 target = 0.278831 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.4811 r_free = 0.4811 target = 0.240487 restraints weight = 4922.778|
|-----------------------------------------------------------------------------|
r_work (start): 0.4810 rms_B_bonded: 1.45
r_work: 0.4432 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.4432
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6925
moved from start:          0.1175

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5581  Z= 0.186
  Angle     :  0.507   7.465   7536  Z= 0.266
  Chirality :  0.043   0.141    882
  Planarity :  0.004   0.060    957
  Dihedral  :  6.614  58.383    746
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 10.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  4.54 %
    Allowed  : 30.63 %
    Favored  : 64.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.46 (0.33), residues: 665
  helix:  0.68 (0.30), residues: 296
  sheet: -2.36 (0.51), residues: 94
  loop : -0.47 (0.39), residues: 275

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D  68 
 HIS   0.003   0.001   HIS D 398 
 PHE   0.011   0.001   PHE A 121 
 TYR   0.014   0.001   TYR A  88 
 ARG   0.006   0.000   ARG D  44 

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

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

  1330 Ramachandran restraints generated.
    665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1330 Ramachandran restraints generated.
    665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 72
  time to evaluate  : 0.662 
Fit side-chains
REVERT: A  115 GLU cc_start: 0.6399 (OUTLIER) cc_final: 0.4396 (mp0)
REVERT: C   30 MET cc_start: 0.5727 (pmm) cc_final: 0.5214 (pmm)
REVERT: D  105 MET cc_start: 0.7070 (OUTLIER) cc_final: 0.6785 (mtm)
REVERT: D  148 ILE cc_start: 0.7721 (OUTLIER) cc_final: 0.7487 (mm)
REVERT: D  213 ASP cc_start: 0.8363 (OUTLIER) cc_final: 0.7612 (t70)
REVERT: D  347 LYS cc_start: 0.6237 (tptp) cc_final: 0.5366 (ttpt)
  outliers start: 28
  outliers final: 13
  residues processed: 94
  average time/residue: 0.2482
  time to fit residues: 28.5605
Evaluate side-chains
  84 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 67
  time to evaluate  : 0.549 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 VAL
Chi-restraints excluded: chain A residue   24 ARG
Chi-restraints excluded: chain A residue  115 GLU
Chi-restraints excluded: chain B residue   30 CYS
Chi-restraints excluded: chain C residue   17 ASP
Chi-restraints excluded: chain C residue   50 VAL
Chi-restraints excluded: chain D residue   84 LEU
Chi-restraints excluded: chain D residue  105 MET
Chi-restraints excluded: chain D residue  131 THR
Chi-restraints excluded: chain D residue  148 ILE
Chi-restraints excluded: chain D residue  193 ILE
Chi-restraints excluded: chain D residue  213 ASP
Chi-restraints excluded: chain D residue  222 VAL
Chi-restraints excluded: chain D residue  250 LEU
Chi-restraints excluded: chain D residue  261 LEU
Chi-restraints excluded: chain D residue  276 VAL
Chi-restraints excluded: chain D residue  284 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 16 optimal weight:    0.8980
   chunk 8 optimal weight:    0.8980
   chunk 47 optimal weight:    2.9990
   chunk 45 optimal weight:    7.9990
   chunk 48 optimal weight:    1.9990
   chunk 3 optimal weight:    7.9990
   chunk 62 optimal weight:    0.6980
   chunk 49 optimal weight:    4.9990
   chunk 37 optimal weight:    3.9990
   chunk 35 optimal weight:    0.8980
   chunk 55 optimal weight:    0.6980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** D  63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  82 HIS
** D 163 ASN ** 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 = 0.5098 r_free = 0.5098 target = 0.280017 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4813 r_free = 0.4813 target = 0.240822 restraints weight = 4954.004|
|-----------------------------------------------------------------------------|
r_work (start): 0.4809 rms_B_bonded: 1.30
r_work: 0.4475 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work (final): 0.4475
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6874
moved from start:          0.1363

