Starting phenix.real_space_refine
on Tue Mar 11 21:05:36 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8spb_40678/03_2025/8spb_40678.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8spb_40678/03_2025/8spb_40678.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8spb_40678/03_2025/8spb_40678.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8spb_40678/03_2025/8spb_40678.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8spb_40678/03_2025/8spb_40678.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8spb_40678/03_2025/8spb_40678.cif"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.065
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      50      5.16       5
     C    4264      2.51       5
     N    1134      2.21       5
     O    1278      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 23 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 6726
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1332
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 166, 1332
          Classifications: {'peptide': 166}
          Link IDs: {'PTRANS': 7, 'TRANS': 158}
    Chain: "B"
      Number of atoms: 731
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 88, 731
          Classifications: {'peptide': 88}
          Link IDs: {'PTRANS': 4, 'TRANS': 83}
    Chain: "C"
      Number of atoms: 1300
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 160, 1300
          Classifications: {'peptide': 160}
          Link IDs: {'PTRANS': 4, 'TRANS': 155}
          Chain breaks: 1
    Chain: "a"
      Number of atoms: 1332
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 166, 1332
          Classifications: {'peptide': 166}
          Link IDs: {'PTRANS': 7, 'TRANS': 158}
    Chain: "b"
      Number of atoms: 731
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 88, 731
          Classifications: {'peptide': 88}
          Link IDs: {'PTRANS': 4, 'TRANS': 83}
    Chain: "c"
      Number of atoms: 1300
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 160, 1300
          Classifications: {'peptide': 160}
          Link IDs: {'PTRANS': 4, 'TRANS': 155}
          Chain breaks: 1
  Time building chain proxies: 4.59, per 1000 atoms: 0.68
  Number of scatterers: 6726
  At special positions: 0
  Unit cell: (72.21, 138.61, 78.02, 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      50     16.00
     O    1278      8.00
     N    1134      7.00
     C    4264      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.45
  Conformation dependent library (CDL) restraints added in 889.5 milliseconds
  

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1596

  Finding SS restraints...
    Secondary structure from input PDB file:
      18 helices and 16 sheets defined
      22.2% alpha, 20.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.82
  Creating SS restraints...
    Processing helix  chain 'A' and resid 110 through 119
      removed outlier: 3.885A  pdb=" N   PHE A 114 " --> pdb=" O   PRO A 110 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   LEU A 115 " --> pdb=" O   HIS A 111 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   CYS A 118 " --> pdb=" O   PHE A 114 " (cutoff:3.500A)
      removed outlier: 4.059A  pdb=" N   LYS A 119 " --> pdb=" O   LEU A 115 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 154 through 169
    Processing helix  chain 'A' and resid 180 through 193
    Processing helix  chain 'A' and resid 194 through 198
    Processing helix  chain 'A' and resid 231 through 238
      removed outlier: 3.597A  pdb=" N   PHE A 238 " --> pdb=" O   ILE A 234 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 243 through 247
      removed outlier: 3.872A  pdb=" N   LYS A 247 " --> pdb=" O   LEU A 244 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 321 through 334
    Processing helix  chain 'B' and resid 338 through 350
    Processing helix  chain 'C' and resid 112 through 116
    Processing helix  chain 'a' and resid 110 through 121
      removed outlier: 3.520A  pdb=" N   CYS a 118 " --> pdb=" O   PHE a 114 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   LYS a 119 " --> pdb=" O   LEU a 115 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 154 through 169
    Processing helix  chain 'a' and resid 180 through 193
    Processing helix  chain 'a' and resid 194 through 200
      removed outlier: 3.522A  pdb=" N   LYS a 198 " --> pdb=" O   PRO a 195 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 231 through 238
    Processing helix  chain 'a' and resid 243 through 247
    Processing helix  chain 'b' and resid 321 through 334
    Processing helix  chain 'b' and resid 338 through 350
    Processing helix  chain 'c' and resid 112 through 116
    Processing sheet with id=AA1, first strand: chain 'A' and resid 172 through 177
      removed outlier: 3.792A  pdb=" N   ALA A 138 " --> pdb=" O   SER A 172 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   PHE A 204 " --> pdb=" O   LEU A 137 " (cutoff:3.500A)
      removed outlier: 6.352A  pdb=" N   THR A 203 " --> pdb=" O   VAL A 252 " (cutoff:3.500A)
      removed outlier: 7.801A  pdb=" N   ILE A 254 " --> pdb=" O   THR A 203 " (cutoff:3.500A)
      removed outlier: 6.059A  pdb=" N   LEU A 205 " --> pdb=" O   ILE A 254 " (cutoff:3.500A)
      removed outlier: 7.436A  pdb=" N   GLN A 256 " --> pdb=" O   LEU A 205 " (cutoff:3.500A)
      removed outlier: 6.868A  pdb=" N   LEU A 207 " --> pdb=" O   GLN A 256 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 215 through 217
    Processing sheet with id=AA3, first strand: chain 'A' and resid 266 through 269
    Processing sheet with id=AA4, first strand: chain 'B' and resid 291 through 294
    Processing sheet with id=AA5, first strand: chain 'B' and resid 319 through 320
    Processing sheet with id=AA6, first strand: chain 'C' and resid 24 through 25
      removed outlier: 3.697A  pdb=" N   ALA C 162 " --> pdb=" O   ILE C 173 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 45 through 46
      removed outlier: 3.526A  pdb=" N   SER C  46 " --> pdb=" O   MET C 186 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'C' and resid 85 through 88
      removed outlier: 5.954A  pdb=" N   ILE C 100 " --> pdb=" O   LEU C 110 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 85 through 88
      removed outlier: 3.603A  pdb=" N   MET C 149 " --> pdb=" O   VAL C 189 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'a' and resid 172 through 176
      removed outlier: 3.832A  pdb=" N   ALA a 138 " --> pdb=" O   SER a 172 " (cutoff:3.500A)
      removed outlier: 7.374A  pdb=" N   LEU a 137 " --> pdb=" O   PHE a 204 " (cutoff:3.500A)
      removed outlier: 8.582A  pdb=" N   VAL a 206 " --> pdb=" O   LEU a 137 " (cutoff:3.500A)
      removed outlier: 6.165A  pdb=" N   LEU a 139 " --> pdb=" O   VAL a 206 " (cutoff:3.500A)
      removed outlier: 7.854A  pdb=" N   MET a 208 " --> pdb=" O   LEU a 139 " (cutoff:3.500A)
      removed outlier: 6.270A  pdb=" N   ILE a 141 " --> pdb=" O   MET a 208 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   ILE b 301 " --> pdb=" O   LYS a 251 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'a' and resid 215 through 217
    Processing sheet with id=AB3, first strand: chain 'b' and resid 319 through 320
    Processing sheet with id=AB4, first strand: chain 'c' and resid 18 through 19
      removed outlier: 6.153A  pdb=" N   LEU c  23 " --> pdb=" O   LEU c 172 " (cutoff:3.500A)
      removed outlier: 4.031A  pdb=" N   LEU c 172 " --> pdb=" O   LEU c  23 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   PHE c  25 " --> pdb=" O   PHE c 170 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   ALA c 162 " --> pdb=" O   ILE c 173 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'c' and resid 45 through 46
      removed outlier: 3.508A  pdb=" N   SER c  46 " --> pdb=" O   MET c 186 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB5
    Processing sheet with id=AB6, first strand: chain 'c' and resid 84 through 88
      removed outlier: 6.122A  pdb=" N   ILE c 100 " --> pdb=" O   LEU c 110 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'c' and resid 84 through 88
      removed outlier: 3.918A  pdb=" N   MET c 149 " --> pdb=" O   VAL c 189 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   VAL c 189 " --> pdb=" O   MET c 149 " (cutoff:3.500A)

