Starting phenix.real_space_refine
on Thu Mar  6 07:26:32 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8s7d_19766/03_2025/8s7d_19766.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8s7d_19766/03_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_19766/03_2025/8s7d_19766.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8s7d_19766/03_2025/8s7d_19766.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8s7d_19766/03_2025/8s7d_19766.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8s7d_19766/03_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-5624/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: 3.94, per 1000 atoms: 0.72
  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: 1.39
  Conformation dependent library (CDL) restraints added in 626.8 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: 0.73
  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: 1.79

  Time building geometry restraints manager: 1.65 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:             0.740
  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:          0.250
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     18.100
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.720
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.070
-------------------------------------------------------------------------------
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  : 0.596 
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: 0.2070
  time to fit residues: 24.1975
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  : 0.549 
-------------------------------------------------------------------------------
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 = 0.233589 restraints weight = 4808.013|
|-----------------------------------------------------------------------------|
r_work (start): 0.4754 rms_B_bonded: 1.34
r_work: 0.4398 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work (final): 0.4398
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6986
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  : 0.615 
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: 0.6527 (OUTLIER) cc_final: 0.4551 (mp0)
REVERT: B   48 LEU cc_start: 0.7551 (OUTLIER) cc_final: 0.6863 (mp)
REVERT: B   93 ILE cc_start: 0.7569 (OUTLIER) cc_final: 0.7289 (mp)
REVERT: C   30 MET cc_start: 0.5666 (pmm) cc_final: 0.5168 (pmm)
REVERT: D   58 ARG cc_start: 0.8034 (ttp-110) cc_final: 0.7631 (ttp-110)
REVERT: D  105 MET cc_start: 0.7140 (OUTLIER) cc_final: 0.6849 (mtm)
REVERT: D  148 ILE cc_start: 0.7836 (OUTLIER) cc_final: 0.7582 (mm)
REVERT: D  213 ASP cc_start: 0.8358 (OUTLIER) cc_final: 0.7633 (t70)
REVERT: D  347 LYS cc_start: 0.6301 (tptp) cc_final: 0.5343 (ttpt)
  outliers start: 32
  outliers final: 20
  residues processed: 91
  average time/residue: 0.2443
  time to fit residues: 27.7394
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  : 0.588 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 8 optimal weight:    0.8980
   chunk 14 optimal weight:    0.9980
   chunk 15 optimal weight:    0.9990
   chunk 10 optimal weight:    3.9990
   chunk 35 optimal weight:    0.8980
   chunk 20 optimal weight:    5.9990
   chunk 23 optimal weight:    4.9990
   chunk 9 optimal weight:    0.9990
   overall best weight:    0.9584

-------------------------------------------------------------------------------
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 = 0.5083 r_free = 0.5083 target = 0.277936 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.4779 r_free = 0.4779 target = 0.236319 restraints weight = 4916.672|
|-----------------------------------------------------------------------------|
r_work (start): 0.4778 rms_B_bonded: 1.51
r_work: 0.4417 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.4417
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6937
moved from start:          0.1161

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5581  Z= 0.195
  Angle     :  0.514   7.404   7536  Z= 0.270
  Chirality :  0.043   0.142    882
  Planarity :  0.004   0.060    957
  Dihedral  :  6.707  59.501    746
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 11.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.46 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  4.70 %
    Allowed  : 30.63 %
    Favored  : 64.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.50 (0.33), residues: 665
  helix:  0.64 (0.30), residues: 296
  sheet: -2.38 (0.52), residues: 94
  loop : -0.49 (0.39), residues: 275

