Starting phenix.real_space_refine
on Wed Sep 17 05:37:27 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8s7d_19766/09_2025/8s7d_19766.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8s7d_19766/09_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_19766/09_2025/8s7d_19766.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8s7d_19766/09_2025/8s7d_19766.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8s7d_19766/09_2025/8s7d_19766.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8s7d_19766/09_2025/8s7d_19766.cif"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.122
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 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: 1.46, per 1000 atoms: 0.27
  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: 0.28
  Conformation dependent library (CDL) restraints added in 134.8 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.25
  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: 0.84

  Time building geometry restraints manager: 0.39 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:             0.720
  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:          0.110
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.710
  Find NCS groups from input model:        0.030
  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:             0.000
  Load rotamer database and sin/cos tables:1.370
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.990
-------------------------------------------------------------------------------
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= 0.115
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.33 (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
 ARG   0.008   0.000   ARG D  58 
 TYR   0.009   0.001   TYR A  88 
 PHE   0.029   0.001   PHE B 108 
 TRP   0.007   0.001   TRP D  68 
 HIS   0.003   0.001   HIS D 398 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 5581)
  covalent geometry    : angle       0.56915 ( 7536)
  hydrogen bonds       : bond        0.16768 (  254)
  hydrogen bonds       : angle       7.32727 (  723)

*********************** 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  : 0.214 
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: 0.0927
  time to fit residues: 10.7296
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  : 0.213 
-------------------------------------------------------------------------------
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 49 optimal weight:    0.9980
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.6980
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9980
   chunk 27 optimal weight:   20.0000
   overall best weight:    0.8982

-------------------------------------------------------------------------------
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
** 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 = 0.5093 r_free = 0.5093 target = 0.279308 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.4803 r_free = 0.4803 target = 0.239246 restraints weight = 4868.874|
|-----------------------------------------------------------------------------|
r_work (start): 0.4802 rms_B_bonded: 1.29
r_work: 0.4467 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work (final): 0.4467
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6882
moved from start:          0.0957

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= 0.125
  Angle     :  0.527   7.493   7536  Z= 0.277
  Chirality :  0.043   0.143    882
  Planarity :  0.004   0.061    957
  Dihedral  :  7.877  75.069    773
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 11.27
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.36 (0.34), residues: 665
  helix:  0.74 (0.31), residues: 296
  sheet: -2.27 (0.53), residues: 96
  loop : -0.39 (0.40), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 136 
 TYR   0.013   0.001   TYR A  88 
 PHE   0.010   0.001   PHE A 121 
 TRP   0.010   0.001   TRP D  68 
 HIS   0.004   0.001   HIS D 398 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 5581)
  covalent geometry    : angle       0.52660 ( 7536)
  hydrogen bonds       : bond        0.03385 (  254)
  hydrogen bonds       : angle       5.55240 (  723)

*********************** 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
  91 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 67
  time to evaluate  : 0.219 
Fit side-chains
REVERT: A  115 GLU cc_start: 0.6375 (OUTLIER) cc_final: 0.4313 (mp0)
REVERT: C   30 MET cc_start: 0.5745 (pmm) cc_final: 0.5212 (pmm)
REVERT: D   58 ARG cc_start: 0.7955 (ttp-110) cc_final: 0.7555 (ttp-110)
REVERT: D  213 ASP cc_start: 0.8348 (OUTLIER) cc_final: 0.7615 (t70)
REVERT: D  347 LYS cc_start: 0.6156 (tptp) cc_final: 0.5098 (ttpt)
  outliers start: 24
  outliers final: 15
  residues processed: 88
  average time/residue: 0.1019
  time to fit residues: 11.0867
Evaluate side-chains
  81 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 64
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
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 C residue   83 ASP
Chi-restraints excluded: chain D residue   84 LEU
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
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 51 optimal weight:    0.0060
   chunk 2 optimal weight:    0.5980
   chunk 15 optimal weight:    5.9990
   chunk 40 optimal weight:    4.9990
   chunk 3 optimal weight:    0.3980
   chunk 55 optimal weight:    2.9990
   chunk 18 optimal weight:    0.8980
   chunk 11 optimal weight:    5.9990
   chunk 16 optimal weight:    3.9990
   chunk 6 optimal weight:    9.9990
   chunk 37 optimal weight:   10.0000
   overall best weight:    0.9798