    219 hydrogen bonds defined for protein.
    561 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: 1.77

  Time building geometry restraints manager: 1.76 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: 2190
        1.34 -     1.46: 942
        1.46 -     1.57: 3650
        1.57 -     1.69: 0
        1.69 -     1.81: 74
  Bond restraints: 6856
  Sorted by residual:
  bond pdb=" N   ILE C  11 "
       pdb=" CA  ILE C  11 "
    ideal  model  delta    sigma   weight residual
    1.459  1.499 -0.040 1.25e-02 6.40e+03 1.02e+01
  bond pdb=" N   LYS a 249 "
       pdb=" CA  LYS a 249 "
    ideal  model  delta    sigma   weight residual
    1.453  1.487 -0.035 1.18e-02 7.18e+03 8.67e+00
  bond pdb=" N   LYS c 148 "
       pdb=" CA  LYS c 148 "
    ideal  model  delta    sigma   weight residual
    1.454  1.485 -0.032 1.18e-02 7.18e+03 7.21e+00
  bond pdb=" N   LYS C 148 "
       pdb=" CA  LYS C 148 "
    ideal  model  delta    sigma   weight residual
    1.455  1.488 -0.033 1.25e-02 6.40e+03 7.15e+00
  bond pdb=" N   ILE a 140 "
       pdb=" CA  ILE a 140 "
    ideal  model  delta    sigma   weight residual
    1.459  1.492 -0.033 1.28e-02 6.10e+03 6.49e+00
  ... (remaining 6851 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.23: 9164
        3.23 -     6.45: 56
        6.45 -     9.68: 8
        9.68 -    12.91: 0
       12.91 -    16.14: 2
  Bond angle restraints: 9230
  Sorted by residual:
  angle pdb=" N   ASN C  12 "
        pdb=" CA  ASN C  12 "
        pdb=" C   ASN C  12 "
      ideal   model   delta    sigma   weight residual
     108.17  124.31  -16.14 1.85e+00 2.92e-01 7.61e+01
  angle pdb=" N   ASN C  12 "
        pdb=" CA  ASN C  12 "
        pdb=" CB  ASN C  12 "
      ideal   model   delta    sigma   weight residual
     110.46  101.21    9.25 1.42e+00 4.96e-01 4.24e+01
  angle pdb=" N   ILE C  11 "
        pdb=" CA  ILE C  11 "
        pdb=" C   ILE C  11 "
      ideal   model   delta    sigma   weight residual
     109.34  122.27  -12.93 2.08e+00 2.31e-01 3.86e+01
  angle pdb=" C   ARG C 167 "
        pdb=" CA  ARG C 167 "
        pdb=" CB  ARG C 167 "
      ideal   model   delta    sigma   weight residual
     117.23  110.34    6.89 1.36e+00 5.41e-01 2.57e+01
  angle pdb=" C   ARG c 167 "
        pdb=" CA  ARG c 167 "
        pdb=" CB  ARG c 167 "
      ideal   model   delta    sigma   weight residual
     117.23  110.39    6.84 1.36e+00 5.41e-01 2.53e+01
  ... (remaining 9225 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.99: 3573
       17.99 -    35.97: 465
       35.97 -    53.96: 132
       53.96 -    71.94: 17
       71.94 -    89.93: 9
  Dihedral angle restraints: 4196
    sinusoidal: 1756
      harmonic: 2440
  Sorted by residual:
  dihedral pdb=" CA  VAL c  47 "
           pdb=" C   VAL c  47 "
           pdb=" N   ILE c  48 "
           pdb=" CA  ILE c  48 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.96  -21.04     0      5.00e+00 4.00e-02 1.77e+01
  dihedral pdb=" CA  VAL C  47 "
           pdb=" C   VAL C  47 "
           pdb=" N   ILE C  48 "
           pdb=" CA  ILE C  48 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.54  -20.46     0      5.00e+00 4.00e-02 1.67e+01
  dihedral pdb=" CA  TYR c  37 "
           pdb=" C   TYR c  37 "
           pdb=" N   PHE c  38 "
           pdb=" CA  PHE c  38 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.85  -18.15     0      5.00e+00 4.00e-02 1.32e+01
  ... (remaining 4193 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.055: 818
       0.055 -    0.109: 162
       0.109 -    0.164: 30
       0.164 -    0.218: 3
       0.218 -    0.273: 3
  Chirality restraints: 1016
  Sorted by residual:
  chirality pdb=" CA  ASN C  12 "
            pdb=" N   ASN C  12 "
            pdb=" C   ASN C  12 "
            pdb=" CB  ASN C  12 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.24    0.27 2.00e-01 2.50e+01 1.86e+00
  chirality pdb=" CA  THR c 188 "
            pdb=" N   THR c 188 "
            pdb=" C   THR c 188 "
            pdb=" CB  THR c 188 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.26    0.26 2.00e-01 2.50e+01 1.74e+00
  chirality pdb=" CA  ILE C  11 "
            pdb=" N   ILE C  11 "
            pdb=" C   ILE C  11 "
            pdb=" CB  ILE C  11 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.21    0.22 2.00e-01 2.50e+01 1.20e+00
  ... (remaining 1013 not shown)