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   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   0.004   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
  99 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 70
  time to evaluate  : 0.613 
Fit side-chains
REVERT: A  115 GLU cc_start: 0.6430 (OUTLIER) cc_final: 0.4435 (mp0)
REVERT: C   30 MET cc_start: 0.5773 (pmm) cc_final: 0.5220 (pmm)
REVERT: D  105 MET cc_start: 0.7088 (OUTLIER) cc_final: 0.6819 (mtm)
REVERT: D  148 ILE cc_start: 0.7763 (OUTLIER) cc_final: 0.7522 (mm)
REVERT: D  213 ASP cc_start: 0.8366 (OUTLIER) cc_final: 0.7623 (t70)
REVERT: D  347 LYS cc_start: 0.6250 (tptp) cc_final: 0.5349 (ttpt)
  outliers start: 29
  outliers final: 15
  residues processed: 93
  average time/residue: 0.2423
  time to fit residues: 27.7031
Evaluate side-chains
  86 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 67
  time to evaluate  : 0.554 
-------------------------------------------------------------------------------
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  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 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  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:    7.9990
   chunk 8 optimal weight:    0.8980
   chunk 47 optimal weight:    2.9990
   chunk 45 optimal weight:    8.9990
   chunk 48 optimal weight:    1.9990
   chunk 3 optimal weight:    6.9990
   chunk 62 optimal weight:    0.6980
   chunk 49 optimal weight:    7.9990
   chunk 37 optimal weight:    3.9990
   chunk 35 optimal weight:    0.7980
   chunk 55 optimal weight:    0.9980
   overall best weight:    1.0782

-------------------------------------------------------------------------------
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 = 0.5085 r_free = 0.5085 target = 0.278238 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4797 r_free = 0.4797 target = 0.238890 restraints weight = 4953.775|
|-----------------------------------------------------------------------------|
r_work (start): 0.4797 rms_B_bonded: 1.60
r_work: 0.4400 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.4400
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6968
moved from start:          0.1354

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5581  Z= 0.207
  Angle     :  0.514   6.939   7536  Z= 0.269
  Chirality :  0.043   0.156    882
  Planarity :  0.004   0.060    957
  Dihedral  :  6.095  54.457    740
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 11.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  5.35 %
    Allowed  : 29.01 %
    Favored  : 65.64 %
  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: -0.43 (0.33), residues: 665
  helix:  0.67 (0.30), residues: 302
  sheet: -2.43 (0.50), residues: 96
  loop : -0.36 (0.40), residues: 267

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   0.012   0.001   PHE A 121 
 TYR   0.015   0.001   TYR D 104 
 ARG   0.007   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
  107 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 74
  time to evaluate  : 0.642 
Fit side-chains
REVERT: A  115 GLU cc_start: 0.6491 (OUTLIER) cc_final: 0.4514 (mp0)
REVERT: C   30 MET cc_start: 0.5755 (OUTLIER) cc_final: 0.5229 (pmm)
REVERT: D   58 ARG cc_start: 0.7976 (ttp-110) cc_final: 0.7764 (ttp-110)
REVERT: D  105 MET cc_start: 0.7092 (OUTLIER) cc_final: 0.6818 (mtm)
REVERT: D  148 ILE cc_start: 0.7794 (OUTLIER) cc_final: 0.7562 (mm)
REVERT: D  178 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.7815 (mt)
REVERT: D  213 ASP cc_start: 0.8435 (OUTLIER) cc_final: 0.7683 (t70)
REVERT: D  347 LYS cc_start: 0.6246 (tptp) cc_final: 0.5366 (ttpt)
  outliers start: 33
  outliers final: 18
  residues processed: 99
  average time/residue: 0.2586
  time to fit residues: 31.0183
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  : 0.651 
-------------------------------------------------------------------------------
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  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   42 LEU
Chi-restraints excluded: chain D residue  105 MET
Chi-restraints excluded: chain D residue  108 SER
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:    0.1980
   chunk 23 optimal weight:    0.6980
   chunk 2 optimal weight:    0.2980
   chunk 21 optimal weight:    0.5980
   chunk 40 optimal weight:    5.9990
   chunk 5 optimal weight:    0.8980
   chunk 56 optimal weight:    0.9990
   chunk 59 optimal weight:    1.9990
   chunk 29 optimal weight:    8.9990
   chunk 17 optimal weight:    9.9990
   chunk 48 optimal weight:    0.9980
   overall best weight:    0.5380

