Starting phenix.real_space_refine
on Thu Mar  6 09:19:26 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7vag_31840/03_2025/7vag_31840.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7vag_31840/03_2025/7vag_31840.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.32
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7vag_31840/03_2025/7vag_31840.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7vag_31840/03_2025/7vag_31840.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7vag_31840/03_2025/7vag_31840.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7vag_31840/03_2025/7vag_31840.cif"
  }
  resolution = 3.32
  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=   0.003
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      43      5.16       5
     C    3676      2.51       5
     N     912      2.21       5
     O    1066      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 5697
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 2344
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 306, 2344
          Classifications: {'peptide': 306}
          Link IDs: {'PTRANS': 17, 'TRANS': 288}
    Chain: "H"
      Number of atoms: 1669
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 221, 1669
          Classifications: {'peptide': 221}
          Link IDs: {'PTRANS': 15, 'TRANS': 205}
    Chain: "L"
      Number of atoms: 1684
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 216, 1684
          Classifications: {'peptide': 216}
          Link IDs: {'PTRANS': 9, 'TRANS': 206}
  Time building chain proxies: 3.65, per 1000 atoms: 0.64
  Number of scatterers: 5697
  At special positions: 0
  Unit cell: (84.66, 72.21, 140.685, 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      43     16.00
     O    1066      8.00
     N     912      7.00
     C    3676      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 148 " - pdb=" SG  CYS H 203 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  94 " distance=2.04

  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: 1.38
  Conformation dependent library (CDL) restraints added in 723.4 milliseconds
  

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1376

  Finding SS restraints...
    Secondary structure from input PDB file:
      21 helices and 9 sheets defined
      38.8% alpha, 20.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.63
  Creating SS restraints...
    Processing helix  chain 'A' and resid 15 through 20
      removed outlier: 3.661A  pdb=" N   GLY A  19 " --> pdb=" O   PRO A  16 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 21 through 45
      removed outlier: 4.106A  pdb=" N   THR A  45 " --> pdb=" O   SER A  41 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 47 through 57
      removed outlier: 3.617A  pdb=" N   ILE A  51 " --> pdb=" O   GLU A  47 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 58 through 71
      removed outlier: 3.840A  pdb=" N   ILE A  71 " --> pdb=" O   ALA A  67 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 71 through 83
    Processing helix  chain 'A' and resid 86 through 99
    Processing helix  chain 'A' and resid 102 through 113
      removed outlier: 3.698A  pdb=" N   ASN A 106 " --> pdb=" O   GLY A 102 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 115 through 142
      Proline residue:  A 135  - end of helix
    Processing helix  chain 'A' and resid 156 through 180
      Proline residue:  A 169  - end of helix
    Processing helix  chain 'A' and resid 183 through 209
      removed outlier: 3.510A  pdb=" N   VAL A 187 " --> pdb=" O   TYR A 183 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 214 through 218
    Processing helix  chain 'A' and resid 219 through 244
      Proline residue:  A 230  - end of helix
      removed outlier: 3.526A  pdb=" N   PHE A 244 " --> pdb=" O   LEU A 240 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 249 through 260
      removed outlier: 4.528A  pdb=" N   THR A 253 " --> pdb=" O   ARG A 249 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 263 through 274
    Processing helix  chain 'A' and resid 280 through 283
    Processing helix  chain 'A' and resid 284 through 310
    Processing helix  chain 'H' and resid 28 through 32
      removed outlier: 3.793A  pdb=" N   TYR H  32 " --> pdb=" O   PHE H  29 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 62 through 66
      removed outlier: 3.743A  pdb=" N   LYS H  65 " --> pdb=" O   GLU H  62 " (cutoff:3.500A)
      removed outlier: 4.229A  pdb=" N   GLY H  66 " --> pdb=" O   LYS H  63 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 62 through 66'
    Processing helix  chain 'H' and resid 87 through 91
      removed outlier: 3.866A  pdb=" N   SER H  91 " --> pdb=" O   SER H  88 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 85 through 89
      removed outlier: 3.952A  pdb=" N   LEU L  89 " --> pdb=" O   ALA L  86 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 126 through 132
      removed outlier: 3.514A  pdb=" N   LEU L 130 " --> pdb=" O   SER L 126 " (cutoff:3.500A)
      removed outlier: 3.820A  pdb=" N   THR L 131 " --> pdb=" O   SER L 127 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'H' and resid 5 through 6
    Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12
      removed outlier: 6.606A  pdb=" N   ILE H  34 " --> pdb=" O   TYR H  50 " (cutoff:3.500A)
      removed outlier: 4.482A  pdb=" N   TYR H  50 " --> pdb=" O   ILE H  34 " (cutoff:3.500A)
      removed outlier: 6.755A  pdb=" N   TRP H  36 " --> pdb=" O   ILE H  48 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 12
      removed outlier: 7.028A  pdb=" N   CYS H  96 " --> pdb=" O   TYR H 110 " (cutoff:3.500A)
      removed outlier: 7.235A  pdb=" N   TYR H 110 " --> pdb=" O   CYS H  96 " (cutoff:3.500A)
      removed outlier: 6.188A  pdb=" N   ARG H  98 " --> pdb=" O   PHE H 108 " (cutoff:3.500A)
      removed outlier: 4.452A  pdb=" N   PHE H 108 " --> pdb=" O   ARG H  98 " (cutoff:3.500A)
      removed outlier: 7.185A  pdb=" N   TYR H 100 " --> pdb=" O   HIS H 106 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'H' and resid 130 through 132
      removed outlier: 4.340A  pdb=" N   GLY H 147 " --> pdb=" O   LEU H 132 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   CYS H 148 " --> pdb=" O   SER H 187 " (cutoff:3.500A)
      removed outlier: 4.504A  pdb=" N   SER H 187 " --> pdb=" O   CYS H 148 " (cutoff:3.500A)
      removed outlier: 6.382A  pdb=" N   THR H 184 " --> pdb=" O   ALA H 176 " (cutoff:3.500A)
      removed outlier: 4.592A  pdb=" N   ALA H 176 " --> pdb=" O   THR H 184 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   SER H 186 " --> pdb=" O   PHE H 174 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'H' and resid 159 through 161
      removed outlier: 3.644A  pdb=" N   LYS H 216 " --> pdb=" O   CYS H 203 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'L' and resid 11 through 12
      removed outlier: 3.527A  pdb=" N   TYR L  92 " --> pdb=" O   THR L 107 " (cutoff:3.500A)
      removed outlier: 6.451A  pdb=" N   TRP L  41 " --> pdb=" O   LEU L  53 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'L' and resid 21 through 23
      removed outlier: 3.673A  pdb=" N   CYS L  23 " --> pdb=" O   PHE L  77 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   PHE L  77 " --> pdb=" O   CYS L  23 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'L' and resid 122 through 123
      removed outlier: 3.574A  pdb=" N   VAL L 138 " --> pdb=" O   PHE L 123 " (cutoff:3.500A)
      removed outlier: 3.996A  pdb=" N   ASN L 143 " --> pdb=" O   TYR L 178 " (cutoff:3.500A)
      removed outlier: 6.253A  pdb=" N   TYR L 178 " --> pdb=" O   ASN L 143 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'L' and resid 158 through 159