  Planarity restraints: 1192
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR b 307 "   -0.044 5.00e-02 4.00e+02   6.61e-02 6.99e+00
        pdb=" N   PRO b 308 "    0.114 5.00e-02 4.00e+02
        pdb=" CA  PRO b 308 "   -0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO b 308 "   -0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO C 124 "    0.041 5.00e-02 4.00e+02   6.16e-02 6.08e+00
        pdb=" N   PRO C 125 "   -0.107 5.00e-02 4.00e+02
        pdb=" CA  PRO C 125 "    0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO C 125 "    0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR c  37 "    0.007 2.00e-02 2.50e+03   1.20e-02 2.88e+00
        pdb=" CG  TYR c  37 "   -0.028 2.00e-02 2.50e+03
        pdb=" CD1 TYR c  37 "    0.014 2.00e-02 2.50e+03
        pdb=" CD2 TYR c  37 "    0.010 2.00e-02 2.50e+03
        pdb=" CE1 TYR c  37 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE2 TYR c  37 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ  TYR c  37 "    0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR c  37 "    0.000 2.00e-02 2.50e+03
  ... (remaining 1189 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 985
        2.76 -     3.30: 6429
        3.30 -     3.83: 10700
        3.83 -     4.37: 12308
        4.37 -     4.90: 21335
  Nonbonded interactions: 51757
  Sorted by model distance:
  nonbonded pdb=" N   GLU C  31 "
            pdb=" OE1 GLU C  31 "
     model   vdw
     2.227 3.120
  nonbonded pdb=" OG  SER c  86 "
            pdb=" OG1 THR c  99 "
     model   vdw
     2.237 3.040
  nonbonded pdb=" OG  SER C  86 "
            pdb=" OG1 THR C  99 "
     model   vdw
     2.261 3.040
  nonbonded pdb=" O   THR A 135 "
            pdb=" OG1 THR A 135 "
     model   vdw
     2.268 3.040
  nonbonded pdb=" O   PHE B 330 "
            pdb=" OG  SER B 334 "
     model   vdw
     2.278 3.040
  ... (remaining 51752 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'a'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'b'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'c'
}

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:             1.120
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     18.710
  Find NCS groups from input model:        0.210
  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:             0.010
  Load rotamer database and sin/cos tables:2.800
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.230
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7575
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   6856  Z= 0.207
  Angle     :  0.731  16.137   9230  Z= 0.430
  Chirality :  0.047   0.273   1016
  Planarity :  0.004   0.066   1192
  Dihedral  : 17.299  89.931   2600
  Min Nonbonded Distance : 2.227

Molprobity Statistics.
  All-atom Clashscore : 10.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.90 %
    Favored  : 93.10 %
  Rotamer:
    Outliers :  1.18 %
    Allowed  : 25.79 %
    Favored  : 73.03 %
  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: -1.37 (0.28), residues: 812
  helix:  0.53 (0.41), residues: 148
  sheet: -0.38 (0.42), residues: 160
  loop : -1.61 (0.26), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP b 335 
 HIS   0.003   0.001   HIS A 148 
 PHE   0.017   0.001   PHE c 170 
 TYR   0.028   0.001   TYR c  37 
 ARG   0.003   0.000   ARG c  49 

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

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

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  247 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 238
  time to evaluate  : 0.636 
Fit side-chains
REVERT: C  138 PHE cc_start: 0.6988 (m-80) cc_final: 0.6609 (m-80)
REVERT: C  152 GLU cc_start: 0.3870 (tp30) cc_final: 0.3668 (tp30)
REVERT: a  182 ARG cc_start: 0.8132 (mmp80) cc_final: 0.7921 (mmt180)
REVERT: c  103 LYS cc_start: 0.5659 (tttt) cc_final: 0.5165 (tttp)
  outliers start: 9
  outliers final: 4
  residues processed: 244
  average time/residue: 0.2104
  time to fit residues: 66.4229
Evaluate side-chains
  218 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 214
  time to evaluate  : 0.731 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue  229 LEU
Chi-restraints excluded: chain b residue  341 GLU
Chi-restraints excluded: chain c residue  119 PHE
Chi-restraints excluded: chain c residue  160 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 67 optimal weight:    3.9990
   chunk 60 optimal weight:    1.9990
   chunk 33 optimal weight:    6.9990
   chunk 20 optimal weight:    2.9990
   chunk 40 optimal weight:    6.9990
   chunk 32 optimal weight:    0.2980
   chunk 62 optimal weight:    2.9990
   chunk 24 optimal weight:    0.7980
   chunk 38 optimal weight:   10.0000
   chunk 46 optimal weight:    0.9980
   chunk 72 optimal weight:    8.9990
   overall best weight:    1.4184

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

Flipped N/Q/H residues before XYZ refinement:
A 262 ASN
C  12 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4238 r_free = 0.4238 target = 0.192877 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.122736 restraints weight = 7214.693|
|-----------------------------------------------------------------------------|
r_work (start): 0.3461 rms_B_bonded: 3.33
r_work: 0.3265 rms_B_bonded: 3.85 restraints_weight: 0.5000
r_work (final): 0.3265
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7349
moved from start:          0.1722