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5581  Z= 0.179
  Angle     :  0.498   7.059   7536  Z= 0.260
  Chirality :  0.043   0.155    882
  Planarity :  0.004   0.060    957
  Dihedral  :  5.922  54.595    740
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 10.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 30.47 %
    Favored  : 65.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.36 (0.34), residues: 665
  helix:  0.71 (0.30), residues: 304
  sheet: -2.40 (0.49), residues: 98
  loop : -0.29 (0.41), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D  68 
 HIS   0.003   0.001   HIS D 398 
 PHE   0.011   0.001   PHE A 121 
 TYR   0.014   0.001   TYR D 104 
 ARG   0.005   0.000   ARG D  44 

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

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

  1330 Ramachandran restraints generated.
    665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1330 Ramachandran restraints generated.
    665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 74
  time to evaluate  : 0.528 
Fit side-chains
REVERT: A  115 GLU cc_start: 0.6382 (OUTLIER) cc_final: 0.4346 (mp0)
REVERT: C   30 MET cc_start: 0.5706 (OUTLIER) cc_final: 0.5189 (pmm)
REVERT: D  105 MET cc_start: 0.6926 (OUTLIER) cc_final: 0.6656 (mtm)
REVERT: D  148 ILE cc_start: 0.7670 (OUTLIER) cc_final: 0.7410 (mm)
REVERT: D  178 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.7820 (mt)
REVERT: D  213 ASP cc_start: 0.8377 (OUTLIER) cc_final: 0.7660 (t70)
REVERT: D  347 LYS cc_start: 0.6123 (tptp) cc_final: 0.5299 (ttpt)
  outliers start: 25
  outliers final: 14
  residues processed: 93
  average time/residue: 0.2506
  time to fit residues: 28.3922
Evaluate side-chains
  90 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 70
  time to evaluate  : 0.647 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 VAL
Chi-restraints excluded: chain A residue   24 ARG
Chi-restraints excluded: chain A residue  115 GLU
Chi-restraints excluded: chain B residue   13 SER
Chi-restraints excluded: chain B residue   30 CYS
Chi-restraints excluded: chain B residue   32 VAL
Chi-restraints excluded: chain C residue   17 ASP
Chi-restraints excluded: chain C residue   30 MET
Chi-restraints excluded: chain C residue   83 ASP
Chi-restraints excluded: chain D residue  105 MET
Chi-restraints excluded: chain D residue  131 THR
Chi-restraints excluded: chain D residue  148 ILE
Chi-restraints excluded: chain D residue  178 LEU
Chi-restraints excluded: chain D residue  193 ILE
Chi-restraints excluded: chain D residue  213 ASP
Chi-restraints excluded: chain D residue  222 VAL
Chi-restraints excluded: chain D residue  250 LEU
Chi-restraints excluded: chain D residue  261 LEU
Chi-restraints excluded: chain D residue  276 VAL
Chi-restraints excluded: chain D residue  284 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 39 optimal weight:    0.9980
   chunk 23 optimal weight:    0.7980
   chunk 2 optimal weight:    0.0070
   chunk 21 optimal weight:    4.9990
   chunk 40 optimal weight:    4.9990
   chunk 5 optimal weight:    0.7980
   chunk 56 optimal weight:    0.4980
   chunk 59 optimal weight:    5.9990
   chunk 29 optimal weight:    9.9990
   chunk 17 optimal weight:    8.9990
   chunk 48 optimal weight:    2.9990
   overall best weight:    0.6198

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

Flipped N/Q/H residues before XYZ refinement:
** D  63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5194 r_free = 0.5194 target = 0.294492 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.4905 r_free = 0.4905 target = 0.252870 restraints weight = 4965.599|
|-----------------------------------------------------------------------------|
r_work (start): 0.4901 rms_B_bonded: 1.48
r_work: 0.4538 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.4538
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6898
moved from start:          0.1473

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   5581  Z= 0.154
  Angle     :  0.482   6.714   7536  Z= 0.253
  Chirality :  0.042   0.165    882
  Planarity :  0.004   0.058    957
  Dihedral  :  5.513  54.613    738
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 10.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  4.38 %
    Allowed  : 29.50 %
    Favored  : 66.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.25 (0.34), residues: 665
  helix:  0.77 (0.30), residues: 306
  sheet: -2.32 (0.49), residues: 98
  loop : -0.22 (0.41), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D  68 
 HIS   0.004   0.001   HIS D 398 
 PHE   0.010   0.001   PHE A 121 
 TYR   0.013   0.001   TYR D 104 
 ARG   0.005   0.000   ARG D  44 