    283 hydrogen bonds defined for protein.
    753 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: 1.47

  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:
        1.23 -     1.35: 1734
        1.35 -     1.46: 1443
        1.46 -     1.58: 2593
        1.58 -     1.70: 0
        1.70 -     1.82: 65
  Bond restraints: 5835
  Sorted by residual:
  bond pdb=" CA  MET A 133 "
       pdb=" CB  MET A 133 "
    ideal  model  delta    sigma   weight residual
    1.530  1.549 -0.019 1.84e-02 2.95e+03 1.08e+00
  bond pdb=" CB  GLN H 179 "
       pdb=" CG  GLN H 179 "
    ideal  model  delta    sigma   weight residual
    1.520  1.550 -0.030 3.00e-02 1.11e+03 1.00e+00
  bond pdb=" CA  GLN H 179 "
       pdb=" CB  GLN H 179 "
    ideal  model  delta    sigma   weight residual
    1.533  1.549 -0.016 1.69e-02 3.50e+03 8.61e-01
  bond pdb=" C   SER L   7 "
       pdb=" N   PRO L   8 "
    ideal  model  delta    sigma   weight residual
    1.334  1.353 -0.019 2.34e-02 1.83e+03 6.57e-01
  bond pdb=" CB  MET A 256 "
       pdb=" CG  MET A 256 "
    ideal  model  delta    sigma   weight residual
    1.520  1.496  0.024 3.00e-02 1.11e+03 6.25e-01
  ... (remaining 5830 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.88: 7752
        1.88 -     3.76: 135
        3.76 -     5.64: 31
        5.64 -     7.52: 9
        7.52 -     9.39: 2
  Bond angle restraints: 7929
  Sorted by residual:
  angle pdb=" CA  GLN H 179 "
        pdb=" CB  GLN H 179 "
        pdb=" CG  GLN H 179 "
      ideal   model   delta    sigma   weight residual
     114.10  119.79   -5.69 2.00e+00 2.50e-01 8.09e+00
  angle pdb=" CA  LEU A 150 "
        pdb=" CB  LEU A 150 "
        pdb=" CG  LEU A 150 "
      ideal   model   delta    sigma   weight residual
     116.30  125.69   -9.39 3.50e+00 8.16e-02 7.20e+00
  angle pdb=" CB  MET A 133 "
        pdb=" CG  MET A 133 "
        pdb=" SD  MET A 133 "
      ideal   model   delta    sigma   weight residual
     112.70  120.74   -8.04 3.00e+00 1.11e-01 7.19e+00
  angle pdb=" N   MET A 133 "
        pdb=" CA  MET A 133 "
        pdb=" CB  MET A 133 "
      ideal   model   delta    sigma   weight residual
     111.66  107.78    3.88 1.56e+00 4.11e-01 6.18e+00
  angle pdb=" CB  MET A  39 "
        pdb=" CG  MET A  39 "
        pdb=" SD  MET A  39 "
      ideal   model   delta    sigma   weight residual
     112.70  119.71   -7.01 3.00e+00 1.11e-01 5.45e+00
  ... (remaining 7924 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.95: 3179
       17.95 -    35.90: 258
       35.90 -    53.85: 33
       53.85 -    71.80: 7
       71.80 -    89.75: 4
  Dihedral angle restraints: 3481
    sinusoidal: 1329
      harmonic: 2152
  Sorted by residual:
  dihedral pdb=" CB  CYS L  23 "
           pdb=" SG  CYS L  23 "
           pdb=" SG  CYS L  94 "
           pdb=" CB  CYS L  94 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  165.03  -72.03     1      1.00e+01 1.00e-02 6.64e+01
  dihedral pdb=" CB  GLU L 192 "
           pdb=" CG  GLU L 192 "
           pdb=" CD  GLU L 192 "
           pdb=" OE1 GLU L 192 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   89.75  -89.75     1      3.00e+01 1.11e-03 1.06e+01
  dihedral pdb=" CA  GLY A 132 "
           pdb=" C   GLY A 132 "
           pdb=" N   MET A 133 "
           pdb=" CA  MET A 133 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -164.19  -15.81     0      5.00e+00 4.00e-02 1.00e+01
  ... (remaining 3478 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 550
       0.029 -    0.058: 230
       0.058 -    0.088: 80
       0.088 -    0.117: 52
       0.117 -    0.146: 6
  Chirality restraints: 918
  Sorted by residual:
  chirality pdb=" CA  ILE H 104 "
            pdb=" N   ILE H 104 "
            pdb=" C   ILE H 104 "
            pdb=" CB  ILE H 104 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.34e-01
  chirality pdb=" CG  LEU A 118 "
            pdb=" CB  LEU A 118 "
            pdb=" CD1 LEU A 118 "
            pdb=" CD2 LEU A 118 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.72    0.13 2.00e-01 2.50e+01 4.21e-01
  chirality pdb=" CB  ILE A 214 "
            pdb=" CA  ILE A 214 "
            pdb=" CG1 ILE A 214 "
            pdb=" CG2 ILE A 214 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.77   -0.13 2.00e-01 2.50e+01 3.98e-01
  ... (remaining 915 not shown)

  Planarity restraints: 980
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR H 213 "   -0.007 2.00e-02 2.50e+03   1.34e-02 1.78e+00
        pdb=" C   THR H 213 "    0.023 2.00e-02 2.50e+03
        pdb=" O   THR H 213 "   -0.009 2.00e-02 2.50e+03
        pdb=" N   VAL H 214 "   -0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE H 174 "   -0.020 5.00e-02 4.00e+02   2.97e-02 1.41e+00
        pdb=" N   PRO H 175 "    0.051 5.00e-02 4.00e+02
        pdb=" CA  PRO H 175 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO H 175 "   -0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 280 "   -0.018 5.00e-02 4.00e+02   2.74e-02 1.20e+00
        pdb=" N   PRO A 281 "    0.047 5.00e-02 4.00e+02
        pdb=" CA  PRO A 281 "   -0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO A 281 "   -0.015 5.00e-02 4.00e+02
  ... (remaining 977 not shown)

  Histogram of nonbonded interaction distances:
        2.11 -     2.67: 77
        2.67 -     3.23: 5522
        3.23 -     3.78: 8655
        3.78 -     4.34: 11118
        4.34 -     4.90: 18741
  Nonbonded interactions: 44113
  Sorted by model distance:
  nonbonded pdb=" OG  SER H 198 "
            pdb=" OE1 GLN H 199 "
     model   vdw
     2.109 3.040
  nonbonded pdb=" OE1 GLN H   6 "
            pdb=" OG1 THR H 115 "
     model   vdw
     2.239 3.040
  nonbonded pdb=" OH  TYR A  69 "
            pdb=" O   SER A 126 "
     model   vdw
     2.293 3.040
  nonbonded pdb=" OE2 GLU A  47 "
            pdb=" NZ  LYS A  50 "
     model   vdw
     2.295 3.120
  nonbonded pdb=" NH2 ARG L  60 "
            pdb=" O   VAL L  64 "
     model   vdw
     2.317 3.120
  ... (remaining 44108 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.520
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     16.450
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.010
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.600
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.940
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7521
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      :  0.002   0.030   5835  Z= 0.150
  Angle     :  0.655   9.395   7929  Z= 0.311
  Chirality :  0.041   0.146    918
  Planarity :  0.004   0.031    980
  Dihedral  : 13.266  89.754   2096
  Min Nonbonded Distance : 2.109

