Starting phenix.real_space_refine
on Sun Apr 27 12:28:46 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9jqt_61741/04_2025/9jqt_61741.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9jqt_61741/04_2025/9jqt_61741.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9jqt_61741/04_2025/9jqt_61741.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9jqt_61741/04_2025/9jqt_61741.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9jqt_61741/04_2025/9jqt_61741.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9jqt_61741/04_2025/9jqt_61741.cif"
  }
  resolution = 2.7
  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=   0.014
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      23      5.16       5
     C    3581      2.51       5
     N     963      2.21       5
     O    1102      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 25 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 5669
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1599
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 188, 1599
          Classifications: {'peptide': 188}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 177}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 1557
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 206, 1557
          Classifications: {'peptide': 206}
          Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 193}
          Chain breaks: 2
    Chain: "C"
      Number of atoms: 1603
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 208, 1603
          Classifications: {'peptide': 208}
          Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 194}
    Chain: "D"
      Number of atoms: 910
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 118, 910
          Classifications: {'peptide': 118}
          Link IDs: {'PTRANS': 3, 'TRANS': 114}
  Time building chain proxies: 4.33, per 1000 atoms: 0.76
  Number of scatterers: 5669
  At special positions: 0
  Unit cell: (80.864, 85.918, 113.354, 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      23     16.00
     O    1102      8.00
     N     963      7.00
     C    3581      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 102 " - pdb=" SG  CYS A 115 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 182 " - pdb=" SG  CYS A 231 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 144 " - pdb=" SG  CYS B 200 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C  23 " - pdb=" SG  CYS C  87 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 133 " - pdb=" SG  CYS C 193 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  24 " - pdb=" SG  CYS D  98 " distance=2.03

  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: 1.47
  Conformation dependent library (CDL) restraints added in 718.1 milliseconds
  

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1354

  Finding SS restraints...
    Secondary structure from input PDB file:
      12 helices and 18 sheets defined
      8.3% alpha, 49.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.10
  Creating SS restraints...
    Processing helix  chain 'A' and resid 75 through 79
      removed outlier: 3.615A  pdb=" N   SER A  78 " --> pdb=" O   ASN A  75 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 118 through 122
    Processing helix  chain 'B' and resid 28 through 32
    Processing helix  chain 'B' and resid 87 through 91
      removed outlier: 3.537A  pdb=" N   THR B  91 " --> pdb=" O   SER B  88 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 160 through 162
      No H-bonds generated for 'chain 'B' and resid 160 through 162'
    Processing helix  chain 'B' and resid 191 through 193
      No H-bonds generated for 'chain 'B' and resid 191 through 193'
    Processing helix  chain 'B' and resid 205 through 208
    Processing helix  chain 'C' and resid 78 through 82
      removed outlier: 3.647A  pdb=" N   PHE C  82 " --> pdb=" O   PRO C  79 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 120 through 127
    Processing helix  chain 'C' and resid 182 through 188
      removed outlier: 3.871A  pdb=" N   HIS C 188 " --> pdb=" O   ASP C 184 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 30 through 34
      removed outlier: 4.175A  pdb=" N   ARG D  33 " --> pdb=" O   THR D  30 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 89 through 93
    Processing sheet with id=AA1, first strand: chain 'A' and resid 105 through 108
      removed outlier: 6.601A  pdb=" N   LEU A 106 " --> pdb=" O   SER A 113 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   TYR A  69 " --> pdb=" O   PHE A  65 " (cutoff:3.500A)
      removed outlier: 7.631A  pdb=" N   ILE A 153 " --> pdb=" O   CYS A  62 " (cutoff:3.500A)
      removed outlier: 5.986A  pdb=" N   VAL A  64 " --> pdb=" O   ILE A 153 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 100 through 101
    Processing sheet with id=AA3, first strand: chain 'A' and resid 158 through 163
      removed outlier: 4.428A  pdb=" N   LEU A 160 " --> pdb=" O   ASN A 173 " (cutoff:3.500A)
      removed outlier: 6.787A  pdb=" N   ASN A 173 " --> pdb=" O   LEU A 160 " (cutoff:3.500A)
      removed outlier: 4.461A  pdb=" N   LEU A 162 " --> pdb=" O   GLU A 171 " (cutoff:3.500A)
      removed outlier: 6.383A  pdb=" N   GLU A 171 " --> pdb=" O   LEU A 162 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 198 through 202
    Processing sheet with id=AA5, first strand: chain 'B' and resid 3 through 6
    Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 12
      removed outlier: 6.530A  pdb=" N   GLU B  10 " --> pdb=" O   THR B 114 " (cutoff:3.500A)
      removed outlier: 5.944A  pdb=" N   ARG B  38 " --> pdb=" O   TRP B  47 " (cutoff:3.500A)
      removed outlier: 4.894A  pdb=" N   TRP B  47 " --> pdb=" O   ARG B  38 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 10 through 12
      removed outlier: 6.530A  pdb=" N   GLU B  10 " --> pdb=" O   THR B 114 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 124 through 128
      removed outlier: 5.927A  pdb=" N   TYR B 180 " --> pdb=" O   ASP B 148 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 124 through 128
      removed outlier: 5.927A  pdb=" N   TYR B 180 " --> pdb=" O   ASP B 148 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 155 through 158
    Processing sheet with id=AB2, first strand: chain 'C' and resid 4 through 7
    Processing sheet with id=AB3, first strand: chain 'C' and resid 10 through 13
      removed outlier: 6.015A  pdb=" N   LEU C  11 " --> pdb=" O   GLU C 104 " (cutoff:3.500A)
      removed outlier: 6.352A  pdb=" N   TRP C  34 " --> pdb=" O   LEU C  46 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 10 through 13
      removed outlier: 6.015A  pdb=" N   LEU C  11 " --> pdb=" O   GLU C 104 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   THR C  96 " --> pdb=" O   GLN C  89 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 113 through 117
      removed outlier: 5.626A  pdb=" N   TYR C 172 " --> pdb=" O   ASN C 137 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'C' and resid 152 through 154
      removed outlier: 4.648A  pdb=" N   TRP C 147 " --> pdb=" O   GLN C 154 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'D' and resid 7 through 9
    Processing sheet with id=AB8, first strand: chain 'D' and resid 60 through 62
      removed outlier: 6.672A  pdb=" N   TRP D  38 " --> pdb=" O   VAL D  50 " (cutoff:3.500A)
      removed outlier: 4.656A  pdb=" N   VAL D  52 " --> pdb=" O   MET D  36 " (cutoff:3.500A)
      removed outlier: 6.405A  pdb=" N   MET D  36 " --> pdb=" O   VAL D  52 " (cutoff:3.500A)
      removed outlier: 3.988A  pdb=" N   ALA D  35 " --> pdb=" O   ASP D 101 " (cutoff:3.500A)
      removed outlier: 4.488A  pdb=" N   TYR D 112 " --> pdb=" O   ILE D 100 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'D' and resid 60 through 62
      removed outlier: 6.672A  pdb=" N   TRP D  38 " --> pdb=" O   VAL D  50 " (cutoff:3.500A)
      removed outlier: 4.656A  pdb=" N   VAL D  52 " --> pdb=" O   MET D  36 " (cutoff:3.500A)
      removed outlier: 6.405A  pdb=" N   MET D  36 " --> pdb=" O   VAL D  52 " (cutoff:3.500A)
      removed outlier: 3.988A  pdb=" N   ALA D  35 " --> pdb=" O   ASP D 101 " (cutoff:3.500A)