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

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

  1330 Ramachandran restraints generated.
    665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1330 Ramachandran restraints generated.
    665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 76
  time to evaluate  : 0.615 
Fit side-chains
REVERT: A  115 GLU cc_start: 0.6331 (OUTLIER) cc_final: 0.4525 (mp0)
REVERT: C   30 MET cc_start: 0.5850 (OUTLIER) cc_final: 0.5289 (pmm)
REVERT: D  144 GLN cc_start: 0.6344 (OUTLIER) cc_final: 0.5727 (mp10)
REVERT: D  148 ILE cc_start: 0.7695 (OUTLIER) cc_final: 0.7483 (mm)
REVERT: D  213 ASP cc_start: 0.8343 (OUTLIER) cc_final: 0.7616 (t70)
REVERT: D  329 ARG cc_start: 0.2806 (OUTLIER) cc_final: 0.2189 (ptp-170)
REVERT: D  347 LYS cc_start: 0.6202 (tptp) cc_final: 0.5417 (ttpt)
  outliers start: 27
  outliers final: 17
  residues processed: 98
  average time/residue: 0.2507
  time to fit residues: 29.9037
Evaluate side-chains
  94 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 71
  time to evaluate  : 0.547 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 VAL
Chi-restraints excluded: chain A residue   24 ARG
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue  115 GLU
Chi-restraints excluded: chain B residue    3 SER
Chi-restraints excluded: chain B residue   13 SER
Chi-restraints excluded: chain B residue   28 VAL
Chi-restraints excluded: chain B residue   30 CYS
Chi-restraints excluded: chain B residue   32 VAL
Chi-restraints excluded: chain C residue   17 ASP
Chi-restraints excluded: chain C residue   30 MET
Chi-restraints excluded: chain C residue   83 ASP
Chi-restraints excluded: chain D residue  108 SER
Chi-restraints excluded: chain D residue  144 GLN
Chi-restraints excluded: chain D residue  148 ILE
Chi-restraints excluded: chain D residue  193 ILE
Chi-restraints excluded: chain D residue  213 ASP
Chi-restraints excluded: chain D residue  222 VAL
Chi-restraints excluded: chain D residue  250 LEU
Chi-restraints excluded: chain D residue  261 LEU
Chi-restraints excluded: chain D residue  276 VAL
Chi-restraints excluded: chain D residue  284 ARG
Chi-restraints excluded: chain D residue  329 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 25 optimal weight:   20.0000
   chunk 40 optimal weight:    3.9990
   chunk 7 optimal weight:    1.9990
   chunk 39 optimal weight:    0.7980
   chunk 63 optimal weight:    0.6980
   chunk 6 optimal weight:    0.0070
   chunk 50 optimal weight:    2.9990
   chunk 2 optimal weight:    8.9990
   chunk 32 optimal weight:    2.9990
   chunk 35 optimal weight:    3.9990
   chunk 23 optimal weight:    0.4980
   overall best weight:    0.8000

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

Flipped N/Q/H residues before XYZ refinement:
A 120 GLN
** D  63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 163 ASN ** 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 = 0.5146 r_free = 0.5146 target = 0.286424 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.4875 r_free = 0.4875 target = 0.247932 restraints weight = 5006.634|
|-----------------------------------------------------------------------------|
r_work (start): 0.4900 rms_B_bonded: 1.24
r_work: 0.4581 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work (final): 0.4581
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6864
moved from start:          0.1605

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5581  Z= 0.174
  Angle     :  0.495   6.492   7536  Z= 0.259
  Chirality :  0.042   0.175    882
  Planarity :  0.004   0.058    957
  Dihedral  :  5.014  54.388    734
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 10.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  5.51 %
    Allowed  : 29.34 %
    Favored  : 65.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.21 (0.34), residues: 665
  helix:  0.80 (0.30), residues: 306
  sheet: -2.27 (0.50), residues: 98
  loop : -0.20 (0.41), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP D  68 
 HIS   0.003   0.001   HIS D 398 
 PHE   0.025   0.001   PHE A 108 
 TYR   0.014   0.001   TYR D 104 
 ARG   0.006   0.000   ARG D  44 