Molprobity Statistics.
  All-atom Clashscore : 7.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.28 %
    Favored  : 91.72 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  0.77 %
    Favored  : 99.07 %
  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:  0.41 (0.32), residues: 737
  helix:  1.46 (0.33), residues: 250
  sheet:  0.88 (0.41), residues: 168
  loop : -1.04 (0.35), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP L  56 
 HIS   0.002   0.000   HIS H  35 
 PHE   0.014   0.001   PHE A 292 
 TYR   0.010   0.001   TYR A 146 
 ARG   0.005   0.001   ARG A 251 

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

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

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 215
  time to evaluate  : 0.586 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  180 ARG cc_start: 0.8007 (mtt90) cc_final: 0.7666 (ttm-80)
REVERT: A  229 MET cc_start: 0.8523 (tpt) cc_final: 0.8039 (tpt)
REVERT: A  308 GLU cc_start: 0.7853 (tm-30) cc_final: 0.7435 (tp30)
REVERT: H   91 SER cc_start: 0.8947 (m) cc_final: 0.8706 (p)
REVERT: H  153 TYR cc_start: 0.6429 (p90) cc_final: 0.5833 (p90)
REVERT: L  144 PHE cc_start: 0.8461 (p90) cc_final: 0.8190 (p90)
REVERT: L  180 MET cc_start: 0.8413 (ttp) cc_final: 0.8086 (ttt)
  outliers start: 1
  outliers final: 0
  residues processed: 215
  average time/residue: 0.1495
  time to fit residues: 42.4888
Evaluate side-chains
  185 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 185
  time to evaluate  : 0.583 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 61 optimal weight:    0.9990
   chunk 55 optimal weight:    2.9990
   chunk 30 optimal weight:    3.9990
   chunk 18 optimal weight:    5.9990
   chunk 37 optimal weight:    3.9990
   chunk 29 optimal weight:    5.9990
   chunk 57 optimal weight:    0.7980
   chunk 22 optimal weight:    0.0770
   chunk 34 optimal weight:    0.7980
   chunk 42 optimal weight:    3.9990
   chunk 66 optimal weight:    3.9990
   overall best weight:    1.1342

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

Flipped N/Q/H residues before XYZ refinement:
A 209 ASN
A 293 GLN
H  39 GLN
H 113 GLN
H 179 GLN
** L  37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 195 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.162325 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.126487 restraints weight = 9276.545|
|-----------------------------------------------------------------------------|
r_work (start): 0.3521 rms_B_bonded: 3.59
r_work: 0.3399 rms_B_bonded: 4.03 restraints_weight: 0.5000
r_work (final): 0.3399
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7583
moved from start:          0.1772

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   5835  Z= 0.263
  Angle     :  0.715   9.912   7929  Z= 0.351
  Chirality :  0.045   0.173    918
  Planarity :  0.004   0.039    980
  Dihedral  :  4.161  17.439    794
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 8.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.19 %
    Favored  : 92.81 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 13.93 %
    Favored  : 84.06 %
  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:  0.47 (0.32), residues: 737
  helix:  1.64 (0.34), residues: 248
  sheet:  0.77 (0.41), residues: 169
  loop : -1.02 (0.35), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP H 196 
 HIS   0.003   0.001   HIS H 207 
 PHE   0.029   0.002   PHE A 274 
 TYR   0.020   0.002   TYR A 146 
 ARG   0.005   0.001   ARG A 251 

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

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

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 207
  time to evaluate  : 0.600 
Fit side-chains
   revert: symmetry clash
REVERT: A  180 ARG cc_start: 0.8100 (mtt90) cc_final: 0.7788 (ttm170)
REVERT: A  182 GLN cc_start: 0.5452 (pm20) cc_final: 0.5190 (pm20)
REVERT: A  184 MET cc_start: 0.5234 (mmp) cc_final: 0.4848 (mmt)
REVERT: A  229 MET cc_start: 0.9005 (tpt) cc_final: 0.8391 (tpt)
REVERT: A  231 PHE cc_start: 0.8590 (t80) cc_final: 0.8205 (t80)
REVERT: A  271 ASN cc_start: 0.8998 (m-40) cc_final: 0.8762 (m-40)
REVERT: H   39 GLN cc_start: 0.8676 (tt0) cc_final: 0.8360 (tt0)
REVERT: H   61 ASN cc_start: 0.8799 (t0) cc_final: 0.8097 (t0)
REVERT: H  153 TYR cc_start: 0.7003 (p90) cc_final: 0.6230 (p90)
REVERT: H  179 GLN cc_start: 0.7238 (OUTLIER) cc_final: 0.6936 (pp30)
REVERT: L    2 ILE cc_start: 0.9189 (mt) cc_final: 0.8952 (mm)
REVERT: L   87 GLU cc_start: 0.8595 (pm20) cc_final: 0.8304 (pm20)
REVERT: L   88 ASP cc_start: 0.8940 (m-30) cc_final: 0.8666 (m-30)
REVERT: L  144 PHE cc_start: 0.8548 (p90) cc_final: 0.8210 (p90)
REVERT: L  161 GLN cc_start: 0.5988 (mp10) cc_final: 0.4949 (pm20)
  outliers start: 13
  outliers final: 10
  residues processed: 210
  average time/residue: 0.1409
  time to fit residues: 40.4677
Evaluate side-chains
  207 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 196
  time to evaluate  : 0.607 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue  129 CYS
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain A residue  293 GLN
Chi-restraints excluded: chain H residue  118 THR
Chi-restraints excluded: chain H residue  179 GLN
Chi-restraints excluded: chain L residue   71 SER
Chi-restraints excluded: chain L residue  110 GLU
Chi-restraints excluded: chain L residue  137 VAL
Chi-restraints excluded: chain L residue  141 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 66 optimal weight:    0.7980
   chunk 45 optimal weight:    1.9990
   chunk 63 optimal weight:    4.9990
   chunk 69 optimal weight:    2.9990
   chunk 55 optimal weight:    3.9990
   chunk 48 optimal weight:    4.9990
   chunk 54 optimal weight:    1.9990
   chunk 67 optimal weight:    0.9990
   chunk 68 optimal weight:    0.7980
   chunk 71 optimal weight:    2.9990
   chunk 0 optimal weight:    7.9990
   overall best weight:    1.3186