    262 hydrogen bonds defined for protein.
    627 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: 1.73

  Time building geometry restraints manager: 1.74 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: 1822
        1.34 -     1.46: 1422
        1.46 -     1.58: 2541
        1.58 -     1.70: 0
        1.70 -     1.82: 30
  Bond restraints: 5815
  Sorted by residual:
  bond pdb=" N   VAL A 223 "
       pdb=" CA  VAL A 223 "
    ideal  model  delta    sigma   weight residual
    1.458  1.495 -0.037 1.18e-02 7.18e+03 1.00e+01
  bond pdb=" N   GLY D 116 "
       pdb=" CA  GLY D 116 "
    ideal  model  delta    sigma   weight residual
    1.446  1.476 -0.030 1.02e-02 9.61e+03 8.91e+00
  bond pdb=" N   VAL B 146 "
       pdb=" CA  VAL B 146 "
    ideal  model  delta    sigma   weight residual
    1.460  1.492 -0.033 1.10e-02 8.26e+03 8.85e+00
  bond pdb=" N   VAL B 125 "
       pdb=" CA  VAL B 125 "
    ideal  model  delta    sigma   weight residual
    1.459  1.495 -0.036 1.24e-02 6.50e+03 8.62e+00
  bond pdb=" N   VAL A 187 "
       pdb=" CA  VAL A 187 "
    ideal  model  delta    sigma   weight residual
    1.459  1.494 -0.035 1.19e-02 7.06e+03 8.52e+00
  ... (remaining 5810 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.35: 7431
        1.35 -     2.70: 387
        2.70 -     4.05: 75
        4.05 -     5.40: 10
        5.40 -     6.76: 7
  Bond angle restraints: 7910
  Sorted by residual:
  angle pdb=" CA  GLY D 116 "
        pdb=" C   GLY D 116 "
        pdb=" O   GLY D 116 "
      ideal   model   delta    sigma   weight residual
     122.23  118.37    3.86 6.90e-01 2.10e+00 3.13e+01
  angle pdb=" CA  GLY B  49 "
        pdb=" C   GLY B  49 "
        pdb=" O   GLY B  49 "
      ideal   model   delta    sigma   weight residual
     121.60  118.12    3.48 9.70e-01 1.06e+00 1.28e+01
  angle pdb=" N   TYR B 106 "
        pdb=" CA  TYR B 106 "
        pdb=" CB  TYR B 106 "
      ideal   model   delta    sigma   weight residual
     110.69  104.95    5.74 1.61e+00 3.86e-01 1.27e+01
  angle pdb=" CA  ASP B  52 "
        pdb=" CB  ASP B  52 "
        pdb=" CG  ASP B  52 "
      ideal   model   delta    sigma   weight residual
     112.60  116.13   -3.53 1.00e+00 1.00e+00 1.25e+01
  angle pdb=" N   PRO A 229 "
        pdb=" CA  PRO A 229 "
        pdb=" CB  PRO A 229 "
      ideal   model   delta    sigma   weight residual
     102.60   99.00    3.60 1.10e+00 8.26e-01 1.07e+01
  ... (remaining 7905 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.94: 3162
       17.94 -    35.88: 229
       35.88 -    53.82: 56
       53.82 -    71.77: 9
       71.77 -    89.71: 4
  Dihedral angle restraints: 3460
    sinusoidal: 1357
      harmonic: 2103
  Sorted by residual:
  dihedral pdb=" CB  CYS B 144 "
           pdb=" SG  CYS B 144 "
           pdb=" SG  CYS B 200 "
           pdb=" CB  CYS B 200 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   54.27   38.73     1      1.00e+01 1.00e-02 2.11e+01
  dihedral pdb=" CA  ASN A 228 "
           pdb=" C   ASN A 228 "
           pdb=" N   PRO A 229 "
           pdb=" CA  PRO A 229 "
      ideal   model   delta  harmonic     sigma   weight residual
       0.00  -20.52   20.52     0      5.00e+00 4.00e-02 1.68e+01
  dihedral pdb=" CB  CYS C  23 "
           pdb=" SG  CYS C  23 "
           pdb=" SG  CYS C  87 "
           pdb=" CB  CYS C  87 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   63.50   29.50     1      1.00e+01 1.00e-02 1.24e+01
  ... (remaining 3457 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.060: 711
       0.060 -    0.120: 129
       0.120 -    0.179: 19
       0.179 -    0.239: 2
       0.239 -    0.299: 2
  Chirality restraints: 863
  Sorted by residual:
  chirality pdb=" CA  ILE D  31 "
            pdb=" N   ILE D  31 "
            pdb=" C   ILE D  31 "
            pdb=" CB  ILE D  31 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.73   -0.30 2.00e-01 2.50e+01 2.23e+00
  chirality pdb=" CA  VAL C 145 "
            pdb=" N   VAL C 145 "
            pdb=" C   VAL C 145 "
            pdb=" CB  VAL C 145 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.74   -0.30 2.00e-01 2.50e+01 2.20e+00
  chirality pdb=" CA  VAL B 146 "
            pdb=" N   VAL B 146 "
            pdb=" C   VAL B 146 "
            pdb=" CB  VAL B 146 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.64   -0.20 2.00e-01 2.50e+01 1.03e+00
  ... (remaining 860 not shown)