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   6856  Z= 0.280
  Angle     :  0.599   7.116   9230  Z= 0.323
  Chirality :  0.043   0.151   1016
  Planarity :  0.004   0.045   1192
  Dihedral  :  6.020  55.808    899
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 11.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.65 %
    Favored  : 93.35 %
  Rotamer:
    Outliers :  5.00 %
    Allowed  : 25.92 %
    Favored  : 69.08 %
  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: -1.20 (0.28), residues: 812
  helix:  0.79 (0.39), residues: 152
  sheet: -0.18 (0.42), residues: 160
  loop : -1.60 (0.26), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP b 335 
 HIS   0.003   0.001   HIS B 309 
 PHE   0.022   0.001   PHE C  13 
 TYR   0.018   0.001   TYR c  37 
 ARG   0.002   0.000   ARG A 269 

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

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

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  252 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 214
  time to evaluate  : 0.790 
Fit side-chains
REVERT: B  373 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8245 (mm)
REVERT: C   31 GLU cc_start: 0.8202 (pm20) cc_final: 0.8001 (pm20)
REVERT: C   45 LEU cc_start: 0.8040 (OUTLIER) cc_final: 0.7807 (pp)
REVERT: C  123 ASN cc_start: 0.7814 (OUTLIER) cc_final: 0.7481 (m110)
REVERT: a  223 GLU cc_start: 0.8305 (mm-30) cc_final: 0.7796 (pm20)
  outliers start: 38
  outliers final: 20
  residues processed: 232
  average time/residue: 0.1866
  time to fit residues: 56.9706
Evaluate side-chains
  228 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 205
  time to evaluate  : 0.689 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  209 SER
Chi-restraints excluded: chain A residue  228 VAL
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  234 ILE
Chi-restraints excluded: chain A residue  236 GLN
Chi-restraints excluded: chain A residue  244 LEU
Chi-restraints excluded: chain B residue  340 GLU
Chi-restraints excluded: chain B residue  349 SER
Chi-restraints excluded: chain B residue  373 LEU
Chi-restraints excluded: chain C residue   45 LEU
Chi-restraints excluded: chain C residue  102 VAL
Chi-restraints excluded: chain C residue  112 CYS
Chi-restraints excluded: chain C residue  123 ASN
Chi-restraints excluded: chain a residue  156 ASP
Chi-restraints excluded: chain a residue  228 VAL
Chi-restraints excluded: chain a residue  229 LEU
Chi-restraints excluded: chain a residue  268 VAL
Chi-restraints excluded: chain b residue  312 SER
Chi-restraints excluded: chain b residue  341 GLU
Chi-restraints excluded: chain b residue  342 VAL
Chi-restraints excluded: chain b residue  349 SER
Chi-restraints excluded: chain c residue   26 ILE
Chi-restraints excluded: chain c residue  104 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 58 optimal weight:    2.9990
   chunk 76 optimal weight:    9.9990
   chunk 27 optimal weight:    5.9990
   chunk 50 optimal weight:    2.9990
   chunk 72 optimal weight:    0.5980
   chunk 19 optimal weight:    0.9990
   chunk 0 optimal weight:   10.0000
   chunk 43 optimal weight:    0.8980
   chunk 34 optimal weight:   10.0000
   chunk 31 optimal weight:    5.9990
   chunk 30 optimal weight:    6.9990
   overall best weight:    1.6986

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

Flipped N/Q/H residues before XYZ refinement:
A 262 ASN
b 310 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4216 r_free = 0.4216 target = 0.191112 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.120389 restraints weight = 7383.248|
|-----------------------------------------------------------------------------|
r_work (start): 0.3430 rms_B_bonded: 3.35
r_work: 0.3233 rms_B_bonded: 3.85 restraints_weight: 0.5000
r_work (final): 0.3233
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7380
moved from start:          0.2175

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   6856  Z= 0.321
  Angle     :  0.616   8.642   9230  Z= 0.326
  Chirality :  0.044   0.145   1016
  Planarity :  0.004   0.040   1192
  Dihedral  :  5.476  48.279    895
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 12.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.53 %
    Favored  : 93.47 %
  Rotamer:
    Outliers :  5.26 %
    Allowed  : 26.71 %
    Favored  : 68.03 %
  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: -1.34 (0.28), residues: 812
  helix:  0.64 (0.39), residues: 154
  sheet: -0.38 (0.42), residues: 164
  loop : -1.64 (0.26), residues: 494

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP b 335 
 HIS   0.003   0.001   HIS B 309 
 PHE   0.016   0.001   PHE C  13 
 TYR   0.012   0.001   TYR c 159 
 ARG   0.004   0.000   ARG A 269 