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

Flipped N/Q/H residues before XYZ refinement:
A 209 ASN
A 293 GLN
** L  37 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 = 0.3912 r_free = 0.3912 target = 0.158978 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.122740 restraints weight = 9356.655|
|-----------------------------------------------------------------------------|
r_work (start): 0.3473 rms_B_bonded: 3.54
r_work: 0.3345 rms_B_bonded: 4.00 restraints_weight: 0.5000
r_work (final): 0.3345
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7640
moved from start:          0.2288

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   5835  Z= 0.293
  Angle     :  0.707   9.104   7929  Z= 0.351
  Chirality :  0.046   0.210    918
  Planarity :  0.004   0.036    980
  Dihedral  :  4.420  17.865    794
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 8.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.60 %
    Favored  : 92.40 %
  Rotamer:
    Outliers :  3.87 %
    Allowed  : 16.72 %
    Favored  : 79.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.37 (0.32), residues: 737
  helix:  1.61 (0.34), residues: 247
  sheet:  0.72 (0.41), residues: 168
  loop : -1.12 (0.35), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP L 153 
 HIS   0.005   0.001   HIS H 207 
 PHE   0.029   0.002   PHE A 292 
 TYR   0.016   0.002   TYR A 146 
 ARG   0.004   0.000   ARG A 251 

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

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

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 196
  time to evaluate  : 0.577 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  139 TYR cc_start: 0.8134 (t80) cc_final: 0.7930 (t80)
REVERT: A  180 ARG cc_start: 0.8285 (mtt90) cc_final: 0.7817 (ttm-80)
REVERT: A  184 MET cc_start: 0.5172 (mmp) cc_final: 0.4828 (mmt)
REVERT: A  229 MET cc_start: 0.9087 (tpt) cc_final: 0.8540 (tpt)
REVERT: H   39 GLN cc_start: 0.8679 (tt0) cc_final: 0.8424 (tt0)
REVERT: H   61 ASN cc_start: 0.8887 (t0) cc_final: 0.8499 (t0)
REVERT: H  153 TYR cc_start: 0.7317 (p90) cc_final: 0.6464 (p90)
REVERT: H  179 GLN cc_start: 0.7772 (OUTLIER) cc_final: 0.7555 (tm-30)
REVERT: L    2 ILE cc_start: 0.9237 (mt) cc_final: 0.8938 (mm)
REVERT: L   27 GLN cc_start: 0.8069 (pm20) cc_final: 0.7455 (pm20)
REVERT: L   88 ASP cc_start: 0.8894 (m-30) cc_final: 0.8691 (m-30)
REVERT: L  144 PHE cc_start: 0.8537 (p90) cc_final: 0.8192 (p90)
  outliers start: 25
  outliers final: 18
  residues processed: 203
  average time/residue: 0.1374
  time to fit residues: 37.9559
Evaluate side-chains
  207 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 188
  time to evaluate  : 0.652 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue  125 CYS
Chi-restraints excluded: chain A residue  129 CYS
Chi-restraints excluded: chain A residue  160 VAL
Chi-restraints excluded: chain A residue  185 ARG
Chi-restraints excluded: chain A residue  219 THR
Chi-restraints excluded: chain A residue  245 CYS
Chi-restraints excluded: chain A residue  258 THR
Chi-restraints excluded: chain A residue  299 LEU
Chi-restraints excluded: chain A residue  303 ILE
Chi-restraints excluded: chain H residue  118 THR
Chi-restraints excluded: chain H residue  179 GLN
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   71 SER
Chi-restraints excluded: chain L residue  110 GLU
Chi-restraints excluded: chain L residue  137 VAL
Chi-restraints excluded: chain L residue  141 LEU
Chi-restraints excluded: chain L residue  194 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 35 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 38 optimal weight:    0.2980
   chunk 41 optimal weight:    0.9990
   chunk 36 optimal weight:    0.9980
   chunk 24 optimal weight:    0.8980
   chunk 46 optimal weight:    0.0870
   chunk 15 optimal weight:    0.6980
   chunk 33 optimal weight:    1.9990
   chunk 71 optimal weight:    6.9990
   chunk 67 optimal weight:    0.7980
   overall best weight:    0.5558

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

Flipped N/Q/H residues before XYZ refinement:
A 209 ASN
A 293 GLN
H 179 GLN
** L  37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.159617 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.123471 restraints weight = 9606.128|
|-----------------------------------------------------------------------------|
r_work (start): 0.3489 rms_B_bonded: 3.62
r_work: 0.3364 rms_B_bonded: 4.05 restraints_weight: 0.5000
r_work (final): 0.3364
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7619
moved from start:          0.2497

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5835  Z= 0.192
  Angle     :  0.689   9.497   7929  Z= 0.330
  Chirality :  0.044   0.200    918
  Planarity :  0.004   0.035    980
  Dihedral  :  4.305  17.661    794
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 8.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.92 %
    Favored  : 93.08 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 20.12 %
    Favored  : 76.16 %
  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 (0.32), residues: 737
  helix:  1.69 (0.34), residues: 253
  sheet:  0.70 (0.42), residues: 162
  loop : -1.27 (0.34), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP L 168 
 HIS   0.002   0.001   HIS A  54 
 PHE   0.020   0.001   PHE A 292 
 TYR   0.016   0.001   TYR L 145 
 ARG   0.002   0.000   ARG A 249 

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

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

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 204
  time to evaluate  : 0.630 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   27 LEU cc_start: 0.6709 (tp) cc_final: 0.6450 (mm)
REVERT: A   42 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8943 (mp)
REVERT: A  180 ARG cc_start: 0.8223 (mtt90) cc_final: 0.7483 (ttm110)
REVERT: A  184 MET cc_start: 0.5232 (mmp) cc_final: 0.4924 (mmt)
REVERT: A  229 MET cc_start: 0.9089 (tpt) cc_final: 0.8557 (tpt)
REVERT: A  253 THR cc_start: 0.9026 (t) cc_final: 0.8755 (t)
REVERT: A  310 PHE cc_start: 0.6835 (m-10) cc_final: 0.6632 (m-80)
REVERT: H   39 GLN cc_start: 0.8654 (tt0) cc_final: 0.8420 (tt0)
REVERT: H   61 ASN cc_start: 0.8896 (t0) cc_final: 0.8501 (t0)
REVERT: H  153 TYR cc_start: 0.7379 (p90) cc_final: 0.6545 (p90)
REVERT: H  185 MET cc_start: 0.8435 (ppp) cc_final: 0.8202 (ppp)
REVERT: L    2 ILE cc_start: 0.9233 (mt) cc_final: 0.8924 (mm)
REVERT: L   27 GLN cc_start: 0.7943 (pm20) cc_final: 0.7483 (pm20)
REVERT: L   88 ASP cc_start: 0.8968 (m-30) cc_final: 0.8725 (m-30)
REVERT: L  144 PHE cc_start: 0.8564 (p90) cc_final: 0.8192 (p90)
REVERT: L  161 GLN cc_start: 0.5982 (mp10) cc_final: 0.4927 (pm20)
  outliers start: 24
  outliers final: 17
  residues processed: 210
  average time/residue: 0.1322
  time to fit residues: 38.0108
Evaluate side-chains
  214 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 196
  time to evaluate  : 0.584 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue   42 LEU
Chi-restraints excluded: chain A residue   71 ILE
Chi-restraints excluded: chain A residue   99 SER
Chi-restraints excluded: chain A residue  129 CYS
Chi-restraints excluded: chain A residue  160 VAL
Chi-restraints excluded: chain A residue  185 ARG
Chi-restraints excluded: chain A residue  219 THR
Chi-restraints excluded: chain A residue  240 LEU
Chi-restraints excluded: chain A residue  303 ILE
Chi-restraints excluded: chain H residue   99 SER
Chi-restraints excluded: chain H residue  118 THR
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   71 SER
Chi-restraints excluded: chain L residue  110 GLU
Chi-restraints excluded: chain L residue  137 VAL
Chi-restraints excluded: chain L residue  141 LEU
Chi-restraints excluded: chain L residue  194 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 50 optimal weight:    0.9980
   chunk 12 optimal weight:    2.9990
   chunk 42 optimal weight:    3.9990
   chunk 40 optimal weight:    2.9990
   chunk 45 optimal weight:    0.5980
   chunk 37 optimal weight:    3.9990
   chunk 35 optimal weight:    3.9990
   chunk 41 optimal weight:    0.9980
   chunk 15 optimal weight:    0.0000
   chunk 9 optimal weight:    0.9980
   chunk 31 optimal weight:    1.9990
   overall best weight:    0.7184