  Planarity restraints: 1014
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU C  78 "   -0.037 5.00e-02 4.00e+02   5.63e-02 5.06e+00
        pdb=" N   PRO C  79 "    0.097 5.00e-02 4.00e+02
        pdb=" CA  PRO C  79 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO C  79 "   -0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR C  50 "    0.010 2.00e-02 2.50e+03   1.96e-02 3.83e+00
        pdb=" C   THR C  50 "   -0.034 2.00e-02 2.50e+03
        pdb=" O   THR C  50 "    0.013 2.00e-02 2.50e+03
        pdb=" N   SER C  51 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP B  61 "    0.028 5.00e-02 4.00e+02   4.32e-02 2.99e+00
        pdb=" N   PRO B  62 "   -0.075 5.00e-02 4.00e+02
        pdb=" CA  PRO B  62 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO B  62 "    0.024 5.00e-02 4.00e+02
  ... (remaining 1011 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 507
        2.75 -     3.29: 5054
        3.29 -     3.82: 9534
        3.82 -     4.36: 12193
        4.36 -     4.90: 20589
  Nonbonded interactions: 47877
  Sorted by model distance:
  nonbonded pdb=" O   PHE B 102 "
            pdb=" OD1 ASP B 105 "
     model   vdw
     2.209 3.040
  nonbonded pdb=" OD1 ASN A 150 "
            pdb=" OG  SER A 233 "
     model   vdw
     2.224 3.040
  nonbonded pdb=" OD1 ASP B  73 "
            pdb=" OG  SER B  75 "
     model   vdw
     2.260 3.040
  nonbonded pdb=" NH1 ARG D  40 "
            pdb=" OD1 ASP D  92 "
     model   vdw
     2.306 3.120
  nonbonded pdb=" O   PRO A 157 "
            pdb=" OG  SER A 241 "
     model   vdw
     2.309 3.040
  ... (remaining 47872 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:             2.250
  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:          0.280
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     18.880
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:12.560
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.180
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5878
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      :  0.005   0.037   5822  Z= 0.318
  Angle     :  0.718   6.756   7924  Z= 0.449
  Chirality :  0.050   0.299    863
  Planarity :  0.005   0.063   1014
  Dihedral  : 13.514  89.707   2085
  Min Nonbonded Distance : 2.209

Molprobity Statistics.
  All-atom Clashscore : 8.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  : 12.60 %
    Favored  : 87.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.79 %
    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:  0.51 (0.32), residues: 706
  helix:  0.65 (1.11), residues: 21
  sheet:  0.47 (0.28), residues: 323
  loop :  0.34 (0.34), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  47 
 HIS   0.006   0.001   HIS C 197 
 PHE   0.014   0.002   PHE C 138 
 TYR   0.010   0.001   TYR C  48 
 ARG   0.003   0.000   ARG C  24 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.12968 (  229)
  hydrogen bonds       : angle       7.39875 (  627)
  SS BOND              : bond        0.00475 (    7)
  SS BOND              : angle       1.18742 (   14)
  covalent geometry    : bond        0.00491 ( 5815)
  covalent geometry    : angle       0.71712 ( 7910)

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

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

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 95
  time to evaluate  : 0.684 
Fit side-chains
REVERT: A  101 LYS cc_start: 0.7565 (mttt) cc_final: 0.7243 (mptm)
REVERT: B   30 GLU cc_start: 0.6940 (pt0) cc_final: 0.6120 (pm20)
REVERT: B   59 ASN cc_start: 0.7210 (m-40) cc_final: 0.6879 (m110)
REVERT: C  168 LYS cc_start: 0.6680 (mttt) cc_final: 0.6369 (ttpp)
  outliers start: 2
  outliers final: 1
  residues processed: 97
  average time/residue: 1.1763
  time to fit residues: 119.5299
Evaluate side-chains
  82 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 81
  time to evaluate  : 0.605 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   75 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 58 optimal weight:    5.9990
   chunk 52 optimal weight:    0.6980
   chunk 29 optimal weight:    6.9990
   chunk 17 optimal weight:    0.9990
   chunk 35 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   chunk 54 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 32 optimal weight:    0.5980
   chunk 40 optimal weight:    1.9990
   chunk 62 optimal weight:    2.9990
   overall best weight:    1.2586

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

Flipped N/Q/H residues before XYZ refinement:
A 100 GLN
B 201 ASN
C  93 ASN
D  84 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4101 r_free = 0.4101 target = 0.187416 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.131807 restraints weight = 5408.417|
|-----------------------------------------------------------------------------|
r_work (start): 0.3604 rms_B_bonded: 2.42
r_work: 0.3477 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3337 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.3337
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7610
moved from start:          0.0954

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.055   5822  Z= 0.195
  Angle     :  0.573   8.703   7924  Z= 0.299
  Chirality :  0.043   0.160    863
  Planarity :  0.005   0.052   1014
  Dihedral  :  4.637  17.002    779
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 7.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.70 %
    Favored  : 98.30 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 12.91 %
    Favored  : 83.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.79 %
    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:  0.54 (0.32), residues: 706
  helix:  0.87 (1.06), residues: 21
  sheet:  0.40 (0.27), residues: 343
  loop :  0.46 (0.35), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  47 
 HIS   0.004   0.001   HIS B  35 
 PHE   0.019   0.002   PHE D  49 
 TYR   0.010   0.002   TYR C  48 
 ARG   0.003   0.001   ARG C  24 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03828 (  229)
  hydrogen bonds       : angle       5.83498 (  627)
  SS BOND              : bond        0.00309 (    7)
  SS BOND              : angle       0.92373 (   14)
  covalent geometry    : bond        0.00452 ( 5815)
  covalent geometry    : angle       0.57226 ( 7910)

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

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

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 88
  time to evaluate  : 0.675 
Fit side-chains
   revert: symmetry clash
REVERT: A   66 ASN cc_start: 0.8712 (OUTLIER) cc_final: 0.8505 (t0)
REVERT: A  101 LYS cc_start: 0.8141 (mttt) cc_final: 0.7831 (mptm)
REVERT: B   19 LYS cc_start: 0.8588 (OUTLIER) cc_final: 0.8319 (tttt)
REVERT: B   30 GLU cc_start: 0.7654 (pt0) cc_final: 0.6959 (pm20)
REVERT: B   59 ASN cc_start: 0.8241 (m-40) cc_final: 0.7980 (m110)
REVERT: D   92 ASP cc_start: 0.7508 (m-30) cc_final: 0.7249 (m-30)
  outliers start: 20
  outliers final: 8
  residues processed: 101
  average time/residue: 1.3487
  time to fit residues: 141.9614
Evaluate side-chains
  92 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 82
  time to evaluate  : 0.684 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 ASN
Chi-restraints excluded: chain A residue  238 SER
Chi-restraints excluded: chain B residue   19 LYS
Chi-restraints excluded: chain B residue   34 LEU
Chi-restraints excluded: chain B residue  155 THR
Chi-restraints excluded: chain B residue  211 VAL
Chi-restraints excluded: chain C residue   62 SER
Chi-restraints excluded: chain C residue  116 ILE
Chi-restraints excluded: chain C residue  180 LEU
Chi-restraints excluded: chain D residue   73 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 60 optimal weight:    6.9990
   chunk 44 optimal weight:    3.9990
   chunk 9 optimal weight:    3.9990
   chunk 5 optimal weight:    4.9990
   chunk 36 optimal weight:    6.9990
   chunk 33 optimal weight:    0.7980
   chunk 40 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 49 optimal weight:    2.9990
   chunk 37 optimal weight:    6.9990
   chunk 59 optimal weight:    3.9990
   overall best weight:    2.3588