-------------------------------------------------------------------------------
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 = 0.5206 r_free = 0.5206 target = 0.295996 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 78)----------------|
| r_work = 0.4902 r_free = 0.4902 target = 0.252018 restraints weight = 4954.817|
|-----------------------------------------------------------------------------|
r_work (start): 0.4851 rms_B_bonded: 1.58
r_work: 0.4483 rms_B_bonded: 4.66 restraints_weight: 0.5000
r_work (final): 0.4483
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6963
moved from start:          0.1535

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= 0.148
  Angle     :  0.487   6.613   7536  Z= 0.254
  Chirality :  0.042   0.166    882
  Planarity :  0.004   0.059    957
  Dihedral  :  5.508  54.648    738
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 10.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  3.89 %
    Allowed  : 30.31 %
    Favored  : 65.80 %
  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: -0.27 (0.34), residues: 665
  helix:  0.77 (0.30), residues: 306
  sheet: -2.38 (0.49), residues: 98
  loop : -0.21 (0.41), residues: 261

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   0.004   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
  100 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 76
  time to evaluate  : 0.637 
Fit side-chains
REVERT: A  115 GLU cc_start: 0.6441 (OUTLIER) cc_final: 0.4686 (mp0)
REVERT: C   30 MET cc_start: 0.5853 (OUTLIER) cc_final: 0.5292 (pmm)
REVERT: D   42 LEU cc_start: 0.7956 (OUTLIER) cc_final: 0.7746 (tt)
REVERT: D  148 ILE cc_start: 0.7754 (OUTLIER) cc_final: 0.7548 (mm)
REVERT: D  213 ASP cc_start: 0.8335 (OUTLIER) cc_final: 0.7610 (t70)
REVERT: D  347 LYS cc_start: 0.6297 (tptp) cc_final: 0.5510 (ttpt)
  outliers start: 24
  outliers final: 16
  residues processed: 95
  average time/residue: 0.2598
  time to fit residues: 30.0826
Evaluate side-chains
  92 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 71
  time to evaluate  : 0.605 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 D residue   42 LEU
Chi-restraints excluded: chain D residue  108 SER
Chi-restraints excluded: chain D residue  148 ILE
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
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 25 optimal weight:    4.9990
   chunk 40 optimal weight:    4.9990
   chunk 7 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9990
   chunk 63 optimal weight:    0.5980
   chunk 6 optimal weight:    0.0020
   chunk 50 optimal weight:    0.9980
   chunk 2 optimal weight:   10.0000
   chunk 32 optimal weight:    0.6980
   chunk 35 optimal weight:    2.9990
   chunk 23 optimal weight:    3.9990
   overall best weight:    0.6590

-------------------------------------------------------------------------------
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 = 0.5195 r_free = 0.5195 target = 0.294741 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 76)----------------|
| r_work = 0.4899 r_free = 0.4899 target = 0.252110 restraints weight = 4986.730|
|-----------------------------------------------------------------------------|
r_work (start): 0.4886 rms_B_bonded: 1.36
r_work: 0.4553 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.4553
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6895
moved from start:          0.1614

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   5581  Z= 0.161
  Angle     :  0.501   8.938   7536  Z= 0.259
  Chirality :  0.042   0.181    882
  Planarity :  0.004   0.057    957
  Dihedral  :  4.998  54.548    734
  Min Nonbonded Distance : 2.338

Molprobity Statistics.
  All-atom Clashscore : 10.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  4.70 %
    Allowed  : 30.96 %
    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: -0.17 (0.34), residues: 665
  helix:  0.84 (0.30), residues: 306
  sheet: -2.29 (0.50), residues: 98
  loop : -0.18 (0.41), residues: 261