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

Flipped N/Q/H residues before XYZ refinement:
A 112 HIS
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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5091 r_free = 0.5091 target = 0.279097 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4800 r_free = 0.4800 target = 0.239127 restraints weight = 4889.923|
|-----------------------------------------------------------------------------|
r_work (start): 0.4799 rms_B_bonded: 1.28
r_work: 0.4469 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work (final): 0.4469
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6886
moved from start:          0.1224

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= 0.124
  Angle     :  0.504   7.521   7536  Z= 0.265
  Chirality :  0.043   0.143    882
  Planarity :  0.004   0.059    957
  Dihedral  :  5.876  55.437    740
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 11.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  4.38 %
    Allowed  : 30.15 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.38 (0.34), residues: 665
  helix:  0.76 (0.30), residues: 296
  sheet: -2.34 (0.51), residues: 96
  loop : -0.41 (0.40), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 136 
 TYR   0.014   0.001   TYR D 104 
 PHE   0.018   0.001   PHE A 108 
 TRP   0.008   0.001   TRP D  68 
 HIS   0.003   0.001   HIS B  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 5581)
  covalent geometry    : angle       0.50356 ( 7536)
  hydrogen bonds       : bond        0.03094 (  254)
  hydrogen bonds       : angle       5.28570 (  723)

*********************** 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
  97 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 70
  time to evaluate  : 0.203 
Fit side-chains
REVERT: A  115 GLU cc_start: 0.6386 (OUTLIER) cc_final: 0.4402 (mp0)
REVERT: C   30 MET cc_start: 0.5729 (pmm) cc_final: 0.5188 (pmm)
REVERT: C  128 LYS cc_start: 0.6699 (mmmm) cc_final: 0.6453 (mmmt)
REVERT: D   58 ARG cc_start: 0.7952 (ttp-110) cc_final: 0.7576 (ttp-110)
REVERT: D  105 MET cc_start: 0.6981 (OUTLIER) cc_final: 0.6733 (mtm)
REVERT: D  213 ASP cc_start: 0.8337 (OUTLIER) cc_final: 0.7622 (t70)
REVERT: D  329 ARG cc_start: 0.3230 (OUTLIER) cc_final: 0.2479 (ptp-170)
REVERT: D  347 LYS cc_start: 0.6110 (tptp) cc_final: 0.5281 (ttpt)
  outliers start: 27
  outliers final: 16
  residues processed: 92
  average time/residue: 0.1042
  time to fit residues: 11.6176
Evaluate side-chains
  86 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 66
  time to evaluate  : 0.137 
-------------------------------------------------------------------------------
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   28 VAL
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 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  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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 15 optimal weight:    1.9990
   chunk 45 optimal weight:    9.9990
   chunk 6 optimal weight:    0.8980
   chunk 11 optimal weight:    4.9990
   chunk 19 optimal weight:    0.7980
   chunk 13 optimal weight:    0.9980
   chunk 49 optimal weight:    9.9990
   chunk 62 optimal weight:    0.8980
   chunk 22 optimal weight:    9.9990
   chunk 40 optimal weight:    1.9990
   chunk 63 optimal weight:    0.7980
   overall best weight:    0.8780

-------------------------------------------------------------------------------
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 = 0.5101 r_free = 0.5101 target = 0.280178 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.4812 r_free = 0.4812 target = 0.240349 restraints weight = 4899.285|
|-----------------------------------------------------------------------------|
r_work (start): 0.4808 rms_B_bonded: 1.30
r_work: 0.4476 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work (final): 0.4476
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6877
moved from start:          0.1371

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= 0.116
  Angle     :  0.489   6.890   7536  Z= 0.258
  Chirality :  0.043   0.158    882
  Planarity :  0.004   0.059    957
  Dihedral  :  5.314  54.561    736
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 10.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 29.82 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.32 (0.33), residues: 665
  helix:  0.75 (0.30), residues: 306
  sheet: -2.39 (0.49), residues: 98
  loop : -0.30 (0.40), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D  44 
 TYR   0.014   0.001   TYR D 104 
 PHE   0.021   0.001   PHE A 108 
 TRP   0.008   0.001   TRP D  68 
 HIS   0.003   0.001   HIS D 398 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 5581)
  covalent geometry    : angle       0.48860 ( 7536)
  hydrogen bonds       : bond        0.02860 (  254)
  hydrogen bonds       : angle       5.15966 (  723)