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

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

  1330 Ramachandran restraints generated.
    665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1330 Ramachandran restraints generated.
    665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 71
  time to evaluate  : 0.622 
Fit side-chains
REVERT: A   54 TYR cc_start: 0.6808 (t80) cc_final: 0.6597 (t80)
REVERT: A  115 GLU cc_start: 0.6391 (OUTLIER) cc_final: 0.4562 (mp0)
REVERT: C   30 MET cc_start: 0.5653 (OUTLIER) cc_final: 0.5197 (pmm)
REVERT: D  144 GLN cc_start: 0.6347 (OUTLIER) cc_final: 0.5755 (mp10)
REVERT: D  178 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.7720 (mt)
REVERT: D  213 ASP cc_start: 0.8358 (OUTLIER) cc_final: 0.7639 (t70)
REVERT: D  329 ARG cc_start: 0.3025 (OUTLIER) cc_final: 0.2508 (ptp-170)
REVERT: D  347 LYS cc_start: 0.6190 (tptp) cc_final: 0.5477 (ttpt)
  outliers start: 34
  outliers final: 22
  residues processed: 99
  average time/residue: 0.2416
  time to fit residues: 29.3774
Evaluate side-chains
  99 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 71
  time to evaluate  : 0.619 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 VAL
Chi-restraints excluded: chain A residue   24 ARG
Chi-restraints excluded: chain A residue   62 GLN
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue  115 GLU
Chi-restraints excluded: chain B residue    3 SER
Chi-restraints excluded: chain B residue   13 SER
Chi-restraints excluded: chain B residue   28 VAL
Chi-restraints excluded: chain B residue   30 CYS
Chi-restraints excluded: chain B residue   32 VAL
Chi-restraints excluded: chain C residue   17 ASP
Chi-restraints excluded: chain C residue   30 MET
Chi-restraints excluded: chain C residue   83 ASP
Chi-restraints excluded: chain D residue   61 ARG
Chi-restraints excluded: chain D residue  108 SER
Chi-restraints excluded: chain D residue  131 THR
Chi-restraints excluded: chain D residue  144 GLN
Chi-restraints excluded: chain D residue  178 LEU
Chi-restraints excluded: chain D residue  185 ILE
Chi-restraints excluded: chain D residue  193 ILE
Chi-restraints excluded: chain D residue  213 ASP
Chi-restraints excluded: chain D residue  222 VAL
Chi-restraints excluded: chain D residue  250 LEU
Chi-restraints excluded: chain D residue  261 LEU
Chi-restraints excluded: chain D residue  276 VAL
Chi-restraints excluded: chain D residue  284 ARG
Chi-restraints excluded: chain D residue  329 ARG
Chi-restraints excluded: chain D residue  362 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 62 optimal weight:    1.9990
   chunk 57 optimal weight:    0.6980
   chunk 31 optimal weight:    5.9990
   chunk 9 optimal weight:    0.9980
   chunk 61 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 2 optimal weight:   10.0000
   chunk 35 optimal weight:    3.9990
   chunk 22 optimal weight:    8.9990
   chunk 16 optimal weight:    3.9990
   chunk 36 optimal weight:    0.9990
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
A 120 GLN
** D  63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 163 ASN ** 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 = 0.5167 r_free = 0.5167 target = 0.290590 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4878 r_free = 0.4878 target = 0.250289 restraints weight = 4958.060|
|-----------------------------------------------------------------------------|
r_work (start): 0.4877 rms_B_bonded: 1.52
r_work: 0.4489 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.4489
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6986
moved from start:          0.1700

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   5581  Z= 0.241
  Angle     :  0.544   8.371   7536  Z= 0.285
  Chirality :  0.044   0.183    882
  Planarity :  0.004   0.058    957
  Dihedral  :  5.247  53.980    734
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 12.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  4.70 %
    Allowed  : 29.82 %
    Favored  : 65.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.37 (0.34), residues: 665
  helix:  0.71 (0.30), residues: 299
  sheet: -2.56 (0.48), residues: 99
  loop : -0.20 (0.40), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP D  68 
 HIS   0.004   0.001   HIS B  56 
 PHE   0.019   0.001   PHE B 108 
 TYR   0.016   0.002   TYR D 104 
 ARG   0.009   0.000   ARG D  44 