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

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

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  261 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 221
  time to evaluate  : 0.797 
Fit side-chains
REVERT: B  373 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8307 (mm)
REVERT: C   45 LEU cc_start: 0.8110 (OUTLIER) cc_final: 0.7861 (pp)
REVERT: C  184 SER cc_start: 0.4459 (m) cc_final: 0.3964 (t)
REVERT: a  223 GLU cc_start: 0.8353 (mm-30) cc_final: 0.7958 (pm20)
REVERT: c  165 LYS cc_start: 0.7399 (tptt) cc_final: 0.7137 (ttmm)
REVERT: c  168 ASP cc_start: 0.7151 (t0) cc_final: 0.6902 (t0)
  outliers start: 40
  outliers final: 29
  residues processed: 234
  average time/residue: 0.2096
  time to fit residues: 64.3043
Evaluate side-chains
  239 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 208
  time to evaluate  : 0.803 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  197 HIS
Chi-restraints excluded: chain A residue  209 SER
Chi-restraints excluded: chain A residue  228 VAL
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  234 ILE
Chi-restraints excluded: chain A residue  236 GLN
Chi-restraints excluded: chain A residue  244 LEU
Chi-restraints excluded: chain A residue  248 ASP
Chi-restraints excluded: chain B residue  340 GLU
Chi-restraints excluded: chain B residue  349 SER
Chi-restraints excluded: chain B residue  373 LEU
Chi-restraints excluded: chain C residue   45 LEU
Chi-restraints excluded: chain C residue   52 ASN
Chi-restraints excluded: chain C residue  102 VAL
Chi-restraints excluded: chain C residue  112 CYS
Chi-restraints excluded: chain C residue  116 ILE
Chi-restraints excluded: chain C residue  119 PHE
Chi-restraints excluded: chain a residue  156 ASP
Chi-restraints excluded: chain a residue  228 VAL
Chi-restraints excluded: chain a residue  229 LEU
Chi-restraints excluded: chain a residue  236 GLN
Chi-restraints excluded: chain a residue  268 VAL
Chi-restraints excluded: chain b residue  312 SER
Chi-restraints excluded: chain b residue  340 GLU
Chi-restraints excluded: chain b residue  341 GLU
Chi-restraints excluded: chain b residue  342 VAL
Chi-restraints excluded: chain b residue  349 SER
Chi-restraints excluded: chain c residue   99 THR
Chi-restraints excluded: chain c residue  104 CYS
Chi-restraints excluded: chain c residue  112 CYS
Chi-restraints excluded: chain c residue  116 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 45 optimal weight:    0.9990
   chunk 22 optimal weight:    0.8980
   chunk 27 optimal weight:    4.9990
   chunk 36 optimal weight:   10.0000
   chunk 66 optimal weight:    3.9990
   chunk 8 optimal weight:    0.5980
   chunk 26 optimal weight:    0.7980
   chunk 0 optimal weight:   10.0000
   chunk 78 optimal weight:    1.9990
   chunk 77 optimal weight:    6.9990
   chunk 37 optimal weight:    3.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
A 262 ASN
B 310 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4232 r_free = 0.4232 target = 0.193039 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.123157 restraints weight = 7407.724|
|-----------------------------------------------------------------------------|
r_work (start): 0.3459 rms_B_bonded: 3.36
r_work: 0.3257 rms_B_bonded: 3.87 restraints_weight: 0.5000
r_work (final): 0.3257
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7344
moved from start:          0.2382

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6856  Z= 0.231
  Angle     :  0.588   8.477   9230  Z= 0.307
  Chirality :  0.043   0.140   1016
  Planarity :  0.003   0.036   1192
  Dihedral  :  5.256  45.232    895
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 11.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.65 %
    Favored  : 93.35 %
  Rotamer:
    Outliers :  5.53 %
    Allowed  : 26.45 %
    Favored  : 68.03 %
  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: -1.33 (0.28), residues: 812
  helix:  0.89 (0.40), residues: 154
  sheet: -0.53 (0.41), residues: 164
  loop : -1.66 (0.26), residues: 494

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP b 335 
 HIS   0.003   0.001   HIS B 295 
 PHE   0.013   0.001   PHE C  13 
 TYR   0.027   0.001   TYR c  37 
 ARG   0.002   0.000   ARG A 269 

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

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

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  252 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 210
  time to evaluate  : 1.060 
Fit side-chains
REVERT: B  314 ARG cc_start: 0.7321 (OUTLIER) cc_final: 0.6022 (ttp80)
REVERT: B  373 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8268 (mm)
REVERT: C   31 GLU cc_start: 0.8221 (pm20) cc_final: 0.8009 (pm20)
REVERT: C   45 LEU cc_start: 0.8107 (OUTLIER) cc_final: 0.7895 (pp)
REVERT: C  123 ASN cc_start: 0.7874 (OUTLIER) cc_final: 0.7565 (m110)
REVERT: C  184 SER cc_start: 0.4694 (m) cc_final: 0.4140 (t)
REVERT: a  223 GLU cc_start: 0.8348 (mm-30) cc_final: 0.7984 (pm20)
REVERT: a  227 ASP cc_start: 0.8121 (t70) cc_final: 0.7892 (t0)
REVERT: b  373 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8473 (mm)
  outliers start: 42
  outliers final: 30
  residues processed: 226
  average time/residue: 0.1843
  time to fit residues: 54.8284
Evaluate side-chains
  245 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 210
  time to evaluate  : 0.699 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  186 SER
Chi-restraints excluded: chain A residue  197 HIS
Chi-restraints excluded: chain A residue  209 SER
Chi-restraints excluded: chain A residue  228 VAL
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  234 ILE
Chi-restraints excluded: chain A residue  236 GLN
Chi-restraints excluded: chain A residue  244 LEU
Chi-restraints excluded: chain A residue  248 ASP
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain B residue  340 GLU
Chi-restraints excluded: chain B residue  349 SER
Chi-restraints excluded: chain B residue  373 LEU
Chi-restraints excluded: chain C residue   45 LEU
Chi-restraints excluded: chain C residue   52 ASN
Chi-restraints excluded: chain C residue  112 CYS
Chi-restraints excluded: chain C residue  116 ILE
Chi-restraints excluded: chain C residue  119 PHE
Chi-restraints excluded: chain C residue  123 ASN
Chi-restraints excluded: chain C residue  148 LYS
Chi-restraints excluded: chain C residue  188 THR
Chi-restraints excluded: chain a residue  156 ASP
Chi-restraints excluded: chain a residue  228 VAL
Chi-restraints excluded: chain a residue  229 LEU
Chi-restraints excluded: chain a residue  236 GLN
Chi-restraints excluded: chain a residue  268 VAL
Chi-restraints excluded: chain b residue  312 SER
Chi-restraints excluded: chain b residue  340 GLU
Chi-restraints excluded: chain b residue  349 SER
Chi-restraints excluded: chain b residue  373 LEU
Chi-restraints excluded: chain c residue   52 ASN
Chi-restraints excluded: chain c residue   99 THR
Chi-restraints excluded: chain c residue  104 CYS
Chi-restraints excluded: chain c residue  110 LEU
Chi-restraints excluded: chain c residue  116 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 41 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9980
   chunk 48 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9990
   chunk 18 optimal weight:    0.6980
   chunk 72 optimal weight:    6.9990
   chunk 74 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9980
   chunk 65 optimal weight:   10.0000
   chunk 34 optimal weight:    2.9990
   chunk 20 optimal weight:    2.9990
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
A 262 ASN
C 123 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4228 r_free = 0.4228 target = 0.192706 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.122307 restraints weight = 7332.521|
|-----------------------------------------------------------------------------|
r_work (start): 0.3454 rms_B_bonded: 3.35
r_work: 0.3253 rms_B_bonded: 3.86 restraints_weight: 0.5000
r_work (final): 0.3253
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7347
moved from start:          0.2520