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

Flipped N/Q/H residues before XYZ refinement:
A 209 ASN
** L   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  37 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 = 0.3916 r_free = 0.3916 target = 0.159206 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.123381 restraints weight = 9429.821|
|-----------------------------------------------------------------------------|
r_work (start): 0.3483 rms_B_bonded: 3.61
r_work: 0.3354 rms_B_bonded: 4.05 restraints_weight: 0.5000
r_work (final): 0.3354
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7610
moved from start:          0.2700

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5835  Z= 0.204
  Angle     :  0.687   8.768   7929  Z= 0.326
  Chirality :  0.044   0.214    918
  Planarity :  0.004   0.036    980
  Dihedral  :  4.271  18.580    794
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 8.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.06 %
    Favored  : 92.94 %
  Rotamer:
    Outliers :  4.33 %
    Allowed  : 20.59 %
    Favored  : 75.08 %
  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 (0.32), residues: 737
  helix:  1.68 (0.34), residues: 254
  sheet:  0.68 (0.42), residues: 162
  loop : -1.26 (0.34), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP L 168 
 HIS   0.003   0.001   HIS H  35 
 PHE   0.022   0.001   PHE A 292 
 TYR   0.018   0.001   TYR L 145 
 ARG   0.002   0.000   ARG A 249 

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

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

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 199
  time to evaluate  : 0.601 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   27 LEU cc_start: 0.6720 (tp) cc_final: 0.6442 (mm)
REVERT: A  127 THR cc_start: 0.8796 (m) cc_final: 0.8489 (p)
REVERT: A  229 MET cc_start: 0.9132 (tpt) cc_final: 0.8611 (tpt)
REVERT: A  253 THR cc_start: 0.9034 (t) cc_final: 0.8763 (t)
REVERT: H   39 GLN cc_start: 0.8660 (tt0) cc_final: 0.8436 (tt0)
REVERT: H   61 ASN cc_start: 0.8907 (t0) cc_final: 0.8507 (t0)
REVERT: H  153 TYR cc_start: 0.7348 (p90) cc_final: 0.6475 (p90)
REVERT: H  185 MET cc_start: 0.8506 (ppp) cc_final: 0.8281 (ppp)
REVERT: L    2 ILE cc_start: 0.9233 (mt) cc_final: 0.8823 (mm)
REVERT: L   27 GLN cc_start: 0.8169 (pm20) cc_final: 0.7193 (pm20)
REVERT: L   61 GLU cc_start: 0.9235 (tp30) cc_final: 0.9034 (tp30)
REVERT: L  144 PHE cc_start: 0.8499 (p90) cc_final: 0.8094 (p90)
  outliers start: 28
  outliers final: 21
  residues processed: 206
  average time/residue: 0.1401
  time to fit residues: 39.1496
Evaluate side-chains
  215 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 194
  time to evaluate  : 0.677 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue   71 ILE
Chi-restraints excluded: chain A residue   99 SER
Chi-restraints excluded: chain A residue  125 CYS
Chi-restraints excluded: chain A residue  129 CYS
Chi-restraints excluded: chain A residue  154 VAL
Chi-restraints excluded: chain A residue  160 VAL
Chi-restraints excluded: chain A residue  185 ARG
Chi-restraints excluded: chain A residue  219 THR
Chi-restraints excluded: chain A residue  258 THR
Chi-restraints excluded: chain A residue  303 ILE
Chi-restraints excluded: chain H residue   99 SER
Chi-restraints excluded: chain H residue  118 THR
Chi-restraints excluded: chain L residue   17 GLU
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   52 LEU
Chi-restraints excluded: chain L residue   71 SER
Chi-restraints excluded: chain L residue  137 VAL
Chi-restraints excluded: chain L residue  141 LEU
Chi-restraints excluded: chain L residue  151 VAL
Chi-restraints excluded: chain L residue  194 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 42 optimal weight:   10.0000
   chunk 40 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9980
   chunk 7 optimal weight:    0.7980
   chunk 55 optimal weight:    2.9990
   chunk 20 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9980
   chunk 36 optimal weight:    0.7980
   chunk 59 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9990
   chunk 33 optimal weight:    1.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
A 209 ASN
A 293 GLN
** L   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  37 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 = 0.3895 r_free = 0.3895 target = 0.157115 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.121276 restraints weight = 9444.152|
|-----------------------------------------------------------------------------|
r_work (start): 0.3460 rms_B_bonded: 3.55
r_work: 0.3334 rms_B_bonded: 4.00 restraints_weight: 0.5000
r_work (final): 0.3334
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7649
moved from start:          0.2974

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   5835  Z= 0.228
  Angle     :  0.718   9.526   7929  Z= 0.339
  Chirality :  0.044   0.208    918
  Planarity :  0.004   0.037    980
  Dihedral  :  4.343  19.152    794
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 9.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.01 %
    Favored  : 91.99 %
  Rotamer:
    Outliers :  4.33 %
    Allowed  : 21.05 %
    Favored  : 74.61 %
  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:  0.35 (0.32), residues: 737
  helix:  1.79 (0.34), residues: 248
  sheet:  0.66 (0.42), residues: 166
  loop : -1.29 (0.34), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP L 168 
 HIS   0.003   0.001   HIS H  35 
 PHE   0.023   0.001   PHE A 292 
 TYR   0.014   0.001   TYR H 183 
 ARG   0.005   0.000   ARG L 113 