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

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

  1330 Ramachandran restraints generated.
    665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1330 Ramachandran restraints generated.
    665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 72
  time to evaluate  : 0.640 
Fit side-chains
REVERT: A   54 TYR cc_start: 0.6938 (t80) cc_final: 0.6647 (t80)
REVERT: A  115 GLU cc_start: 0.6500 (OUTLIER) cc_final: 0.4765 (mp0)
REVERT: C   30 MET cc_start: 0.5608 (OUTLIER) cc_final: 0.5110 (pmm)
REVERT: D  178 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.7782 (mt)
REVERT: D  213 ASP cc_start: 0.8400 (OUTLIER) cc_final: 0.7695 (t70)
REVERT: D  329 ARG cc_start: 0.3271 (OUTLIER) cc_final: 0.2384 (ptp-110)
REVERT: D  347 LYS cc_start: 0.6290 (tptp) cc_final: 0.5545 (ttpt)
  outliers start: 29
  outliers final: 22
  residues processed: 95
  average time/residue: 0.2469
  time to fit residues: 28.6389
Evaluate side-chains
  96 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 69
  time to evaluate  : 0.588 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 VAL
Chi-restraints excluded: chain A residue   18 LEU
Chi-restraints excluded: chain A residue   24 ARG
Chi-restraints excluded: chain A residue   28 VAL
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue   62 GLN
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue  115 GLU
Chi-restraints excluded: chain B residue    3 SER
Chi-restraints excluded: chain B residue   13 SER
Chi-restraints excluded: chain B residue   28 VAL
Chi-restraints excluded: chain B residue   30 CYS
Chi-restraints excluded: chain B residue   32 VAL
Chi-restraints excluded: chain C residue   17 ASP
Chi-restraints excluded: chain C residue   30 MET
Chi-restraints excluded: chain C residue   83 ASP
Chi-restraints excluded: chain D residue  108 SER
Chi-restraints excluded: chain D residue  131 THR
Chi-restraints excluded: chain D residue  178 LEU
Chi-restraints excluded: chain D residue  193 ILE
Chi-restraints excluded: chain D residue  213 ASP
Chi-restraints excluded: chain D residue  222 VAL
Chi-restraints excluded: chain D residue  250 LEU
Chi-restraints excluded: chain D residue  261 LEU
Chi-restraints excluded: chain D residue  276 VAL
Chi-restraints excluded: chain D residue  284 ARG
Chi-restraints excluded: chain D residue  329 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 37 optimal weight:    0.9990
   chunk 49 optimal weight:    6.9990
   chunk 54 optimal weight:    0.3980
   chunk 45 optimal weight:    5.9990
   chunk 44 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 65 optimal weight:    3.9990
   chunk 2 optimal weight:    0.0370
   chunk 36 optimal weight:    0.8980
   chunk 19 optimal weight:    5.9990
   chunk 58 optimal weight:    0.8980
   overall best weight:    0.6460

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

Flipped N/Q/H residues before XYZ refinement:
** D  63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5198 r_free = 0.5198 target = 0.294921 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.4903 r_free = 0.4903 target = 0.252360 restraints weight = 4938.748|
|-----------------------------------------------------------------------------|
r_work (start): 0.4895 rms_B_bonded: 1.45
r_work: 0.4553 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.4553
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6887
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      :  0.003   0.028   5581  Z= 0.172
  Angle     :  0.524   8.144   7536  Z= 0.272
  Chirality :  0.043   0.184    882
  Planarity :  0.004   0.058    957
  Dihedral  :  5.044  54.448    734
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 11.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  4.21 %
    Allowed  : 30.47 %
    Favored  : 65.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.22 (0.34), residues: 665
  helix:  0.79 (0.30), residues: 301
  sheet: -2.35 (0.49), residues: 98
  loop : -0.16 (0.41), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D  68 
 HIS   0.003   0.001   HIS D 398 
 PHE   0.029   0.001   PHE A 108 
 TYR   0.013   0.001   TYR D 104 
 ARG   0.007   0.000   ARG D  44 