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   6856  Z= 0.240
  Angle     :  0.588   7.863   9230  Z= 0.308
  Chirality :  0.043   0.138   1016
  Planarity :  0.003   0.035   1192
  Dihedral  :  4.906  44.839    892
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 11.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.51 %
    Favored  : 92.49 %
  Rotamer:
    Outliers :  6.18 %
    Allowed  : 26.18 %
    Favored  : 67.63 %
  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: -1.37 (0.28), residues: 812
  helix:  0.84 (0.39), residues: 154
  sheet: -0.64 (0.41), residues: 164
  loop : -1.66 (0.26), residues: 494

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP b 335 
 HIS   0.003   0.001   HIS A 148 
 PHE   0.012   0.001   PHE C  13 
 TYR   0.018   0.001   TYR c  37 
 ARG   0.005   0.000   ARG C  49 

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

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

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  273 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 226
  time to evaluate  : 1.014 
Fit side-chains
REVERT: A  227 ASP cc_start: 0.8074 (t0) cc_final: 0.7645 (t0)
REVERT: B  314 ARG cc_start: 0.7329 (OUTLIER) cc_final: 0.6008 (ttp80)
REVERT: B  373 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8304 (mm)
REVERT: C  192 GLU cc_start: 0.8240 (mm-30) cc_final: 0.7887 (mm-30)
REVERT: a  123 GLU cc_start: 0.8649 (pm20) cc_final: 0.8344 (pm20)
REVERT: a  157 PHE cc_start: 0.8315 (m-80) cc_final: 0.7931 (m-80)
REVERT: a  223 GLU cc_start: 0.8309 (mm-30) cc_final: 0.7971 (pm20)
REVERT: a  227 ASP cc_start: 0.8124 (t70) cc_final: 0.7886 (t0)
REVERT: b  373 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8486 (mm)
REVERT: c   87 MET cc_start: 0.6338 (ppp) cc_final: 0.6125 (pmm)
  outliers start: 47
  outliers final: 32
  residues processed: 242
  average time/residue: 0.1930
  time to fit residues: 60.9641
Evaluate side-chains
  241 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 206
  time to evaluate  : 0.790 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  186 SER
Chi-restraints excluded: chain A residue  197 HIS
Chi-restraints excluded: chain A residue  209 SER
Chi-restraints excluded: chain A residue  228 VAL
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  234 ILE
Chi-restraints excluded: chain A residue  236 GLN
Chi-restraints excluded: chain A residue  244 LEU
Chi-restraints excluded: chain A residue  248 ASP
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain B residue  340 GLU
Chi-restraints excluded: chain B residue  349 SER
Chi-restraints excluded: chain B residue  373 LEU
Chi-restraints excluded: chain C residue   52 ASN
Chi-restraints excluded: chain C residue  112 CYS
Chi-restraints excluded: chain C residue  116 ILE
Chi-restraints excluded: chain C residue  119 PHE
Chi-restraints excluded: chain C residue  148 LYS
Chi-restraints excluded: chain C residue  188 THR
Chi-restraints excluded: chain a residue  156 ASP
Chi-restraints excluded: chain a residue  186 SER
Chi-restraints excluded: chain a residue  228 VAL
Chi-restraints excluded: chain a residue  229 LEU
Chi-restraints excluded: chain a residue  236 GLN
Chi-restraints excluded: chain a residue  268 VAL
Chi-restraints excluded: chain b residue  312 SER
Chi-restraints excluded: chain b residue  340 GLU
Chi-restraints excluded: chain b residue  349 SER
Chi-restraints excluded: chain b residue  368 THR
Chi-restraints excluded: chain b residue  373 LEU
Chi-restraints excluded: chain c residue   19 ILE
Chi-restraints excluded: chain c residue   46 SER
Chi-restraints excluded: chain c residue   99 THR
Chi-restraints excluded: chain c residue  110 LEU
Chi-restraints excluded: chain c residue  116 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 32 optimal weight:    7.9990
   chunk 17 optimal weight:    2.9990
   chunk 7 optimal weight:    6.9990
   chunk 30 optimal weight:    8.9990
   chunk 37 optimal weight:    0.0870
   chunk 48 optimal weight:    7.9990
   chunk 76 optimal weight:    0.3980
   chunk 68 optimal weight:    0.5980
   chunk 6 optimal weight:    1.9990
   chunk 57 optimal weight:    1.9990
   chunk 79 optimal weight:    6.9990
   overall best weight:    1.0162

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

Flipped N/Q/H residues before XYZ refinement:
A 262 ASN
C  12 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4244 r_free = 0.4244 target = 0.193329 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.123721 restraints weight = 7248.129|
|-----------------------------------------------------------------------------|
r_work (start): 0.3482 rms_B_bonded: 3.25
r_work: 0.3286 rms_B_bonded: 3.77 restraints_weight: 0.5000
r_work (final): 0.3286
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7397
moved from start:          0.2681

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6856  Z= 0.229
  Angle     :  0.603   8.174   9230  Z= 0.314
  Chirality :  0.043   0.137   1016
  Planarity :  0.003   0.034   1192
  Dihedral  :  4.869  43.959    892
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 11.53
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  6.77 %
    Favored  : 93.10 %
  Rotamer:
    Outliers :  5.00 %
    Allowed  : 27.37 %
    Favored  : 67.63 %
  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: -1.40 (0.28), residues: 812
  helix:  0.93 (0.39), residues: 154
  sheet: -0.80 (0.40), residues: 170
  loop : -1.65 (0.26), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP b 335 
 HIS   0.003   0.001   HIS b 338 
 PHE   0.011   0.001   PHE c  13 
 TYR   0.020   0.001   TYR c  37 
 ARG   0.006   0.000   ARG C  49 