*********************** 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
  97 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 72
  time to evaluate  : 0.218 
Fit side-chains
REVERT: A  115 GLU cc_start: 0.6358 (OUTLIER) cc_final: 0.4423 (mp0)
REVERT: C   30 MET cc_start: 0.5780 (OUTLIER) cc_final: 0.5261 (pmm)
REVERT: D  105 MET cc_start: 0.6882 (OUTLIER) cc_final: 0.6590 (mtm)
REVERT: D  213 ASP cc_start: 0.8387 (OUTLIER) cc_final: 0.7675 (t70)
REVERT: D  329 ARG cc_start: 0.3008 (OUTLIER) cc_final: 0.2391 (ptp-170)
REVERT: D  347 LYS cc_start: 0.6129 (tptp) cc_final: 0.5321 (ttpt)
  outliers start: 25
  outliers final: 15
  residues processed: 91
  average time/residue: 0.1254
  time to fit residues: 13.7610
Evaluate side-chains
  89 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 69
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
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   28 VAL
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 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  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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 21 optimal weight:    0.0270
   chunk 49 optimal weight:    9.9990
   chunk 44 optimal weight:    0.0870
   chunk 40 optimal weight:    0.3980
   chunk 50 optimal weight:    0.6980
   chunk 20 optimal weight:    7.9990
   chunk 56 optimal weight:    0.9990
   chunk 16 optimal weight:    0.9980
   chunk 58 optimal weight:    2.9990
   chunk 43 optimal weight:    0.7980
   chunk 23 optimal weight:    6.9990
   overall best weight:    0.4016

-------------------------------------------------------------------------------
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 = 0.5176 r_free = 0.5176 target = 0.290475 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.4914 r_free = 0.4914 target = 0.252659 restraints weight = 5068.454|
|-----------------------------------------------------------------------------|
r_work (start): 0.4944 rms_B_bonded: 1.26
r_work: 0.4608 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.4608
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6807
moved from start:          0.1584

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   5581  Z= 0.091
  Angle     :  0.468   7.041   7536  Z= 0.245
  Chirality :  0.042   0.173    882
  Planarity :  0.004   0.058    957
  Dihedral  :  4.854  54.699    734
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 9.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 30.63 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.07 (0.34), residues: 665
  helix:  0.94 (0.30), residues: 306
  sheet: -2.20 (0.50), residues: 98
  loop : -0.17 (0.41), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D  44 
 TYR   0.013   0.001   TYR D 104 
 PHE   0.023   0.001   PHE A 108 
 TRP   0.008   0.001   TRP D  68 
 HIS   0.003   0.001   HIS D 398 

Details of bonding type rmsd
  covalent geometry    : bond        0.00202 ( 5581)
  covalent geometry    : angle       0.46790 ( 7536)
  hydrogen bonds       : bond        0.02566 (  254)
  hydrogen bonds       : angle       4.89673 (  723)

*********************** 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: 20
    poor density    : 80
  time to evaluate  : 0.220 
Fit side-chains
REVERT: A  115 GLU cc_start: 0.6153 (OUTLIER) cc_final: 0.4489 (mp0)
REVERT: C   30 MET cc_start: 0.5654 (OUTLIER) cc_final: 0.5185 (pmm)
REVERT: D  178 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.7732 (mt)
REVERT: D  213 ASP cc_start: 0.8306 (OUTLIER) cc_final: 0.7603 (t70)
  outliers start: 20
  outliers final: 14
  residues processed: 95
  average time/residue: 0.1136
  time to fit residues: 13.0982
Evaluate side-chains
  92 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 74
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 ARG
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 C residue   17 ASP
Chi-restraints excluded: chain C residue   30 MET
Chi-restraints excluded: chain D residue   61 ARG
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 5 optimal weight:    4.9990
   chunk 35 optimal weight:    3.9990
   chunk 53 optimal weight:    0.7980
   chunk 0 optimal weight:   20.0000
   chunk 27 optimal weight:    3.9990
   chunk 19 optimal weight:    0.0770
   chunk 45 optimal weight:   10.0000
   chunk 37 optimal weight:    6.9990
   chunk 64 optimal weight:    2.9990
   chunk 34 optimal weight:    0.0060
   chunk 29 optimal weight:    2.9990
   overall best weight:    1.3758