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

Flipped N/Q/H residues before XYZ refinement:
A  61 GLN
A  88 HIS
** A 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 201 ASN
C  93 ASN
C 123 GLN
D  79 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4075 r_free = 0.4075 target = 0.184948 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.127849 restraints weight = 5394.198|
|-----------------------------------------------------------------------------|
r_work (start): 0.3531 rms_B_bonded: 2.45
r_work: 0.3398 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3259 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.3259
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7703
moved from start:          0.1535

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.082   5822  Z= 0.322
  Angle     :  0.684  11.203   7924  Z= 0.353
  Chirality :  0.047   0.196    863
  Planarity :  0.006   0.053   1014
  Dihedral  :  5.136  19.350    778
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 8.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  3.94 %
    Allowed  : 14.80 %
    Favored  : 81.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.79 %
    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:  0.34 (0.31), residues: 706
  helix:  0.44 (1.06), residues: 21
  sheet:  0.43 (0.28), residues: 333
  loop :  0.15 (0.34), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B  47 
 HIS   0.005   0.002   HIS C 197 
 PHE   0.025   0.003   PHE D  49 
 TYR   0.012   0.003   TYR C  85 
 ARG   0.005   0.001   ARG C  24 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04392 (  229)
  hydrogen bonds       : angle       6.17987 (  627)
  SS BOND              : bond        0.00504 (    7)
  SS BOND              : angle       1.25941 (   14)
  covalent geometry    : bond        0.00757 ( 5815)
  covalent geometry    : angle       0.68292 ( 7910)

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

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

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 85
  time to evaluate  : 0.655 
Fit side-chains
REVERT: A   66 ASN cc_start: 0.8781 (OUTLIER) cc_final: 0.8574 (t0)
REVERT: A  149 GLN cc_start: 0.7735 (OUTLIER) cc_final: 0.7529 (pt0)
REVERT: B   19 LYS cc_start: 0.8596 (OUTLIER) cc_final: 0.8317 (tttt)
REVERT: B   30 GLU cc_start: 0.7657 (pt0) cc_final: 0.6971 (pm20)
REVERT: B   59 ASN cc_start: 0.8310 (m-40) cc_final: 0.8028 (m110)
REVERT: B  210 LYS cc_start: 0.7730 (tttt) cc_final: 0.7212 (tptt)
REVERT: C   80 GLU cc_start: 0.8326 (pm20) cc_final: 0.7860 (pm20)
REVERT: C  168 LYS cc_start: 0.7769 (ttmt) cc_final: 0.6885 (ttpp)
REVERT: D   92 ASP cc_start: 0.7465 (m-30) cc_final: 0.7257 (m-30)
  outliers start: 25
  outliers final: 12
  residues processed: 101
  average time/residue: 1.2793
  time to fit residues: 134.8258
Evaluate side-chains
  99 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 84
  time to evaluate  : 0.671 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 ASN
Chi-restraints excluded: chain A residue  127 THR
Chi-restraints excluded: chain A residue  149 GLN
Chi-restraints excluded: chain A residue  201 SER
Chi-restraints excluded: chain A residue  238 SER
Chi-restraints excluded: chain B residue   19 LYS
Chi-restraints excluded: chain B residue   34 LEU
Chi-restraints excluded: chain B residue   50 ARG
Chi-restraints excluded: chain B residue   74 THR
Chi-restraints excluded: chain B residue  155 THR
Chi-restraints excluded: chain B residue  211 VAL
Chi-restraints excluded: chain C residue   62 SER
Chi-restraints excluded: chain C residue   90 TRP
Chi-restraints excluded: chain C residue  180 LEU
Chi-restraints excluded: chain D residue   73 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 37 optimal weight:    9.9990
   chunk 68 optimal weight:    3.9990
   chunk 31 optimal weight:    1.9990
   chunk 9 optimal weight:    0.6980
   chunk 19 optimal weight:    0.0370
   chunk 25 optimal weight:    0.8980
   chunk 53 optimal weight:    4.9990
   chunk 44 optimal weight:    0.8980
   chunk 32 optimal weight:    0.7980
   chunk 11 optimal weight:    2.9990
   chunk 27 optimal weight:    0.6980
   overall best weight:    0.6258

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

Flipped N/Q/H residues before XYZ refinement:
A  61 GLN
A  88 HIS
** A 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 201 ASN
C  93 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4117 r_free = 0.4117 target = 0.189697 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.134444 restraints weight = 5462.789|
|-----------------------------------------------------------------------------|
r_work (start): 0.3650 rms_B_bonded: 2.44
r_work: 0.3521 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3380 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.3380
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7592
moved from start:          0.1462

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   5822  Z= 0.123
  Angle     :  0.509   7.034   7924  Z= 0.265
  Chirality :  0.041   0.146    863
  Planarity :  0.005   0.057   1014
  Dihedral  :  4.462  15.452    778
  Min Nonbonded Distance : 2.618

Molprobity Statistics.
  All-atom Clashscore : 6.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 15.59 %
    Favored  : 81.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.79 %
    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:  0.42 (0.32), residues: 706
  helix:  0.78 (1.06), residues: 22
  sheet:  0.39 (0.27), residues: 346
  loop :  0.30 (0.35), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  47 
 HIS   0.003   0.001   HIS A 123 
 PHE   0.014   0.002   PHE D  49 
 TYR   0.010   0.001   TYR A 189 
 ARG   0.003   0.000   ARG C  24 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03173 (  229)
  hydrogen bonds       : angle       5.53794 (  627)
  SS BOND              : bond        0.00269 (    7)
  SS BOND              : angle       0.66504 (   14)
  covalent geometry    : bond        0.00278 ( 5815)
  covalent geometry    : angle       0.50859 ( 7910)