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   0.025   0.001   PHE A 108 
 TYR   0.013   0.001   TYR D 104 
 ARG   0.008   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
  103 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 74
  time to evaluate  : 0.578 
Fit side-chains
REVERT: A   54 TYR cc_start: 0.6864 (t80) cc_final: 0.6572 (t80)
REVERT: A  115 GLU cc_start: 0.6360 (OUTLIER) cc_final: 0.4563 (mp0)
REVERT: C   30 MET cc_start: 0.5746 (OUTLIER) cc_final: 0.5236 (pmm)
REVERT: D  109 GLU cc_start: 0.6723 (pp20) cc_final: 0.6499 (tp30)
REVERT: D  178 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.7745 (mt)
REVERT: D  213 ASP cc_start: 0.8346 (OUTLIER) cc_final: 0.7625 (t70)
REVERT: D  347 LYS cc_start: 0.6217 (tptp) cc_final: 0.5508 (ttpt)
  outliers start: 29
  outliers final: 20
  residues processed: 96
  average time/residue: 0.2414
  time to fit residues: 28.6055
Evaluate side-chains
  95 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 71
  time to evaluate  : 0.468 
-------------------------------------------------------------------------------
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 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  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  362 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 62 optimal weight:    0.8980
   chunk 57 optimal weight:    0.9980
   chunk 31 optimal weight:    4.9990
   chunk 9 optimal weight:    0.8980
   chunk 61 optimal weight:    0.9990
   chunk 51 optimal weight:    0.0070
   chunk 2 optimal weight:   10.0000
   chunk 35 optimal weight:    2.9990
   chunk 22 optimal weight:    0.0870
   chunk 16 optimal weight:    3.9990
   chunk 36 optimal weight:    0.5980
   overall best weight:    0.4976

-------------------------------------------------------------------------------
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 = 0.5205 r_free = 0.5205 target = 0.296176 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 72)----------------|
| r_work = 0.4908 r_free = 0.4908 target = 0.252755 restraints weight = 4973.496|
|-----------------------------------------------------------------------------|
r_work (start): 0.4894 rms_B_bonded: 1.40
r_work: 0.4561 rms_B_bonded: 3.70 restraints_weight: 0.5000
r_work (final): 0.4561
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6870
moved from start:          0.1731

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   5581  Z= 0.145
  Angle     :  0.492   8.357   7536  Z= 0.257
  Chirality :  0.042   0.189    882
  Planarity :  0.004   0.057    957
  Dihedral  :  4.924  54.507    734
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 10.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  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: -0.05 (0.34), residues: 665
  helix:  0.92 (0.31), residues: 301
  sheet: -2.18 (0.50), residues: 98
  loop : -0.08 (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   0.019   0.001   PHE A 108 
 TYR   0.013   0.001   TYR D 104 
 ARG   0.005   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
  107 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 79
  time to evaluate  : 0.622 
Fit side-chains
REVERT: A  115 GLU cc_start: 0.6274 (OUTLIER) cc_final: 0.4463 (mp0)
REVERT: C   30 MET cc_start: 0.5776 (OUTLIER) cc_final: 0.5270 (pmm)
REVERT: D  109 GLU cc_start: 0.6789 (pp20) cc_final: 0.6534 (tp30)
REVERT: D  178 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.7749 (mt)
REVERT: D  213 ASP cc_start: 0.8338 (OUTLIER) cc_final: 0.7635 (t70)
  outliers start: 28
  outliers final: 20
  residues processed: 101
  average time/residue: 0.2289
  time to fit residues: 28.6651
Evaluate side-chains
  97 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 73
  time to evaluate  : 0.612 
-------------------------------------------------------------------------------
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   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 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  362 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 37 optimal weight:    1.9990
   chunk 49 optimal weight:    0.0050
   chunk 54 optimal weight:    0.9990
   chunk 45 optimal weight:    8.9990
   chunk 44 optimal weight:    0.9980
   chunk 53 optimal weight:    1.9990
   chunk 65 optimal weight:    2.9990
   chunk 2 optimal weight:   10.0000
   chunk 36 optimal weight:    2.9990
   chunk 19 optimal weight:    0.8980
   chunk 58 optimal weight:    1.9990
   overall best weight:    0.9798

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

Flipped N/Q/H residues before XYZ refinement:
B  56 HIS
** 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5187 r_free = 0.5187 target = 0.293579 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.4887 r_free = 0.4887 target = 0.250371 restraints weight = 4952.612|
|-----------------------------------------------------------------------------|
r_work (start): 0.4885 rms_B_bonded: 1.36
r_work: 0.4549 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.4549
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6898
moved from start:          0.1770