-------------------------------------------------------------------------------
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  82 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 = 0.5171 r_free = 0.5171 target = 0.291897 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4882 r_free = 0.4882 target = 0.250431 restraints weight = 4972.409|
|-----------------------------------------------------------------------------|
r_work (start): 0.4882 rms_B_bonded: 1.92
r_work: 0.4468 rms_B_bonded: 3.85 restraints_weight: 0.5000
r_work (final): 0.4468
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6990
moved from start:          0.1652

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= 0.151
  Angle     :  0.536   6.468   7536  Z= 0.280
  Chirality :  0.043   0.178    882
  Planarity :  0.004   0.059    957
  Dihedral  :  5.083  54.150    734
  Min Nonbonded Distance : 2.322

Molprobity Statistics.
  All-atom Clashscore : 12.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.06 %
    Favored  : 95.94 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.25 (0.34), residues: 665
  helix:  0.83 (0.30), residues: 306
  sheet: -2.39 (0.49), residues: 98
  loop : -0.27 (0.40), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D  44 
 TYR   0.028   0.002   TYR A  54 
 PHE   0.018   0.001   PHE B 108 
 TRP   0.008   0.001   TRP D  68 
 HIS   0.004   0.001   HIS D  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 ( 5581)
  covalent geometry    : angle       0.53582 ( 7536)
  hydrogen bonds       : bond        0.02901 (  254)
  hydrogen bonds       : angle       5.08570 (  723)

*********************** 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
  102 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 72
  time to evaluate  : 0.228 
Fit side-chains
REVERT: A  115 GLU cc_start: 0.6479 (OUTLIER) cc_final: 0.4444 (mp0)
REVERT: C   30 MET cc_start: 0.5900 (OUTLIER) cc_final: 0.5329 (pmm)
REVERT: D  105 MET cc_start: 0.7112 (OUTLIER) cc_final: 0.6848 (mtm)
REVERT: D  178 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.7808 (mt)
REVERT: D  213 ASP cc_start: 0.8386 (OUTLIER) cc_final: 0.7671 (t70)
REVERT: D  329 ARG cc_start: 0.3267 (OUTLIER) cc_final: 0.2551 (ptp-170)
  outliers start: 30
  outliers final: 20
  residues processed: 95
  average time/residue: 0.1215
  time to fit residues: 13.9360
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  : 0.220 
-------------------------------------------------------------------------------
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   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   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  105 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  329 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 54 optimal weight:    4.9990
   chunk 55 optimal weight:    1.9990
   chunk 66 optimal weight:    2.9990
   chunk 65 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9980
   chunk 17 optimal weight:    7.9990
   chunk 61 optimal weight:    0.3980
   chunk 10 optimal weight:    0.7980
   chunk 3 optimal weight:    4.9990
   chunk 18 optimal weight:    0.7980
   chunk 0 optimal weight:   10.0000
   overall best weight:    0.9982

-------------------------------------------------------------------------------
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 = 0.5178 r_free = 0.5178 target = 0.292626 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.4876 r_free = 0.4876 target = 0.249334 restraints weight = 5020.021|
|-----------------------------------------------------------------------------|
r_work (start): 0.4872 rms_B_bonded: 1.65
r_work: 0.4493 rms_B_bonded: 3.99 restraints_weight: 0.5000
r_work (final): 0.4493
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6970
moved from start:          0.1693