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

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

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 85
  time to evaluate  : 0.581 
Fit side-chains
REVERT: A   66 ASN cc_start: 0.8687 (OUTLIER) cc_final: 0.8465 (t0)
REVERT: A  101 LYS cc_start: 0.8325 (mttp) cc_final: 0.7996 (mptm)
REVERT: A  149 GLN cc_start: 0.7686 (OUTLIER) cc_final: 0.7444 (pt0)
REVERT: B   19 LYS cc_start: 0.8558 (OUTLIER) cc_final: 0.8282 (tttt)
REVERT: B   30 GLU cc_start: 0.7628 (pt0) cc_final: 0.6929 (pm20)
REVERT: B   59 ASN cc_start: 0.8273 (m-40) cc_final: 0.8038 (m110)
REVERT: B  210 LYS cc_start: 0.7672 (tttt) cc_final: 0.7029 (tptm)
REVERT: C   80 GLU cc_start: 0.8208 (pm20) cc_final: 0.7699 (pm20)
REVERT: C  104 GLU cc_start: 0.8021 (tt0) cc_final: 0.7711 (tt0)
REVERT: C  168 LYS cc_start: 0.7731 (ttmt) cc_final: 0.6839 (ttpp)
  outliers start: 19
  outliers final: 10
  residues processed: 98
  average time/residue: 1.3878
  time to fit residues: 142.1189
Evaluate side-chains
  96 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 83
  time to evaluate  : 0.574 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 ASN
Chi-restraints excluded: chain A residue  127 THR
Chi-restraints excluded: chain A residue  130 VAL
Chi-restraints excluded: chain A residue  149 GLN
Chi-restraints excluded: chain A residue  238 SER
Chi-restraints excluded: chain B residue   19 LYS
Chi-restraints excluded: chain B residue   34 LEU
Chi-restraints excluded: chain B residue   50 ARG
Chi-restraints excluded: chain B residue  211 VAL
Chi-restraints excluded: chain C residue   62 SER
Chi-restraints excluded: chain C residue   71 THR
Chi-restraints excluded: chain C residue   90 TRP
Chi-restraints excluded: chain C residue  180 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 35 optimal weight:    3.9990
   chunk 16 optimal weight:    4.9990
   chunk 47 optimal weight:    2.9990
   chunk 46 optimal weight:    0.9990
   chunk 67 optimal weight:    0.7980
   chunk 29 optimal weight:    6.9990
   chunk 25 optimal weight:    3.9990
   chunk 2 optimal weight:    5.9990
   chunk 32 optimal weight:    0.8980
   chunk 45 optimal weight:    0.7980
   chunk 59 optimal weight:    0.9990
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
** A 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 201 ASN
C  93 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4126 r_free = 0.4126 target = 0.190196 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.133933 restraints weight = 5372.831|
|-----------------------------------------------------------------------------|
r_work (start): 0.3616 rms_B_bonded: 2.45
r_work: 0.3485 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3348 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.3348
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7612
moved from start:          0.1552

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   5822  Z= 0.152
  Angle     :  0.529   7.255   7924  Z= 0.274
  Chirality :  0.042   0.155    863
  Planarity :  0.005   0.056   1014
  Dihedral  :  4.467  16.017    778
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 6.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  3.94 %
    Allowed  : 15.59 %
    Favored  : 80.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.79 %
    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:  0.48 (0.32), residues: 706
  helix:  1.23 (1.10), residues: 21
  sheet:  0.42 (0.27), residues: 350
  loop :  0.32 (0.35), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  47 
 HIS   0.003   0.001   HIS A 123 
 PHE   0.016   0.002   PHE D  49 
 TYR   0.010   0.001   TYR C  85 
 ARG   0.005   0.000   ARG C  24 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03338 (  229)
  hydrogen bonds       : angle       5.49999 (  627)
  SS BOND              : bond        0.00327 (    7)
  SS BOND              : angle       0.68317 (   14)
  covalent geometry    : bond        0.00350 ( 5815)
  covalent geometry    : angle       0.52857 ( 7910)

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

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

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 84
  time to evaluate  : 0.648 
Fit side-chains
REVERT: A   66 ASN cc_start: 0.8695 (OUTLIER) cc_final: 0.8468 (t0)
REVERT: A  101 LYS cc_start: 0.8354 (mttp) cc_final: 0.8033 (mptm)
REVERT: A  149 GLN cc_start: 0.7700 (OUTLIER) cc_final: 0.7434 (pt0)
REVERT: B   19 LYS cc_start: 0.8569 (OUTLIER) cc_final: 0.8294 (tttt)
REVERT: B   30 GLU cc_start: 0.7628 (pt0) cc_final: 0.6939 (pm20)
REVERT: B   59 ASN cc_start: 0.8267 (m-40) cc_final: 0.8045 (m110)
REVERT: B  210 LYS cc_start: 0.7698 (tttt) cc_final: 0.7054 (tptm)
REVERT: C  168 LYS cc_start: 0.7757 (ttmt) cc_final: 0.6874 (ttpp)
  outliers start: 25
  outliers final: 11
  residues processed: 101
  average time/residue: 1.5310
  time to fit residues: 161.2112
Evaluate side-chains
  96 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 82
  time to evaluate  : 0.822 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 ASN
Chi-restraints excluded: chain A residue   67 VAL
Chi-restraints excluded: chain A residue  149 GLN
Chi-restraints excluded: chain A residue  201 SER
Chi-restraints excluded: chain A residue  238 SER
Chi-restraints excluded: chain B residue   19 LYS
Chi-restraints excluded: chain B residue   34 LEU
Chi-restraints excluded: chain B residue  211 VAL
Chi-restraints excluded: chain C residue   30 SER
Chi-restraints excluded: chain C residue   62 SER
Chi-restraints excluded: chain C residue   71 THR
Chi-restraints excluded: chain C residue   90 TRP
Chi-restraints excluded: chain C residue  180 LEU
Chi-restraints excluded: chain D residue   73 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 33 optimal weight:    0.0370
   chunk 19 optimal weight:    0.0070
   chunk 27 optimal weight:    3.9990
   chunk 41 optimal weight:    1.9990
   chunk 49 optimal weight:    0.6980
   chunk 16 optimal weight:    4.9990
   chunk 20 optimal weight:    0.6980
   chunk 46 optimal weight:    0.8980
   chunk 15 optimal weight:    0.9990
   chunk 23 optimal weight:    0.7980
   chunk 45 optimal weight:    0.7980
   overall best weight:    0.4476

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

Flipped N/Q/H residues before XYZ refinement:
** A 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 201 ASN
C  93 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4159 r_free = 0.4159 target = 0.193950 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.138893 restraints weight = 5325.465|
|-----------------------------------------------------------------------------|
r_work (start): 0.3672 rms_B_bonded: 2.43
r_work: 0.3544 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3406 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.3406
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7572
moved from start:          0.1661

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   5822  Z= 0.101
  Angle     :  0.478   6.437   7924  Z= 0.249
  Chirality :  0.041   0.141    863
  Planarity :  0.004   0.058   1014
  Dihedral  :  4.185  14.050    778
  Min Nonbonded Distance : 2.622