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5581  Z= 0.207
  Angle     :  0.542   7.564   7536  Z= 0.283
  Chirality :  0.043   0.187    882
  Planarity :  0.004   0.057    957
  Dihedral  :  5.069  54.229    734
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 11.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  4.21 %
    Allowed  : 31.12 %
    Favored  : 64.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.18 (0.34), residues: 665
  helix:  0.86 (0.31), residues: 301
  sheet: -2.38 (0.49), residues: 98
  loop : -0.15 (0.41), residues: 266

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   0.029   0.001   PHE A 108 
 TYR   0.032   0.002   TYR A  54 
 ARG   0.011   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
  99 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 73
  time to evaluate  : 0.562 
Fit side-chains
REVERT: A  115 GLU cc_start: 0.6451 (OUTLIER) cc_final: 0.4612 (mp0)
REVERT: C   30 MET cc_start: 0.5737 (OUTLIER) cc_final: 0.5197 (pmm)
REVERT: D  178 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.7757 (mt)
REVERT: D  213 ASP cc_start: 0.8386 (OUTLIER) cc_final: 0.7682 (t70)
  outliers start: 26
  outliers final: 22
  residues processed: 93
  average time/residue: 0.2511
  time to fit residues: 28.5685
Evaluate side-chains
  98 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 72
  time to evaluate  : 0.600 
-------------------------------------------------------------------------------
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   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 B residue   56 HIS
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  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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 19 optimal weight:    0.9990
   chunk 8 optimal weight:    0.9980
   chunk 28 optimal weight:    3.9990
   chunk 58 optimal weight:    0.9980
   chunk 33 optimal weight:    0.7980
   chunk 10 optimal weight:    0.7980
   chunk 31 optimal weight:    0.9990
   chunk 36 optimal weight:    0.9990
   chunk 52 optimal weight:    1.9990
   chunk 51 optimal weight:    0.6980
   chunk 0 optimal weight:   10.0000
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
B  56 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 = 0.5192 r_free = 0.5192 target = 0.293923 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.4886 r_free = 0.4886 target = 0.249504 restraints weight = 5011.373|
|-----------------------------------------------------------------------------|
r_work (start): 0.4867 rms_B_bonded: 1.64
r_work: 0.4489 rms_B_bonded: 4.28 restraints_weight: 0.5000
r_work (final): 0.4489
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6965
moved from start:          0.1839

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= 0.192
  Angle     :  0.535   7.552   7536  Z= 0.280
  Chirality :  0.043   0.195    882
  Planarity :  0.004   0.057    957
  Dihedral  :  5.046  54.240    734
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 12.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.46 %
    Favored  : 96.54 %
  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: -0.17 (0.34), residues: 665
  helix:  0.85 (0.31), residues: 301
  sheet: -2.37 (0.48), residues: 98
  loop : -0.13 (0.41), residues: 266

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   0.026   0.001   PHE A 108 
 TYR   0.026   0.002   TYR A  54 
 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
  96 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 70
  time to evaluate  : 0.564 
Fit side-chains
REVERT: A   58 ARG cc_start: 0.5923 (mmm160) cc_final: 0.5376 (mmm-85)
REVERT: A  115 GLU cc_start: 0.6508 (OUTLIER) cc_final: 0.4782 (mp0)
REVERT: C   30 MET cc_start: 0.5726 (OUTLIER) cc_final: 0.5170 (pmm)
REVERT: C   56 LYS cc_start: 0.8157 (tmmt) cc_final: 0.7863 (tptp)
REVERT: D  178 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.7748 (mt)
REVERT: D  213 ASP cc_start: 0.8418 (OUTLIER) cc_final: 0.7705 (t70)
  outliers start: 26
  outliers final: 22
  residues processed: 90
  average time/residue: 0.2381
  time to fit residues: 26.3270
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  : 0.551 
-------------------------------------------------------------------------------
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   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 B residue   56 HIS
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  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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 21 optimal weight:    0.1980
   chunk 40 optimal weight:    2.9990
   chunk 8 optimal weight:    0.0670
   chunk 39 optimal weight:   10.0000
   chunk 18 optimal weight:    0.9990
   chunk 43 optimal weight:    0.8980
   chunk 9 optimal weight:    0.6980
   chunk 31 optimal weight:    5.9990
   chunk 41 optimal weight:    3.9990
   chunk 66 optimal weight:    3.9990
   chunk 10 optimal weight:    0.7980
   overall best weight:    0.5318