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

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

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 198
  time to evaluate  : 0.647 
Fit side-chains
   revert: symmetry clash
REVERT: A   34 MET cc_start: 0.8819 (tmm) cc_final: 0.8593 (ttt)
REVERT: A  163 LEU cc_start: 0.8970 (tp) cc_final: 0.8639 (mp)
REVERT: A  180 ARG cc_start: 0.8371 (ttm170) cc_final: 0.7741 (ttm110)
REVERT: A  229 MET cc_start: 0.9133 (tpt) cc_final: 0.8630 (tpt)
REVERT: A  253 THR cc_start: 0.9206 (t) cc_final: 0.8920 (t)
REVERT: H   39 GLN cc_start: 0.8681 (tt0) cc_final: 0.8457 (tt0)
REVERT: H   61 ASN cc_start: 0.8895 (t0) cc_final: 0.8514 (t0)
REVERT: H  153 TYR cc_start: 0.7454 (p90) cc_final: 0.6514 (p90)
REVERT: L    2 ILE cc_start: 0.9239 (mt) cc_final: 0.8831 (mm)
REVERT: L   27 GLN cc_start: 0.8195 (pm20) cc_final: 0.7105 (pm20)
REVERT: L   61 GLU cc_start: 0.9296 (tp30) cc_final: 0.9078 (tp30)
REVERT: L   88 ASP cc_start: 0.8891 (m-30) cc_final: 0.8659 (m-30)
REVERT: L  144 PHE cc_start: 0.8420 (p90) cc_final: 0.8118 (p90)
REVERT: L  161 GLN cc_start: 0.5910 (mp10) cc_final: 0.5688 (mp10)
  outliers start: 28
  outliers final: 25
  residues processed: 206
  average time/residue: 0.1428
  time to fit residues: 39.7632
Evaluate side-chains
  219 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 194
  time to evaluate  : 0.650 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue   71 ILE
Chi-restraints excluded: chain A residue   99 SER
Chi-restraints excluded: chain A residue  125 CYS
Chi-restraints excluded: chain A residue  129 CYS
Chi-restraints excluded: chain A residue  137 LEU
Chi-restraints excluded: chain A residue  154 VAL
Chi-restraints excluded: chain A residue  160 VAL
Chi-restraints excluded: chain A residue  174 ILE
Chi-restraints excluded: chain A residue  258 THR
Chi-restraints excluded: chain A residue  293 GLN
Chi-restraints excluded: chain A residue  300 LEU
Chi-restraints excluded: chain A residue  303 ILE
Chi-restraints excluded: chain H residue   99 SER
Chi-restraints excluded: chain H residue  104 ILE
Chi-restraints excluded: chain H residue  118 THR
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   52 LEU
Chi-restraints excluded: chain L residue   71 SER
Chi-restraints excluded: chain L residue  110 GLU
Chi-restraints excluded: chain L residue  137 VAL
Chi-restraints excluded: chain L residue  141 LEU
Chi-restraints excluded: chain L residue  151 VAL
Chi-restraints excluded: chain L residue  194 HIS
Chi-restraints excluded: chain L residue  214 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 61 optimal weight:    1.9990
   chunk 54 optimal weight:    0.7980
   chunk 0 optimal weight:    7.9990
   chunk 25 optimal weight:    1.9990
   chunk 34 optimal weight:    0.0870
   chunk 42 optimal weight:    8.9990
   chunk 58 optimal weight:    0.2980
   chunk 69 optimal weight:    0.0000
   chunk 21 optimal weight:    0.7980
   chunk 32 optimal weight:    2.9990
   chunk 5 optimal weight:    0.4980
   overall best weight:    0.3362

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

Flipped N/Q/H residues before XYZ refinement:
A 209 ASN
** L  37 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 = 0.3926 r_free = 0.3926 target = 0.160315 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.123928 restraints weight = 9466.290|
|-----------------------------------------------------------------------------|
r_work (start): 0.3491 rms_B_bonded: 3.62
r_work: 0.3366 rms_B_bonded: 4.05 restraints_weight: 0.5000
r_work (final): 0.3366
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7621
moved from start:          0.3001

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5835  Z= 0.180
  Angle     :  0.714  11.103   7929  Z= 0.333
  Chirality :  0.044   0.217    918
  Planarity :  0.004   0.035    980
  Dihedral  :  4.283  19.066    794
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 9.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.78 %
    Favored  : 93.22 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 23.37 %
    Favored  : 73.37 %
  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:  0.38 (0.32), residues: 737
  helix:  1.81 (0.34), residues: 247
  sheet:  0.69 (0.42), residues: 164
  loop : -1.26 (0.34), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP L 168 
 HIS   0.002   0.001   HIS A  54 
 PHE   0.020   0.001   PHE A 292 
 TYR   0.021   0.001   TYR L 145 
 ARG   0.007   0.000   ARG A 249 

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

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

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 200
  time to evaluate  : 0.652 
Fit side-chains
   revert: symmetry clash
REVERT: A   27 LEU cc_start: 0.6576 (tp) cc_final: 0.6272 (mm)
REVERT: A  180 ARG cc_start: 0.8290 (ttm170) cc_final: 0.7674 (ttm110)
REVERT: A  229 MET cc_start: 0.9081 (tpt) cc_final: 0.8623 (tpt)
REVERT: A  253 THR cc_start: 0.9137 (t) cc_final: 0.8803 (t)
REVERT: H   39 GLN cc_start: 0.8664 (tt0) cc_final: 0.8462 (tt0)
REVERT: H   61 ASN cc_start: 0.8858 (t0) cc_final: 0.8469 (t0)
REVERT: H  100 TYR cc_start: 0.8750 (t80) cc_final: 0.8484 (t80)
REVERT: H  153 TYR cc_start: 0.7382 (p90) cc_final: 0.6458 (p90)
REVERT: L    2 ILE cc_start: 0.9221 (mt) cc_final: 0.8810 (mm)
REVERT: L   27 GLN cc_start: 0.8162 (pm20) cc_final: 0.7135 (pm20)
REVERT: L   61 GLU cc_start: 0.9305 (tp30) cc_final: 0.9091 (tp30)
REVERT: L   88 ASP cc_start: 0.8873 (m-30) cc_final: 0.8666 (m-30)
REVERT: L  144 PHE cc_start: 0.8459 (p90) cc_final: 0.8106 (p90)
REVERT: L  161 GLN cc_start: 0.6100 (mp10) cc_final: 0.5028 (pm20)
  outliers start: 21
  outliers final: 16
  residues processed: 206
  average time/residue: 0.1397
  time to fit residues: 39.5724
Evaluate side-chains
  211 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 195
  time to evaluate  : 0.639 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue   71 ILE
Chi-restraints excluded: chain A residue  125 CYS
Chi-restraints excluded: chain A residue  129 CYS
Chi-restraints excluded: chain A residue  154 VAL
Chi-restraints excluded: chain A residue  160 VAL
Chi-restraints excluded: chain H residue   99 SER
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   52 LEU
Chi-restraints excluded: chain L residue   71 SER
Chi-restraints excluded: chain L residue  110 GLU
Chi-restraints excluded: chain L residue  137 VAL
Chi-restraints excluded: chain L residue  141 LEU
Chi-restraints excluded: chain L residue  151 VAL
Chi-restraints excluded: chain L residue  194 HIS
Chi-restraints excluded: chain L residue  214 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 55 optimal weight:    3.9990
   chunk 9 optimal weight:    0.7980
   chunk 10 optimal weight:    0.9990
   chunk 70 optimal weight:    3.9990
   chunk 47 optimal weight:    0.9980
   chunk 54 optimal weight:    3.9990
   chunk 38 optimal weight:    0.5980
   chunk 36 optimal weight:    0.0770
   chunk 20 optimal weight:    5.9990
   chunk 32 optimal weight:    2.9990
   chunk 11 optimal weight:    0.6980
   overall best weight:    0.6338