Molprobity Statistics.
  All-atom Clashscore : 6.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.70 %
    Favored  : 98.30 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 15.91 %
    Favored  : 80.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.79 %
    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:  0.70 (0.32), residues: 706
  helix:  1.57 (1.15), residues: 21
  sheet:  0.53 (0.28), residues: 343
  loop :  0.49 (0.36), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A  90 
 HIS   0.002   0.001   HIS A 123 
 PHE   0.012   0.001   PHE D  49 
 TYR   0.010   0.001   TYR A 189 
 ARG   0.004   0.000   ARG C  24 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02921 (  229)
  hydrogen bonds       : angle       5.20222 (  627)
  SS BOND              : bond        0.00226 (    7)
  SS BOND              : angle       0.50798 (   14)
  covalent geometry    : bond        0.00229 ( 5815)
  covalent geometry    : angle       0.47809 ( 7910)

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

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

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 87
  time to evaluate  : 0.607 
Fit side-chains
REVERT: A  101 LYS cc_start: 0.8331 (mttp) cc_final: 0.8043 (mptm)
REVERT: A  149 GLN cc_start: 0.7680 (OUTLIER) cc_final: 0.7431 (pt0)
REVERT: B   30 GLU cc_start: 0.7555 (pt0) cc_final: 0.6894 (pm20)
REVERT: B   59 ASN cc_start: 0.8276 (m-40) cc_final: 0.8066 (m110)
REVERT: B  210 LYS cc_start: 0.7678 (tttt) cc_final: 0.7073 (tptm)
REVERT: C   80 GLU cc_start: 0.8292 (pm20) cc_final: 0.7858 (pm20)
REVERT: C  148 LYS cc_start: 0.7493 (mmtp) cc_final: 0.7223 (mmtt)
REVERT: D  110 TYR cc_start: 0.8196 (m-80) cc_final: 0.7951 (m-80)
  outliers start: 20
  outliers final: 12
  residues processed: 100
  average time/residue: 1.3351
  time to fit residues: 139.2774
Evaluate side-chains
  93 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 80
  time to evaluate  : 0.695 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  130 VAL
Chi-restraints excluded: chain A residue  149 GLN
Chi-restraints excluded: chain A residue  201 SER
Chi-restraints excluded: chain B residue   34 LEU
Chi-restraints excluded: chain B residue  154 VAL
Chi-restraints excluded: chain B residue  211 VAL
Chi-restraints excluded: chain C residue   30 SER
Chi-restraints excluded: chain C residue   62 SER
Chi-restraints excluded: chain C residue   71 THR
Chi-restraints excluded: chain C residue   90 TRP
Chi-restraints excluded: chain C residue  180 LEU
Chi-restraints excluded: chain D residue   73 SER
Chi-restraints excluded: chain D residue   85 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 36 optimal weight:    0.0980
   chunk 6 optimal weight:    3.9990
   chunk 28 optimal weight:    0.8980
   chunk 67 optimal weight:    5.9990
   chunk 20 optimal weight:    3.9990
   chunk 23 optimal weight:    0.6980
   chunk 65 optimal weight:    0.0970
   chunk 1 optimal weight:    0.9980
   chunk 46 optimal weight:    0.8980
   chunk 11 optimal weight:   10.0000
   chunk 9 optimal weight:    0.7980
   overall best weight:    0.5178

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

Flipped N/Q/H residues before XYZ refinement:
B 201 ASN
C  93 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.193308 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.137483 restraints weight = 5402.832|
|-----------------------------------------------------------------------------|
r_work (start): 0.3659 rms_B_bonded: 2.45
r_work: 0.3533 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3397 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.3397
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7616
moved from start:          0.1731

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041   5822  Z= 0.108
  Angle     :  0.485   6.367   7924  Z= 0.251
  Chirality :  0.041   0.144    863
  Planarity :  0.005   0.057   1014
  Dihedral  :  4.144  14.021    778
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 5.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 16.69 %
    Favored  : 80.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.79 %
    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:  0.74 (0.32), residues: 706
  helix:  1.74 (1.18), residues: 21
  sheet:  0.53 (0.27), residues: 343
  loop :  0.53 (0.36), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A  90 
 HIS   0.002   0.001   HIS A 123 
 PHE   0.012   0.001   PHE D  49 
 TYR   0.010   0.001   TYR D  97 
 ARG   0.006   0.000   ARG C  24 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02956 (  229)
  hydrogen bonds       : angle       5.17130 (  627)
  SS BOND              : bond        0.00251 (    7)
  SS BOND              : angle       0.68278 (   14)
  covalent geometry    : bond        0.00247 ( 5815)
  covalent geometry    : angle       0.48497 ( 7910)

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

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

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 82
  time to evaluate  : 0.739 
Fit side-chains
REVERT: A  101 LYS cc_start: 0.8372 (mttp) cc_final: 0.8107 (mptm)
REVERT: A  133 GLN cc_start: 0.6481 (mm-40) cc_final: 0.6210 (mm110)
REVERT: A  149 GLN cc_start: 0.7704 (OUTLIER) cc_final: 0.7446 (pt0)
REVERT: B   30 GLU cc_start: 0.7514 (pt0) cc_final: 0.6890 (pm20)
REVERT: B   59 ASN cc_start: 0.8301 (m-40) cc_final: 0.8100 (m110)
REVERT: B  210 LYS cc_start: 0.7663 (tttt) cc_final: 0.7080 (tptm)
REVERT: C   80 GLU cc_start: 0.8300 (pm20) cc_final: 0.7939 (pm20)
  outliers start: 18
  outliers final: 13
  residues processed: 95
  average time/residue: 1.7154
  time to fit residues: 170.9231
Evaluate side-chains
  95 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 81
  time to evaluate  : 0.601 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 VAL
Chi-restraints excluded: chain A residue  130 VAL
Chi-restraints excluded: chain A residue  149 GLN
Chi-restraints excluded: chain A residue  201 SER
Chi-restraints excluded: chain A residue  238 SER
Chi-restraints excluded: chain B residue   34 LEU
Chi-restraints excluded: chain B residue  154 VAL
Chi-restraints excluded: chain B residue  211 VAL
Chi-restraints excluded: chain C residue   62 SER
Chi-restraints excluded: chain C residue   71 THR
Chi-restraints excluded: chain C residue   90 TRP
Chi-restraints excluded: chain C residue  180 LEU
Chi-restraints excluded: chain D residue   73 SER
Chi-restraints excluded: chain D residue   85 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 63 optimal weight:    0.1980
   chunk 29 optimal weight:    6.9990
   chunk 23 optimal weight:    0.7980
   chunk 6 optimal weight:    3.9990
   chunk 28 optimal weight:    0.5980
   chunk 37 optimal weight:    6.9990
   chunk 24 optimal weight:    0.7980
   chunk 21 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9980
   chunk 33 optimal weight:    1.9990
   chunk 12 optimal weight:    7.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** A 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 201 ASN
C  93 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.192738 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.136620 restraints weight = 5309.415|
|-----------------------------------------------------------------------------|
r_work (start): 0.3655 rms_B_bonded: 2.45
r_work: 0.3528 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3387 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.3387
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7574
moved from start:          0.1769