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

Flipped N/Q/H residues before XYZ refinement:
A 120 GLN
B  56 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5206 r_free = 0.5206 target = 0.296190 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.4914 r_free = 0.4914 target = 0.253549 restraints weight = 4969.706|
|-----------------------------------------------------------------------------|
r_work (start): 0.4909 rms_B_bonded: 1.56
r_work: 0.4553 rms_B_bonded: 3.55 restraints_weight: 0.5000
r_work (final): 0.4553
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6865
moved from start:          0.1938

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5581  Z= 0.169
  Angle     :  0.538   8.200   7536  Z= 0.279
  Chirality :  0.043   0.197    882
  Planarity :  0.004   0.057    957
  Dihedral  :  4.972  54.416    734
  Min Nonbonded Distance : 2.293

Molprobity Statistics.
  All-atom Clashscore : 11.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.46 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  4.21 %
    Allowed  : 30.96 %
    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: -0.07 (0.34), residues: 665
  helix:  0.91 (0.31), residues: 301
  sheet: -2.23 (0.49), residues: 98
  loop : -0.08 (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   0.025   0.001   PHE A 108 
 TYR   0.023   0.002   TYR A  54 
 ARG   0.009   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
  97 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 71
  time to evaluate  : 0.562 
Fit side-chains
REVERT: A   58 ARG cc_start: 0.5851 (mmm160) cc_final: 0.5499 (mmm-85)
REVERT: A  115 GLU cc_start: 0.6337 (OUTLIER) cc_final: 0.4629 (mp0)
REVERT: C   30 MET cc_start: 0.5723 (OUTLIER) cc_final: 0.5186 (pmm)
REVERT: C   56 LYS cc_start: 0.8162 (tmmt) cc_final: 0.7866 (tptp)
REVERT: D  178 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.7719 (mt)
REVERT: D  213 ASP cc_start: 0.8368 (OUTLIER) cc_final: 0.7680 (t70)
  outliers start: 26
  outliers final: 21
  residues processed: 89
  average time/residue: 0.2503
  time to fit residues: 27.4636
Evaluate side-chains
  95 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 70
  time to evaluate  : 0.552 
-------------------------------------------------------------------------------
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   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 B residue   56 HIS
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  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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 26 optimal weight:    6.9990
   chunk 32 optimal weight:    9.9990
   chunk 6 optimal weight:    0.3980
   chunk 4 optimal weight:    2.9990
   chunk 3 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9980
   chunk 57 optimal weight:    0.9980
   chunk 24 optimal weight:    3.9990
   chunk 12 optimal weight:    4.9990
   chunk 58 optimal weight:    2.9990
   chunk 63 optimal weight:    0.0970
   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 120 GLN
B  56 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5195 r_free = 0.5195 target = 0.294178 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.4903 r_free = 0.4903 target = 0.251945 restraints weight = 4967.046|
|-----------------------------------------------------------------------------|
r_work (start): 0.4898 rms_B_bonded: 1.53
r_work: 0.4544 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.4544
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6885
moved from start:          0.1934

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   5581  Z= 0.196
  Angle     :  0.555   8.122   7536  Z= 0.288
  Chirality :  0.043   0.200    882
  Planarity :  0.004   0.057    957
  Dihedral  :  5.057  54.256    734
  Min Nonbonded Distance : 2.219

Molprobity Statistics.
  All-atom Clashscore : 12.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  4.54 %
    Allowed  : 30.47 %
    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: -0.16 (0.34), residues: 665
  helix:  0.86 (0.31), residues: 301
  sheet: -2.31 (0.49), residues: 98
  loop : -0.15 (0.41), residues: 266

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   0.020   0.001   PHE B 108 
 TYR   0.021   0.002   TYR A  54 
 ARG   0.007   0.000   ARG D  44 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3314.78 seconds
wall clock time: 57 minutes 36.86 seconds (3456.86 seconds total)