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

Flipped N/Q/H residues before XYZ refinement:
A 209 ASN
** L   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  37 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 = 0.3928 r_free = 0.3928 target = 0.159845 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.122902 restraints weight = 9322.531|
|-----------------------------------------------------------------------------|
r_work (start): 0.3484 rms_B_bonded: 3.68
r_work: 0.3355 rms_B_bonded: 4.13 restraints_weight: 0.5000
r_work (final): 0.3355
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7583
moved from start:          0.3212

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5835  Z= 0.198
  Angle     :  0.724  10.050   7929  Z= 0.339
  Chirality :  0.044   0.214    918
  Planarity :  0.004   0.039    980
  Dihedral  :  4.294  19.494    794
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 9.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.46 %
    Favored  : 92.54 %
  Rotamer:
    Outliers :  4.02 %
    Allowed  : 23.53 %
    Favored  : 72.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.29 (0.32), residues: 737
  helix:  1.80 (0.35), residues: 247
  sheet:  0.54 (0.42), residues: 162
  loop : -1.29 (0.34), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP L 168 
 HIS   0.002   0.001   HIS H  35 
 PHE   0.023   0.001   PHE A 292 
 TYR   0.020   0.001   TYR L 145 
 ARG   0.008   0.001   ARG A 249 

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

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

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 195
  time to evaluate  : 0.654 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  180 ARG cc_start: 0.8247 (ttm170) cc_final: 0.7629 (ttm110)
REVERT: A  229 MET cc_start: 0.9088 (tpt) cc_final: 0.8596 (tpt)
REVERT: A  253 THR cc_start: 0.9178 (t) cc_final: 0.8846 (t)
REVERT: H   61 ASN cc_start: 0.8929 (t0) cc_final: 0.8536 (t0)
REVERT: H  100 TYR cc_start: 0.8763 (t80) cc_final: 0.8478 (t80)
REVERT: H  153 TYR cc_start: 0.7415 (p90) cc_final: 0.6482 (p90)
REVERT: L    2 ILE cc_start: 0.9242 (mt) cc_final: 0.8914 (mm)
REVERT: L   61 GLU cc_start: 0.9282 (tp30) cc_final: 0.9059 (tp30)
REVERT: L  144 PHE cc_start: 0.8306 (p90) cc_final: 0.8065 (p90)
  outliers start: 26
  outliers final: 25
  residues processed: 203
  average time/residue: 0.1397
  time to fit residues: 38.8805
Evaluate side-chains
  214 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 189
  time to evaluate  : 0.653 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue   47 GLU
Chi-restraints excluded: chain A residue   71 ILE
Chi-restraints excluded: chain A residue   99 SER
Chi-restraints excluded: chain A residue  125 CYS
Chi-restraints excluded: chain A residue  129 CYS
Chi-restraints excluded: chain A residue  137 LEU
Chi-restraints excluded: chain A residue  154 VAL
Chi-restraints excluded: chain A residue  160 VAL
Chi-restraints excluded: chain A residue  174 ILE
Chi-restraints excluded: chain A residue  258 THR
Chi-restraints excluded: chain A residue  300 LEU
Chi-restraints excluded: chain H residue   99 SER
Chi-restraints excluded: chain H residue  104 ILE
Chi-restraints excluded: chain H residue  118 THR
Chi-restraints excluded: chain L residue   17 GLU
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   52 LEU
Chi-restraints excluded: chain L residue   71 SER
Chi-restraints excluded: chain L residue  110 GLU
Chi-restraints excluded: chain L residue  137 VAL
Chi-restraints excluded: chain L residue  141 LEU
Chi-restraints excluded: chain L residue  151 VAL
Chi-restraints excluded: chain L residue  194 HIS
Chi-restraints excluded: chain L residue  214 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 34 optimal weight:    0.0770
   chunk 65 optimal weight:    0.4980
   chunk 16 optimal weight:    0.8980
   chunk 33 optimal weight:    0.7980
   chunk 43 optimal weight:    0.0010
   chunk 69 optimal weight:    0.9990
   chunk 3 optimal weight:    0.8980
   chunk 37 optimal weight:    0.9980
   chunk 21 optimal weight:    0.0870
   chunk 19 optimal weight:    2.9990
   chunk 60 optimal weight:    3.9990
   overall best weight:    0.2922

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

Flipped N/Q/H residues before XYZ refinement:
A 106 ASN
A 209 ASN
A 293 GLN
** L  37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.161913 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.125040 restraints weight = 9254.201|
|-----------------------------------------------------------------------------|
r_work (start): 0.3516 rms_B_bonded: 3.67
r_work: 0.3391 rms_B_bonded: 4.11 restraints_weight: 0.5000
r_work (final): 0.3391
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7549
moved from start:          0.3210

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5835  Z= 0.179
  Angle     :  0.719  10.197   7929  Z= 0.334
  Chirality :  0.043   0.216    918
  Planarity :  0.004   0.036    980
  Dihedral  :  4.182  19.332    794
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 9.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.65 %
    Favored  : 93.35 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 24.61 %
    Favored  : 71.98 %
  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:  0.26 (0.32), residues: 737
  helix:  1.75 (0.35), residues: 247
  sheet:  0.63 (0.43), residues: 162
  loop : -1.36 (0.34), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP L 168 
 HIS   0.002   0.001   HIS H  35 
 PHE   0.017   0.001   PHE A 292 
 TYR   0.019   0.001   TYR L 145 
 ARG   0.007   0.001   ARG A 249 