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= 0.129
  Angle     :  0.532   8.079   7536  Z= 0.277
  Chirality :  0.044   0.191    882
  Planarity :  0.004   0.059    957
  Dihedral  :  5.032  54.269    734
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 11.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  4.86 %
    Allowed  : 29.50 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.28 (0.34), residues: 665
  helix:  0.80 (0.30), residues: 306
  sheet: -2.46 (0.49), residues: 98
  loop : -0.25 (0.41), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG D  44 
 TYR   0.018   0.002   TYR A  54 
 PHE   0.027   0.001   PHE A 108 
 TRP   0.008   0.001   TRP D  68 
 HIS   0.007   0.001   HIS B  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 5581)
  covalent geometry    : angle       0.53196 ( 7536)
  hydrogen bonds       : bond        0.02849 (  254)
  hydrogen bonds       : angle       5.03490 (  723)

*********************** 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: 30
    poor density    : 71
  time to evaluate  : 0.218 
Fit side-chains
REVERT: A  115 GLU cc_start: 0.6391 (OUTLIER) cc_final: 0.4365 (mp0)
REVERT: C   30 MET cc_start: 0.5702 (OUTLIER) cc_final: 0.5156 (pmm)
REVERT: D  105 MET cc_start: 0.7061 (OUTLIER) cc_final: 0.6793 (mtm)
REVERT: D  178 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.7774 (mt)
REVERT: D  213 ASP cc_start: 0.8361 (OUTLIER) cc_final: 0.7621 (t70)
REVERT: D  329 ARG cc_start: 0.2985 (OUTLIER) cc_final: 0.2406 (ptp-170)
REVERT: D  347 LYS cc_start: 0.6213 (tptp) cc_final: 0.5341 (ttpt)
  outliers start: 30
  outliers final: 20
  residues processed: 94
  average time/residue: 0.1171
  time to fit residues: 13.2855
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  : 0.223 
-------------------------------------------------------------------------------
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   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   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  105 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  329 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 45 optimal weight:    8.9990
   chunk 11 optimal weight:    4.9990
   chunk 34 optimal weight:    6.9990
   chunk 46 optimal weight:    4.9990
   chunk 53 optimal weight:    1.9990
   chunk 6 optimal weight:    4.9990
   chunk 47 optimal weight:    1.9990
   chunk 3 optimal weight:    0.7980
   chunk 38 optimal weight:    1.9990
   chunk 43 optimal weight:    0.3980
   chunk 20 optimal weight:    7.9990
   overall best weight:    1.4386

-------------------------------------------------------------------------------
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 = 0.5168 r_free = 0.5168 target = 0.291148 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4899 r_free = 0.4899 target = 0.253258 restraints weight = 4988.179|
|-----------------------------------------------------------------------------|
r_work (start): 0.4899 rms_B_bonded: 1.70
r_work: 0.4475 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.4475
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6979
moved from start:          0.1795

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= 0.158
  Angle     :  0.572   7.458   7536  Z= 0.297
  Chirality :  0.045   0.197    882
  Planarity :  0.004   0.064    957
  Dihedral  :  5.185  53.926    734
  Min Nonbonded Distance : 2.372

Molprobity Statistics.
  All-atom Clashscore : 12.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.06 %
    Favored  : 95.94 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.39 (0.34), residues: 665
  helix:  0.73 (0.30), residues: 299
  sheet: -2.69 (0.48), residues: 99
  loop : -0.21 (0.40), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG D  44 
 TYR   0.018   0.002   TYR A  54 
 PHE   0.022   0.002   PHE A 108 
 TRP   0.008   0.001   TRP D  68 
 HIS   0.004   0.001   HIS D 398 

Details of bonding type rmsd
  covalent geometry    : bond        0.00384 ( 5581)
  covalent geometry    : angle       0.57210 ( 7536)
  hydrogen bonds       : bond        0.02998 (  254)
  hydrogen bonds       : angle       5.22021 (  723)