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

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

  1330 Ramachandran restraints generated.
    665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1330 Ramachandran restraints generated.
    665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 74
  time to evaluate  : 0.615 
Fit side-chains
REVERT: A   54 TYR cc_start: 0.6816 (t80) cc_final: 0.6517 (t80)
REVERT: A   58 ARG cc_start: 0.5961 (mmm160) cc_final: 0.5575 (mmm-85)
REVERT: A  115 GLU cc_start: 0.6354 (OUTLIER) cc_final: 0.4569 (mp0)
REVERT: C   30 MET cc_start: 0.5728 (OUTLIER) cc_final: 0.5176 (pmm)
REVERT: C   56 LYS cc_start: 0.8186 (tmmt) cc_final: 0.7891 (tptp)
REVERT: D  213 ASP cc_start: 0.8344 (OUTLIER) cc_final: 0.7657 (t70)
REVERT: D  329 ARG cc_start: 0.2726 (OUTLIER) cc_final: 0.1828 (ptm160)
REVERT: D  347 LYS cc_start: 0.6150 (tptp) cc_final: 0.5440 (ttpt)
  outliers start: 26
  outliers final: 20
  residues processed: 95
  average time/residue: 0.2772
  time to fit residues: 31.8645
Evaluate side-chains
  94 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 70
  time to evaluate  : 0.554 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 VAL
Chi-restraints excluded: chain A residue   24 ARG
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue   62 GLN
Chi-restraints excluded: chain A residue  115 GLU
Chi-restraints excluded: chain B residue    3 SER
Chi-restraints excluded: chain B residue   13 SER
Chi-restraints excluded: chain B residue   28 VAL
Chi-restraints excluded: chain B residue   30 CYS
Chi-restraints excluded: chain B residue   32 VAL
Chi-restraints excluded: chain C residue   17 ASP
Chi-restraints excluded: chain C residue   30 MET
Chi-restraints excluded: chain C residue   83 ASP
Chi-restraints excluded: chain D residue   29 VAL
Chi-restraints excluded: chain D residue  108 SER
Chi-restraints excluded: chain D residue  131 THR
Chi-restraints excluded: chain D residue  193 ILE
Chi-restraints excluded: chain D residue  213 ASP
Chi-restraints excluded: chain D residue  222 VAL
Chi-restraints excluded: chain D residue  250 LEU
Chi-restraints excluded: chain D residue  261 LEU
Chi-restraints excluded: chain D residue  276 VAL
Chi-restraints excluded: chain D residue  284 ARG
Chi-restraints excluded: chain D residue  329 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 19 optimal weight:    0.9980
   chunk 8 optimal weight:    1.9990
   chunk 28 optimal weight:    4.9990
   chunk 58 optimal weight:    4.9990
   chunk 33 optimal weight:    2.9990
   chunk 10 optimal weight:    6.9990
   chunk 31 optimal weight:    0.7980
   chunk 36 optimal weight:    0.2980
   chunk 52 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9980
   chunk 0 optimal weight:    5.9990
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
** D  63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5186 r_free = 0.5186 target = 0.292598 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 91)----------------|
| r_work = 0.4747 r_free = 0.4747 target = 0.239491 restraints weight = 5011.316|
|-----------------------------------------------------------------------------|
r_work (start): 0.4771 rms_B_bonded: 2.07
r_work: 0.4458 rms_B_bonded: 3.97 restraints_weight: 0.5000
r_work (final): 0.4458
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6956
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      :  0.003   0.037   5581  Z= 0.211
  Angle     :  0.543   7.494   7536  Z= 0.284
  Chirality :  0.043   0.186    882
  Planarity :  0.004   0.058    957
  Dihedral  :  5.132  54.164    734
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 12.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  3.89 %
    Allowed  : 31.12 %
    Favored  : 64.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.29 (0.34), residues: 665
  helix:  0.75 (0.30), residues: 301
  sheet: -2.40 (0.49), residues: 98
  loop : -0.20 (0.41), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D  68 
 HIS   0.003   0.001   HIS B  56 
 PHE   0.025   0.001   PHE A 108 
 TYR   0.014   0.001   TYR D 104 
 ARG   0.008   0.000   ARG D  44 