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

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

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 188
  time to evaluate  : 0.633 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  180 ARG cc_start: 0.8219 (ttm170) cc_final: 0.7759 (ttm110)
REVERT: A  229 MET cc_start: 0.9102 (tpt) cc_final: 0.8664 (tpt)
REVERT: A  253 THR cc_start: 0.9126 (t) cc_final: 0.8810 (t)
REVERT: H   61 ASN cc_start: 0.8909 (t0) cc_final: 0.8520 (t0)
REVERT: H  100 TYR cc_start: 0.8741 (t80) cc_final: 0.8466 (t80)
REVERT: H  153 TYR cc_start: 0.7335 (p90) cc_final: 0.6354 (p90)
REVERT: L    2 ILE cc_start: 0.9217 (mt) cc_final: 0.8881 (mm)
REVERT: L   61 GLU cc_start: 0.9274 (tp30) cc_final: 0.9051 (tp30)
REVERT: L  180 MET cc_start: 0.8472 (ttt) cc_final: 0.7813 (ttt)
  outliers start: 22
  outliers final: 19
  residues processed: 194
  average time/residue: 0.1360
  time to fit residues: 36.0381
Evaluate side-chains
  203 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 184
  time to evaluate  : 0.679 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 ILE
Chi-restraints excluded: chain A residue  125 CYS
Chi-restraints excluded: chain A residue  129 CYS
Chi-restraints excluded: chain A residue  137 LEU
Chi-restraints excluded: chain A residue  154 VAL
Chi-restraints excluded: chain A residue  163 LEU
Chi-restraints excluded: chain A residue  185 ARG
Chi-restraints excluded: chain A residue  300 LEU
Chi-restraints excluded: chain H residue   99 SER
Chi-restraints excluded: chain H residue  118 THR
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   52 LEU
Chi-restraints excluded: chain L residue   71 SER
Chi-restraints excluded: chain L residue  110 GLU
Chi-restraints excluded: chain L residue  137 VAL
Chi-restraints excluded: chain L residue  141 LEU
Chi-restraints excluded: chain L residue  151 VAL
Chi-restraints excluded: chain L residue  194 HIS
Chi-restraints excluded: chain L residue  214 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 64 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 5 optimal weight:    0.8980
   chunk 19 optimal weight:    2.9990
   chunk 70 optimal weight:    1.9990
   chunk 20 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 34 optimal weight:    0.8980
   chunk 41 optimal weight:    0.5980
   chunk 37 optimal weight:    0.7980
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
A 106 ASN
A 209 ASN
A 293 GLN
** L   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.157372 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.121039 restraints weight = 9421.747|
|-----------------------------------------------------------------------------|
r_work (start): 0.3450 rms_B_bonded: 3.62
r_work: 0.3321 rms_B_bonded: 4.05 restraints_weight: 0.5000
r_work (final): 0.3321
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7660
moved from start:          0.3456

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   5835  Z= 0.249
  Angle     :  0.758  11.162   7929  Z= 0.361
  Chirality :  0.045   0.209    918
  Planarity :  0.004   0.043    980
  Dihedral  :  4.397  20.599    794
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 11.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.87 %
    Favored  : 92.13 %
  Rotamer:
    Outliers :  3.87 %
    Allowed  : 24.46 %
    Favored  : 71.67 %
  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:  0.09 (0.32), residues: 737
  helix:  1.63 (0.34), residues: 247
  sheet:  0.39 (0.41), residues: 169
  loop : -1.42 (0.34), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP L 168 
 HIS   0.003   0.001   HIS H  35 
 PHE   0.028   0.002   PHE A 292 
 TYR   0.024   0.002   TYR L 145 
 ARG   0.009   0.001   ARG A 249 

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

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

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 194
  time to evaluate  : 1.121 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  229 MET cc_start: 0.9143 (tpt) cc_final: 0.8688 (tpt)
REVERT: A  253 THR cc_start: 0.9246 (t) cc_final: 0.8944 (t)
REVERT: H   61 ASN cc_start: 0.8973 (t0) cc_final: 0.8330 (t0)
REVERT: H  153 TYR cc_start: 0.7514 (p90) cc_final: 0.6602 (p90)
REVERT: L    2 ILE cc_start: 0.9247 (mt) cc_final: 0.8838 (mm)
REVERT: L   27 GLN cc_start: 0.8198 (pm20) cc_final: 0.7184 (pm20)
REVERT: L   61 GLU cc_start: 0.9316 (tp30) cc_final: 0.9104 (tp30)
REVERT: L  179 SER cc_start: 0.8906 (m) cc_final: 0.8466 (m)
REVERT: L  180 MET cc_start: 0.8438 (ttt) cc_final: 0.7860 (ttt)
  outliers start: 25
  outliers final: 23
  residues processed: 200
  average time/residue: 0.1661
  time to fit residues: 46.0291
Evaluate side-chains
  215 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 192
  time to evaluate  : 0.669 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 ILE
Chi-restraints excluded: chain A residue   99 SER
Chi-restraints excluded: chain A residue  125 CYS
Chi-restraints excluded: chain A residue  129 CYS
Chi-restraints excluded: chain A residue  137 LEU
Chi-restraints excluded: chain A residue  154 VAL
Chi-restraints excluded: chain A residue  163 LEU
Chi-restraints excluded: chain A residue  174 ILE
Chi-restraints excluded: chain A residue  185 ARG
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain A residue  300 LEU
Chi-restraints excluded: chain A residue  303 ILE
Chi-restraints excluded: chain H residue   99 SER
Chi-restraints excluded: chain H residue  118 THR
Chi-restraints excluded: chain L residue   52 LEU
Chi-restraints excluded: chain L residue   71 SER
Chi-restraints excluded: chain L residue   84 VAL
Chi-restraints excluded: chain L residue  110 GLU
Chi-restraints excluded: chain L residue  137 VAL
Chi-restraints excluded: chain L residue  141 LEU
Chi-restraints excluded: chain L residue  151 VAL
Chi-restraints excluded: chain L residue  194 HIS
Chi-restraints excluded: chain L residue  214 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 26 optimal weight:    0.9980
   chunk 2 optimal weight:    2.9990
   chunk 55 optimal weight:    0.0050
   chunk 47 optimal weight:    1.9990
   chunk 72 optimal weight:    4.9990
   chunk 3 optimal weight:    1.9990
   chunk 24 optimal weight:    3.9990
   chunk 38 optimal weight:    2.9990
   chunk 50 optimal weight:    4.9990
   chunk 33 optimal weight:    0.8980
   chunk 10 optimal weight:    1.9990
   overall best weight:    1.1798

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

Flipped N/Q/H residues before XYZ refinement:
A 106 ASN
A 209 ASN
A 293 GLN
** L   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.156083 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.119071 restraints weight = 9431.100|
|-----------------------------------------------------------------------------|
r_work (start): 0.3424 rms_B_bonded: 3.59
r_work: 0.3296 rms_B_bonded: 4.02 restraints_weight: 0.5000
r_work (final): 0.3296
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7679
moved from start:          0.3642

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   5835  Z= 0.268
  Angle     :  0.777  12.769   7929  Z= 0.367
  Chirality :  0.046   0.213    918
  Planarity :  0.004   0.043    980
  Dihedral  :  4.505  20.898    794
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 11.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.55 %
    Favored  : 91.45 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 25.23 %
    Favored  : 71.05 %
  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: -0.01 (0.32), residues: 737
  helix:  1.55 (0.34), residues: 247
  sheet:  0.20 (0.40), residues: 176
  loop : -1.44 (0.34), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP L 168 
 HIS   0.004   0.001   HIS H  35 
 PHE   0.027   0.002   PHE A 292 
 TYR   0.021   0.002   TYR L 145 
 ARG   0.010   0.001   ARG A 249 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3138.49 seconds
wall clock time: 55 minutes 0.67 seconds (3300.67 seconds total)