*********************** 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
  96 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 67
  time to evaluate  : 0.225 
Fit side-chains
REVERT: A  115 GLU cc_start: 0.6466 (OUTLIER) cc_final: 0.4463 (mp0)
REVERT: C   30 MET cc_start: 0.5678 (OUTLIER) cc_final: 0.5127 (pmm)
REVERT: D  105 MET cc_start: 0.7181 (OUTLIER) cc_final: 0.6837 (mtm)
REVERT: D  178 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.7797 (mt)
REVERT: D  202 GLU cc_start: 0.7296 (OUTLIER) cc_final: 0.6947 (mp0)
REVERT: D  213 ASP cc_start: 0.8433 (OUTLIER) cc_final: 0.7724 (t70)
REVERT: D  329 ARG cc_start: 0.3265 (OUTLIER) cc_final: 0.2392 (ptp-170)
REVERT: D  347 LYS cc_start: 0.6256 (tptp) cc_final: 0.5376 (ttpt)
  outliers start: 29
  outliers final: 21
  residues processed: 90
  average time/residue: 0.1299
  time to fit residues: 14.1134
Evaluate side-chains
  95 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 67
  time to evaluate  : 0.226 
-------------------------------------------------------------------------------
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   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   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  105 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  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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 59 optimal weight:    0.8980
   chunk 46 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9980
   chunk 64 optimal weight:    3.9990
   chunk 16 optimal weight:    0.0070
   chunk 40 optimal weight:    6.9990
   chunk 58 optimal weight:    0.8980
   chunk 31 optimal weight:    5.9990
   chunk 48 optimal weight:    2.9990
   chunk 38 optimal weight:    4.9990
   chunk 28 optimal weight:    5.9990
   overall best weight:    0.9600

-------------------------------------------------------------------------------
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 = 0.5178 r_free = 0.5178 target = 0.292256 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 92)----------------|
| r_work = 0.4902 r_free = 0.4902 target = 0.253666 restraints weight = 4974.664|
|-----------------------------------------------------------------------------|
r_work (start): 0.4894 rms_B_bonded: 1.07
r_work: 0.4591 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work (final): 0.4591
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6860
moved from start:          0.1765

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= 0.129
  Angle     :  0.554   7.473   7536  Z= 0.287
  Chirality :  0.044   0.183    882
  Planarity :  0.004   0.060    957
  Dihedral  :  5.099  54.138    734
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 12.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 30.63 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.32 (0.34), residues: 665
  helix:  0.75 (0.31), residues: 301
  sheet: -2.55 (0.49), residues: 98
  loop : -0.20 (0.41), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG D  44 
 TYR   0.035   0.002   TYR A  54 
 PHE   0.020   0.001   PHE A 108 
 TRP   0.009   0.001   TRP D  68 
 HIS   0.003   0.001   HIS D 398 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 5581)
  covalent geometry    : angle       0.55419 ( 7536)
  hydrogen bonds       : bond        0.02927 (  254)
  hydrogen bonds       : angle       5.14089 (  723)

*********************** 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
  94 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 69
  time to evaluate  : 0.215 
Fit side-chains
REVERT: A  115 GLU cc_start: 0.6327 (OUTLIER) cc_final: 0.4425 (mp0)
REVERT: C   30 MET cc_start: 0.5513 (OUTLIER) cc_final: 0.5073 (pmm)
REVERT: D  105 MET cc_start: 0.6927 (OUTLIER) cc_final: 0.6623 (mtt)
REVERT: D  178 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.7709 (mt)
REVERT: D  213 ASP cc_start: 0.8361 (OUTLIER) cc_final: 0.7643 (t70)
REVERT: D  347 LYS cc_start: 0.6208 (tptp) cc_final: 0.5432 (ttpt)
  outliers start: 25
  outliers final: 20
  residues processed: 87
  average time/residue: 0.1274
  time to fit residues: 13.4141
Evaluate side-chains
  94 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 69
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
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   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   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  105 MET
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 53 optimal weight:    1.9990
   chunk 12 optimal weight:    4.9990
   chunk 51 optimal weight:    0.8980
   chunk 14 optimal weight:    0.6980
   chunk 9 optimal weight:    0.8980
   chunk 38 optimal weight:    3.9990
   chunk 3 optimal weight:    4.9990
   chunk 31 optimal weight:    5.9990
   chunk 64 optimal weight:    2.9990
   chunk 15 optimal weight:    3.9990
   chunk 49 optimal weight:    0.0050
   overall best weight:    0.8996

-------------------------------------------------------------------------------
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 = 0.5178 r_free = 0.5178 target = 0.292847 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.4890 r_free = 0.4890 target = 0.251240 restraints weight = 4983.461|
|-----------------------------------------------------------------------------|
r_work (start): 0.4890 rms_B_bonded: 1.56
r_work: 0.4514 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.4514
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6930
moved from start:          0.1853