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

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

  1330 Ramachandran restraints generated.
    665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1330 Ramachandran restraints generated.
    665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 69
  time to evaluate  : 0.674 
Fit side-chains
REVERT: A   54 TYR cc_start: 0.6901 (t80) cc_final: 0.6504 (t80)
REVERT: A   58 ARG cc_start: 0.5818 (mmm160) cc_final: 0.5339 (mmm-85)
REVERT: A  115 GLU cc_start: 0.6479 (OUTLIER) cc_final: 0.4752 (mp0)
REVERT: C   30 MET cc_start: 0.5933 (OUTLIER) cc_final: 0.5294 (pmm)
REVERT: D  105 MET cc_start: 0.7014 (mtm) cc_final: 0.6754 (mtt)
REVERT: D  213 ASP cc_start: 0.8354 (OUTLIER) cc_final: 0.7631 (t70)
REVERT: D  329 ARG cc_start: 0.2919 (OUTLIER) cc_final: 0.1751 (ptm160)
REVERT: D  347 LYS cc_start: 0.6127 (tptp) cc_final: 0.5376 (ttpt)
  outliers start: 24
  outliers final: 20
  residues processed: 88
  average time/residue: 0.2671
  time to fit residues: 28.6989
Evaluate side-chains
  92 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 68
  time to evaluate  : 0.615 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 VAL
Chi-restraints excluded: chain A residue   24 ARG
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue   62 GLN
Chi-restraints excluded: chain A residue  115 GLU
Chi-restraints excluded: chain B residue    3 SER
Chi-restraints excluded: chain B residue   13 SER
Chi-restraints excluded: chain B residue   28 VAL
Chi-restraints excluded: chain B residue   30 CYS
Chi-restraints excluded: chain B residue   32 VAL
Chi-restraints excluded: chain C residue   17 ASP
Chi-restraints excluded: chain C residue   30 MET
Chi-restraints excluded: chain C residue   83 ASP
Chi-restraints excluded: chain D residue   29 VAL
Chi-restraints excluded: chain D residue  131 THR
Chi-restraints excluded: chain D residue  185 ILE
Chi-restraints excluded: chain D residue  193 ILE
Chi-restraints excluded: chain D residue  213 ASP
Chi-restraints excluded: chain D residue  222 VAL
Chi-restraints excluded: chain D residue  250 LEU
Chi-restraints excluded: chain D residue  261 LEU
Chi-restraints excluded: chain D residue  276 VAL
Chi-restraints excluded: chain D residue  284 ARG
Chi-restraints excluded: chain D residue  329 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 21 optimal weight:    9.9990
   chunk 40 optimal weight:    2.9990
   chunk 8 optimal weight:    2.9990
   chunk 39 optimal weight:    0.0970
   chunk 18 optimal weight:    0.7980
   chunk 43 optimal weight:    0.9990
   chunk 9 optimal weight:    2.9990
   chunk 31 optimal weight:    3.9990
   chunk 41 optimal weight:    0.7980
   chunk 66 optimal weight:    3.9990
   chunk 10 optimal weight:    1.9990
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
** D  63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5183 r_free = 0.5183 target = 0.292470 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.4877 r_free = 0.4877 target = 0.248482 restraints weight = 4968.246|
|-----------------------------------------------------------------------------|
r_work (start): 0.4872 rms_B_bonded: 1.68
r_work: 0.4503 rms_B_bonded: 3.73 restraints_weight: 0.5000
r_work (final): 0.4503
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6945
moved from start:          0.1820

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5581  Z= 0.201
  Angle     :  0.542   8.060   7536  Z= 0.281
  Chirality :  0.043   0.187    882
  Planarity :  0.004   0.058    957
  Dihedral  :  5.113  54.225    734
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 12.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  4.21 %
    Allowed  : 30.63 %
    Favored  : 65.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.29 (0.34), residues: 665
  helix:  0.76 (0.30), residues: 301
  sheet: -2.41 (0.48), residues: 98
  loop : -0.22 (0.40), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D  68 
 HIS   0.003   0.001   HIS D 398 
 PHE   0.024   0.001   PHE A 108 
 TYR   0.013   0.001   TYR D 104 
 ARG   0.010   0.000   ARG D  44 