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   5822  Z= 0.126
  Angle     :  0.499   6.780   7924  Z= 0.258
  Chirality :  0.041   0.148    863
  Planarity :  0.005   0.057   1014
  Dihedral  :  4.230  14.480    778
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 6.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 16.54 %
    Favored  : 80.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.79 %
    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:  0.73 (0.32), residues: 706
  helix:  1.76 (1.19), residues: 21
  sheet:  0.52 (0.27), residues: 343
  loop :  0.53 (0.36), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  47 
 HIS   0.003   0.001   HIS A 123 
 PHE   0.014   0.002   PHE D  49 
 TYR   0.009   0.001   TYR C  85 
 ARG   0.005   0.000   ARG C  24 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03091 (  229)
  hydrogen bonds       : angle       5.22572 (  627)
  SS BOND              : bond        0.00307 (    7)
  SS BOND              : angle       0.74669 (   14)
  covalent geometry    : bond        0.00288 ( 5815)
  covalent geometry    : angle       0.49842 ( 7910)

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

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

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 78
  time to evaluate  : 0.518 
Fit side-chains
REVERT: A  101 LYS cc_start: 0.8332 (mttp) cc_final: 0.8055 (mptm)
REVERT: A  149 GLN cc_start: 0.7669 (OUTLIER) cc_final: 0.7400 (pt0)
REVERT: B   19 LYS cc_start: 0.8551 (OUTLIER) cc_final: 0.8272 (tttt)
REVERT: B   30 GLU cc_start: 0.7462 (pt0) cc_final: 0.6820 (pm20)
REVERT: B   59 ASN cc_start: 0.8269 (m-40) cc_final: 0.8044 (m110)
REVERT: B  210 LYS cc_start: 0.7612 (tttt) cc_final: 0.6997 (tptm)
REVERT: C   80 GLU cc_start: 0.8277 (pm20) cc_final: 0.7883 (pm20)
REVERT: D   40 ARG cc_start: 0.8195 (OUTLIER) cc_final: 0.7718 (ptt180)
  outliers start: 20
  outliers final: 13
  residues processed: 91
  average time/residue: 1.7260
  time to fit residues: 163.7308
Evaluate side-chains
  93 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 77
  time to evaluate  : 1.009 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 VAL
Chi-restraints excluded: chain A residue  130 VAL
Chi-restraints excluded: chain A residue  149 GLN
Chi-restraints excluded: chain A residue  201 SER
Chi-restraints excluded: chain A residue  238 SER
Chi-restraints excluded: chain B residue   19 LYS
Chi-restraints excluded: chain B residue   34 LEU
Chi-restraints excluded: chain B residue  211 VAL
Chi-restraints excluded: chain C residue   30 SER
Chi-restraints excluded: chain C residue   62 SER
Chi-restraints excluded: chain C residue   71 THR
Chi-restraints excluded: chain C residue   90 TRP
Chi-restraints excluded: chain C residue  180 LEU
Chi-restraints excluded: chain D residue   40 ARG
Chi-restraints excluded: chain D residue   73 SER
Chi-restraints excluded: chain D residue   85 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 59 optimal weight:    0.9990
   chunk 21 optimal weight:    3.9990
   chunk 37 optimal weight:    8.9990
   chunk 66 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9980
   chunk 11 optimal weight:    9.9990
   chunk 42 optimal weight:    0.7980
   chunk 9 optimal weight:    0.2980
   chunk 4 optimal weight:    0.5980
   chunk 50 optimal weight:    0.0670
   chunk 46 optimal weight:    0.9990
   overall best weight:    0.5318

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

Flipped N/Q/H residues before XYZ refinement:
B 201 ASN
C  93 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4156 r_free = 0.4156 target = 0.193520 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.137489 restraints weight = 5354.636|
|-----------------------------------------------------------------------------|
r_work (start): 0.3662 rms_B_bonded: 2.46
r_work: 0.3537 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3402 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.3402
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7546
moved from start:          0.1824

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042   5822  Z= 0.109
  Angle     :  0.483   6.271   7924  Z= 0.250
  Chirality :  0.041   0.144    863
  Planarity :  0.005   0.056   1014
  Dihedral  :  4.158  13.688    778
  Min Nonbonded Distance : 2.621

Molprobity Statistics.
  All-atom Clashscore : 6.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 17.17 %
    Favored  : 79.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.79 %
    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:  0.78 (0.32), residues: 706
  helix:  1.85 (1.20), residues: 21
  sheet:  0.55 (0.27), residues: 343
  loop :  0.57 (0.36), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B  47 
 HIS   0.002   0.001   HIS A 123 
 PHE   0.013   0.001   PHE D  49 
 TYR   0.010   0.001   TYR D  97 
 ARG   0.006   0.000   ARG C  24 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02939 (  229)
  hydrogen bonds       : angle       5.16244 (  627)
  SS BOND              : bond        0.00267 (    7)
  SS BOND              : angle       0.62311 (   14)
  covalent geometry    : bond        0.00249 ( 5815)
  covalent geometry    : angle       0.48242 ( 7910)