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

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

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 205
  time to evaluate  : 0.733 
Fit side-chains
REVERT: A  223 GLU cc_start: 0.8383 (mp0) cc_final: 0.7978 (pm20)
REVERT: A  227 ASP cc_start: 0.8075 (t0) cc_final: 0.7696 (t0)
REVERT: B  314 ARG cc_start: 0.7354 (OUTLIER) cc_final: 0.6035 (ttp80)
REVERT: B  373 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8321 (mm)
REVERT: C  192 GLU cc_start: 0.8239 (mm-30) cc_final: 0.7993 (mm-30)
REVERT: a  157 PHE cc_start: 0.8243 (m-80) cc_final: 0.7888 (m-80)
REVERT: a  223 GLU cc_start: 0.8309 (mm-30) cc_final: 0.7996 (pm20)
REVERT: a  227 ASP cc_start: 0.8119 (t70) cc_final: 0.7890 (t0)
REVERT: b  373 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8516 (mm)
  outliers start: 38
  outliers final: 32
  residues processed: 217
  average time/residue: 0.1869
  time to fit residues: 53.1672
Evaluate side-chains
  235 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 200
  time to evaluate  : 0.717 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  186 SER
Chi-restraints excluded: chain A residue  197 HIS
Chi-restraints excluded: chain A residue  209 SER
Chi-restraints excluded: chain A residue  228 VAL
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  234 ILE
Chi-restraints excluded: chain A residue  236 GLN
Chi-restraints excluded: chain A residue  244 LEU
Chi-restraints excluded: chain A residue  248 ASP
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain B residue  340 GLU
Chi-restraints excluded: chain B residue  349 SER
Chi-restraints excluded: chain B residue  373 LEU
Chi-restraints excluded: chain C residue   52 ASN
Chi-restraints excluded: chain C residue  116 ILE
Chi-restraints excluded: chain C residue  148 LYS
Chi-restraints excluded: chain C residue  188 THR
Chi-restraints excluded: chain a residue  156 ASP
Chi-restraints excluded: chain a residue  186 SER
Chi-restraints excluded: chain a residue  228 VAL
Chi-restraints excluded: chain a residue  229 LEU
Chi-restraints excluded: chain a residue  236 GLN
Chi-restraints excluded: chain a residue  268 VAL
Chi-restraints excluded: chain b residue  312 SER
Chi-restraints excluded: chain b residue  340 GLU
Chi-restraints excluded: chain b residue  349 SER
Chi-restraints excluded: chain b residue  368 THR
Chi-restraints excluded: chain b residue  373 LEU
Chi-restraints excluded: chain c residue   19 ILE
Chi-restraints excluded: chain c residue   46 SER
Chi-restraints excluded: chain c residue   99 THR
Chi-restraints excluded: chain c residue  110 LEU
Chi-restraints excluded: chain c residue  116 ILE
Chi-restraints excluded: chain c residue  123 ASN
Chi-restraints excluded: chain c residue  188 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 6 optimal weight:    0.4980
   chunk 58 optimal weight:    3.9990
   chunk 30 optimal weight:    8.9990
   chunk 68 optimal weight:    0.0270
   chunk 45 optimal weight:    1.9990
   chunk 73 optimal weight:    7.9990
   chunk 27 optimal weight:    4.9990
   chunk 28 optimal weight:    2.9990
   chunk 61 optimal weight:    1.9990
   chunk 66 optimal weight:   10.0000
   chunk 25 optimal weight:    6.9990
   overall best weight:    1.5044

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

Flipped N/Q/H residues before XYZ refinement:
A 262 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4221 r_free = 0.4221 target = 0.190984 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.120737 restraints weight = 7264.561|
|-----------------------------------------------------------------------------|
r_work (start): 0.3450 rms_B_bonded: 3.23
r_work: 0.3255 rms_B_bonded: 3.77 restraints_weight: 0.5000
r_work (final): 0.3255
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7427
moved from start:          0.2854

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.030   6856  Z= 0.298
  Angle     :  0.639   7.827   9230  Z= 0.334
  Chirality :  0.044   0.152   1016
  Planarity :  0.003   0.036   1192
  Dihedral  :  5.069  45.488    892
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 11.90
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  6.77 %
    Favored  : 93.10 %
  Rotamer:
    Outliers :  5.66 %
    Allowed  : 27.37 %
    Favored  : 66.97 %
  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: -1.50 (0.27), residues: 812
  helix:  0.75 (0.39), residues: 154
  sheet: -0.89 (0.41), residues: 166
  loop : -1.68 (0.25), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP b 335 
 HIS   0.003   0.001   HIS A 221 
 PHE   0.010   0.001   PHE C  13 
 TYR   0.022   0.001   TYR c  37 
 ARG   0.005   0.000   ARG C  49 