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= 0.127
  Angle     :  0.572  10.176   7536  Z= 0.292
  Chirality :  0.044   0.186    882
  Planarity :  0.004   0.060    957
  Dihedral  :  5.057  54.192    734
  Min Nonbonded Distance : 2.294

Molprobity Statistics.
  All-atom Clashscore : 12.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.29 (0.34), residues: 665
  helix:  0.76 (0.31), residues: 301
  sheet: -2.49 (0.49), residues: 98
  loop : -0.18 (0.41), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG D  44 
 TYR   0.037   0.002   TYR A  54 
 PHE   0.020   0.001   PHE B 108 
 TRP   0.009   0.001   TRP D  68 
 HIS   0.004   0.001   HIS B  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 5581)
  covalent geometry    : angle       0.57191 ( 7536)
  hydrogen bonds       : bond        0.02905 (  254)
  hydrogen bonds       : angle       5.15733 (  723)

********************** 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: 28
    poor density    : 66
  time to evaluate  : 0.251 
Fit side-chains
REVERT: A  115 GLU cc_start: 0.6326 (OUTLIER) cc_final: 0.4244 (mp0)
REVERT: C   30 MET cc_start: 0.5761 (OUTLIER) cc_final: 0.5200 (pmm)
REVERT: C  147 GLU cc_start: 0.6738 (pm20) cc_final: 0.6517 (pm20)
REVERT: D  105 MET cc_start: 0.7075 (OUTLIER) cc_final: 0.6771 (mtt)
REVERT: D  178 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.7766 (mt)
REVERT: D  213 ASP cc_start: 0.8364 (OUTLIER) cc_final: 0.7645 (t70)
REVERT: D  329 ARG cc_start: 0.2836 (OUTLIER) cc_final: 0.1722 (ptm160)
REVERT: D  347 LYS cc_start: 0.6156 (tptp) cc_final: 0.5303 (ttpt)
  outliers start: 28
  outliers final: 20
  residues processed: 86
  average time/residue: 0.1173
  time to fit residues: 12.3602
Evaluate side-chains
  90 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 64
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
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   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  105 MET
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 20 optimal weight:    5.9990
   chunk 46 optimal weight:    0.7980
   chunk 13 optimal weight:    7.9990
   chunk 65 optimal weight:    2.9990
   chunk 66 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9990
   chunk 18 optimal weight:    0.9980
   chunk 3 optimal weight:    4.9990
   chunk 62 optimal weight:    0.6980
   chunk 8 optimal weight:    4.9990
   chunk 63 optimal weight:    0.7980
   overall best weight:    0.8582

-------------------------------------------------------------------------------
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 = 0.5185 r_free = 0.5185 target = 0.293640 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4893 r_free = 0.4893 target = 0.251122 restraints weight = 4993.873|
|-----------------------------------------------------------------------------|
r_work (start): 0.4886 rms_B_bonded: 1.78
r_work: 0.4499 rms_B_bonded: 3.81 restraints_weight: 0.5000
r_work (final): 0.4499
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6948
moved from start:          0.1878

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= 0.124
  Angle     :  0.560   8.039   7536  Z= 0.287
  Chirality :  0.043   0.182    882
  Planarity :  0.004   0.059    957
  Dihedral  :  5.015  54.181    734
  Min Nonbonded Distance : 2.297

Molprobity Statistics.
  All-atom Clashscore : 11.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  4.54 %
    Allowed  : 30.31 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.24 (0.34), residues: 665
  helix:  0.79 (0.31), residues: 301
  sheet: -2.45 (0.50), residues: 98
  loop : -0.15 (0.41), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG D  44 
 TYR   0.033   0.002   TYR A  54 
 PHE   0.020   0.001   PHE B 108 
 TRP   0.009   0.001   TRP D  68 
 HIS   0.003   0.001   HIS D 398 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 5581)
  covalent geometry    : angle       0.55960 ( 7536)
  hydrogen bonds       : bond        0.02872 (  254)
  hydrogen bonds       : angle       5.13332 (  723)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1711.01 seconds
wall clock time: 30 minutes 1.82 seconds (1801.82 seconds total)