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

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

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 76
  time to evaluate  : 0.590 
Fit side-chains
REVERT: A  101 LYS cc_start: 0.8331 (mttp) cc_final: 0.8065 (mptm)
REVERT: A  133 GLN cc_start: 0.6536 (mm-40) cc_final: 0.5898 (mp-120)
REVERT: A  149 GLN cc_start: 0.7655 (OUTLIER) cc_final: 0.7404 (pt0)
REVERT: B   19 LYS cc_start: 0.8542 (OUTLIER) cc_final: 0.8265 (tttt)
REVERT: B   30 GLU cc_start: 0.7419 (pt0) cc_final: 0.6814 (pm20)
REVERT: B   59 ASN cc_start: 0.8259 (m-40) cc_final: 0.8050 (m110)
REVERT: B  210 LYS cc_start: 0.7624 (tttt) cc_final: 0.7031 (tptm)
REVERT: C   80 GLU cc_start: 0.8242 (pm20) cc_final: 0.7856 (pm20)
REVERT: D   40 ARG cc_start: 0.8183 (OUTLIER) cc_final: 0.7704 (ptt180)
  outliers start: 19
  outliers final: 13
  residues processed: 91
  average time/residue: 1.2387
  time to fit residues: 117.9456
Evaluate side-chains
  92 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 76
  time to evaluate  : 0.573 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 VAL
Chi-restraints excluded: chain A residue  130 VAL
Chi-restraints excluded: chain A residue  149 GLN
Chi-restraints excluded: chain A residue  201 SER
Chi-restraints excluded: chain A residue  238 SER
Chi-restraints excluded: chain B residue   19 LYS
Chi-restraints excluded: chain B residue   34 LEU
Chi-restraints excluded: chain B residue  211 VAL
Chi-restraints excluded: chain C residue   30 SER
Chi-restraints excluded: chain C residue   62 SER
Chi-restraints excluded: chain C residue   71 THR
Chi-restraints excluded: chain C residue   90 TRP
Chi-restraints excluded: chain C residue  180 LEU
Chi-restraints excluded: chain D residue   40 ARG
Chi-restraints excluded: chain D residue   73 SER
Chi-restraints excluded: chain D residue   85 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 13 optimal weight:    8.9990
   chunk 0 optimal weight:    6.9990
   chunk 37 optimal weight:    6.9990
   chunk 46 optimal weight:    1.9990
   chunk 67 optimal weight:    0.8980
   chunk 53 optimal weight:    3.9990
   chunk 56 optimal weight:    5.9990
   chunk 33 optimal weight:    2.9990
   chunk 5 optimal weight:    5.9990
   chunk 36 optimal weight:    2.9990
   chunk 32 optimal weight:    0.0070
   overall best weight:    1.7804

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

Flipped N/Q/H residues before XYZ refinement:
** A 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 201 ASN
C  93 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4105 r_free = 0.4105 target = 0.187729 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.130098 restraints weight = 5435.649|
|-----------------------------------------------------------------------------|
r_work (start): 0.3575 rms_B_bonded: 2.49
r_work: 0.3447 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3307 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.3307
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7647
moved from start:          0.1827

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.073   5822  Z= 0.254
  Angle     :  0.615   9.581   7924  Z= 0.315
  Chirality :  0.045   0.181    863
  Planarity :  0.005   0.072   1014
  Dihedral  :  4.759  17.117    778
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 7.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 17.32 %
    Favored  : 79.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.79 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.43 (0.32), residues: 706
  helix:  1.36 (1.13), residues: 21
  sheet:  0.37 (0.27), residues: 350
  loop :  0.28 (0.35), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP B  47 
 HIS   0.004   0.001   HIS A 123 
 PHE   0.020   0.003   PHE D  49 
 TYR   0.015   0.002   TYR C  48 
 ARG   0.009   0.001   ARG C  24 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03827 (  229)
  hydrogen bonds       : angle       5.74978 (  627)
  SS BOND              : bond        0.00505 (    7)
  SS BOND              : angle       1.19915 (   14)
  covalent geometry    : bond        0.00596 ( 5815)
  covalent geometry    : angle       0.61356 ( 7910)

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

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

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 81
  time to evaluate  : 0.635 
Fit side-chains
REVERT: A  101 LYS cc_start: 0.8343 (mttp) cc_final: 0.8019 (mptm)
REVERT: B   19 LYS cc_start: 0.8586 (OUTLIER) cc_final: 0.8312 (tttt)
REVERT: B   30 GLU cc_start: 0.7491 (pt0) cc_final: 0.6868 (pm20)
REVERT: B   59 ASN cc_start: 0.8302 (m-40) cc_final: 0.8029 (m110)
REVERT: B  210 LYS cc_start: 0.7700 (tttt) cc_final: 0.7178 (tptt)
REVERT: C   80 GLU cc_start: 0.8292 (pm20) cc_final: 0.7801 (pm20)
REVERT: D   40 ARG cc_start: 0.8308 (OUTLIER) cc_final: 0.8020 (ptt180)
  outliers start: 19
  outliers final: 13
  residues processed: 94
  average time/residue: 1.2771
  time to fit residues: 125.3757
Evaluate side-chains
  94 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 79
  time to evaluate  : 0.666 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 VAL
Chi-restraints excluded: chain A residue  201 SER
Chi-restraints excluded: chain A residue  238 SER
Chi-restraints excluded: chain B residue   19 LYS
Chi-restraints excluded: chain B residue   34 LEU
Chi-restraints excluded: chain B residue  211 VAL
Chi-restraints excluded: chain C residue   30 SER
Chi-restraints excluded: chain C residue   62 SER
Chi-restraints excluded: chain C residue   71 THR
Chi-restraints excluded: chain C residue   90 TRP
Chi-restraints excluded: chain C residue  180 LEU
Chi-restraints excluded: chain D residue   40 ARG
Chi-restraints excluded: chain D residue   73 SER
Chi-restraints excluded: chain D residue   85 MET
Chi-restraints excluded: chain D residue  100 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 6 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9990
   chunk 44 optimal weight:    2.9990
   chunk 67 optimal weight:    0.9980
   chunk 17 optimal weight:    0.0470
   chunk 2 optimal weight:    0.5980
   chunk 12 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9990
   chunk 18 optimal weight:    2.9990
   chunk 10 optimal weight:    8.9990
   chunk 62 optimal weight:    1.9990
   overall best weight:    0.7282

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

Flipped N/Q/H residues before XYZ refinement:
A 133 GLN
** A 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 201 ASN
C  93 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4137 r_free = 0.4137 target = 0.191423 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.135158 restraints weight = 5435.980|
|-----------------------------------------------------------------------------|
r_work (start): 0.3629 rms_B_bonded: 2.45
r_work: 0.3504 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3367 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.3367
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7645
moved from start:          0.1803

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   5822  Z= 0.135
  Angle     :  0.517   6.769   7924  Z= 0.268
  Chirality :  0.042   0.149    863
  Planarity :  0.005   0.058   1014
  Dihedral  :  4.434  15.001    778
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 17.01 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.79 %
    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:  0.55 (0.32), residues: 706
  helix:  1.24 (1.15), residues: 22
  sheet:  0.41 (0.27), residues: 348
  loop :  0.43 (0.36), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  47 
 HIS   0.003   0.001   HIS A 123 
 PHE   0.014   0.002   PHE D  49 
 TYR   0.009   0.001   TYR D  97 
 ARG   0.008   0.000   ARG C  24 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03171 (  229)
  hydrogen bonds       : angle       5.46017 (  627)
  SS BOND              : bond        0.00291 (    7)
  SS BOND              : angle       0.73523 (   14)
  covalent geometry    : bond        0.00314 ( 5815)
  covalent geometry    : angle       0.51677 ( 7910)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6358.37 seconds
wall clock time: 111 minutes 2.10 seconds (6662.10 seconds total)