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

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

  1330 Ramachandran restraints generated.
    665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1330 Ramachandran restraints generated.
    665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 68
  time to evaluate  : 0.579 
Fit side-chains
REVERT: A   54 TYR cc_start: 0.6893 (t80) cc_final: 0.6500 (t80)
REVERT: A  115 GLU cc_start: 0.6425 (OUTLIER) cc_final: 0.4694 (mp0)
REVERT: C   30 MET cc_start: 0.5742 (OUTLIER) cc_final: 0.5191 (pmm)
REVERT: C   56 LYS cc_start: 0.8226 (tmmt) cc_final: 0.7911 (tptp)
REVERT: D  178 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.7785 (mt)
REVERT: D  202 GLU cc_start: 0.7378 (OUTLIER) cc_final: 0.7039 (mp0)
REVERT: D  213 ASP cc_start: 0.8334 (OUTLIER) cc_final: 0.7643 (t70)
REVERT: D  329 ARG cc_start: 0.2855 (OUTLIER) cc_final: 0.1924 (ptm160)
REVERT: D  347 LYS cc_start: 0.6194 (tptp) cc_final: 0.5461 (ttpt)
  outliers start: 26
  outliers final: 20
  residues processed: 89
  average time/residue: 0.2504
  time to fit residues: 27.3813
Evaluate side-chains
  92 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 66
  time to evaluate  : 0.624 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 VAL
Chi-restraints excluded: chain A residue   24 ARG
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue   62 GLN
Chi-restraints excluded: chain A residue  115 GLU
Chi-restraints excluded: chain B residue    3 SER
Chi-restraints excluded: chain B residue   13 SER
Chi-restraints excluded: chain B residue   28 VAL
Chi-restraints excluded: chain B residue   30 CYS
Chi-restraints excluded: chain B residue   32 VAL
Chi-restraints excluded: chain C residue   17 ASP
Chi-restraints excluded: chain C residue   30 MET
Chi-restraints excluded: chain C residue   83 ASP
Chi-restraints excluded: chain D residue   29 VAL
Chi-restraints excluded: chain D residue  131 THR
Chi-restraints excluded: chain D residue  178 LEU
Chi-restraints excluded: chain D residue  185 ILE
Chi-restraints excluded: chain D residue  193 ILE
Chi-restraints excluded: chain D residue  202 GLU
Chi-restraints excluded: chain D residue  213 ASP
Chi-restraints excluded: chain D residue  222 VAL
Chi-restraints excluded: chain D residue  250 LEU
Chi-restraints excluded: chain D residue  261 LEU
Chi-restraints excluded: chain D residue  276 VAL
Chi-restraints excluded: chain D residue  284 ARG
Chi-restraints excluded: chain D residue  329 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 26 optimal weight:    7.9990
   chunk 32 optimal weight:    6.9990
   chunk 6 optimal weight:   10.0000
   chunk 4 optimal weight:    2.9990
   chunk 3 optimal weight:    3.9990
   chunk 7 optimal weight:    0.6980
   chunk 57 optimal weight:    0.8980
   chunk 24 optimal weight:    5.9990
   chunk 12 optimal weight:    4.9990
   chunk 58 optimal weight:    0.8980
   chunk 63 optimal weight:    1.9990
   overall best weight:    1.4984

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

Flipped N/Q/H residues before XYZ refinement:
** D  63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5136 r_free = 0.5136 target = 0.284161 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4853 r_free = 0.4853 target = 0.244733 restraints weight = 4959.404|
|-----------------------------------------------------------------------------|
r_work (start): 0.4869 rms_B_bonded: 1.32
r_work: 0.4517 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.4517
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6957
moved from start:          0.1888

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   5581  Z= 0.269
  Angle     :  0.586   8.104   7536  Z= 0.305
  Chirality :  0.044   0.186    882
  Planarity :  0.004   0.070    957
  Dihedral  :  5.313  53.847    734
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 13.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.81 %
    Favored  : 95.19 %
  Rotamer:
    Outliers :  4.86 %
    Allowed  : 29.98 %
    Favored  : 65.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.46 (0.33), residues: 665
  helix:  0.67 (0.30), residues: 299
  sheet: -2.67 (0.48), residues: 99
  loop : -0.27 (0.40), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP C 159 
 HIS   0.005   0.001   HIS B  56 
 PHE   0.032   0.002   PHE A 108 
 TYR   0.016   0.002   TYR D 104 
 ARG   0.012   0.000   ARG D  44 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3221.23 seconds
wall clock time: 58 minutes 5.53 seconds (3485.53 seconds total)