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

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

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  254 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 211
  time to evaluate  : 0.826 
Fit side-chains
REVERT: A  223 GLU cc_start: 0.8376 (mp0) cc_final: 0.8115 (pm20)
REVERT: A  227 ASP cc_start: 0.8168 (t70) cc_final: 0.7698 (t0)
REVERT: B  314 ARG cc_start: 0.7397 (OUTLIER) cc_final: 0.6108 (ttp80)
REVERT: B  373 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8374 (mm)
REVERT: C  122 MET cc_start: 0.7586 (mmt) cc_final: 0.6890 (tpt)
REVERT: C  192 GLU cc_start: 0.8310 (mm-30) cc_final: 0.7929 (mm-30)
REVERT: a  124 GLU cc_start: 0.8345 (mp0) cc_final: 0.8070 (mp0)
REVERT: a  223 GLU cc_start: 0.8464 (mm-30) cc_final: 0.8169 (pm20)
REVERT: a  227 ASP cc_start: 0.8180 (t70) cc_final: 0.7962 (t0)
REVERT: b  373 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8498 (mm)
REVERT: c  123 ASN cc_start: 0.8596 (OUTLIER) cc_final: 0.8363 (m-40)
  outliers start: 43
  outliers final: 31
  residues processed: 223
  average time/residue: 0.1896
  time to fit residues: 55.6451
Evaluate side-chains
  239 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 204
  time to evaluate  : 0.788 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  186 SER
Chi-restraints excluded: chain A residue  197 HIS
Chi-restraints excluded: chain A residue  209 SER
Chi-restraints excluded: chain A residue  228 VAL
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  234 ILE
Chi-restraints excluded: chain A residue  236 GLN
Chi-restraints excluded: chain A residue  244 LEU
Chi-restraints excluded: chain A residue  248 ASP
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain B residue  340 GLU
Chi-restraints excluded: chain B residue  349 SER
Chi-restraints excluded: chain B residue  373 LEU
Chi-restraints excluded: chain C residue   46 SER
Chi-restraints excluded: chain C residue   52 ASN
Chi-restraints excluded: chain C residue  112 CYS
Chi-restraints excluded: chain C residue  116 ILE
Chi-restraints excluded: chain C residue  148 LYS
Chi-restraints excluded: chain C residue  188 THR
Chi-restraints excluded: chain a residue  156 ASP
Chi-restraints excluded: chain a residue  186 SER
Chi-restraints excluded: chain a residue  228 VAL
Chi-restraints excluded: chain a residue  229 LEU
Chi-restraints excluded: chain a residue  236 GLN
Chi-restraints excluded: chain a residue  268 VAL
Chi-restraints excluded: chain b residue  312 SER
Chi-restraints excluded: chain b residue  340 GLU
Chi-restraints excluded: chain b residue  349 SER
Chi-restraints excluded: chain b residue  368 THR
Chi-restraints excluded: chain b residue  373 LEU
Chi-restraints excluded: chain c residue   19 ILE
Chi-restraints excluded: chain c residue   38 PHE
Chi-restraints excluded: chain c residue  116 ILE
Chi-restraints excluded: chain c residue  123 ASN
Chi-restraints excluded: chain c residue  188 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 51 optimal weight:    0.9980
   chunk 42 optimal weight:    0.9990
   chunk 26 optimal weight:    4.9990
   chunk 69 optimal weight:    4.9990
   chunk 39 optimal weight:    7.9990
   chunk 17 optimal weight:    0.0570
   chunk 44 optimal weight:    0.6980
   chunk 63 optimal weight:    0.9980
   chunk 34 optimal weight:    5.9990
   chunk 7 optimal weight:    2.9990
   chunk 29 optimal weight:    5.9990
   overall best weight:    0.7500

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

Flipped N/Q/H residues before XYZ refinement:
A 262 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4251 r_free = 0.4251 target = 0.194092 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.124565 restraints weight = 7300.227|
|-----------------------------------------------------------------------------|
r_work (start): 0.3494 rms_B_bonded: 3.27
r_work: 0.3293 rms_B_bonded: 3.81 restraints_weight: 0.5000
r_work (final): 0.3293
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7376
moved from start:          0.2887

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6856  Z= 0.205
  Angle     :  0.619   8.327   9230  Z= 0.322
  Chirality :  0.043   0.144   1016
  Planarity :  0.003   0.033   1192
  Dihedral  :  4.869  44.746    892
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 11.15
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  6.53 %
    Favored  : 93.35 %
  Rotamer:
    Outliers :  5.13 %
    Allowed  : 28.68 %
    Favored  : 66.18 %
  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: -1.34 (0.28), residues: 812
  helix:  0.96 (0.39), residues: 154
  sheet: -0.73 (0.42), residues: 162
  loop : -1.62 (0.25), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP b 335 
 HIS   0.003   0.001   HIS A 148 
 PHE   0.010   0.001   PHE C  13 
 TYR   0.020   0.001   TYR c  37 
 ARG   0.007   0.000   ARG C  49 

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

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

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  253 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 214
  time to evaluate  : 0.748 
Fit side-chains
REVERT: A  123 GLU cc_start: 0.8909 (pm20) cc_final: 0.8679 (pm20)
REVERT: A  223 GLU cc_start: 0.8373 (mp0) cc_final: 0.7969 (pm20)
REVERT: A  227 ASP cc_start: 0.8027 (t70) cc_final: 0.7420 (t0)
REVERT: B  314 ARG cc_start: 0.7369 (OUTLIER) cc_final: 0.6039 (ttp80)
REVERT: B  373 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8322 (mm)
REVERT: C  121 GLU cc_start: 0.6687 (pt0) cc_final: 0.6481 (pt0)
REVERT: C  122 MET cc_start: 0.7531 (mmt) cc_final: 0.6920 (tpt)
REVERT: a  123 GLU cc_start: 0.8611 (pm20) cc_final: 0.8302 (pm20)
REVERT: a  157 PHE cc_start: 0.8277 (m-80) cc_final: 0.7969 (m-80)
REVERT: a  223 GLU cc_start: 0.8440 (mm-30) cc_final: 0.8162 (pm20)
REVERT: a  227 ASP cc_start: 0.8193 (t70) cc_final: 0.7865 (t0)
REVERT: b  373 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8552 (mm)
REVERT: c   87 MET cc_start: 0.5323 (pmm) cc_final: 0.4328 (ppp)
REVERT: c  165 LYS cc_start: 0.7414 (tptt) cc_final: 0.7011 (ptmm)
  outliers start: 39
  outliers final: 32
  residues processed: 229
  average time/residue: 0.2002
  time to fit residues: 59.5566
Evaluate side-chains
  247 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 212
  time to evaluate  : 0.720 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  186 SER
Chi-restraints excluded: chain A residue  197 HIS
Chi-restraints excluded: chain A residue  209 SER
Chi-restraints excluded: chain A residue  228 VAL
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  234 ILE
Chi-restraints excluded: chain A residue  236 GLN
Chi-restraints excluded: chain A residue  244 LEU
Chi-restraints excluded: chain A residue  248 ASP
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain B residue  340 GLU
Chi-restraints excluded: chain B residue  349 SER
Chi-restraints excluded: chain B residue  373 LEU
Chi-restraints excluded: chain C residue   46 SER
Chi-restraints excluded: chain C residue   52 ASN
Chi-restraints excluded: chain C residue  116 ILE
Chi-restraints excluded: chain C residue  119 PHE
Chi-restraints excluded: chain C residue  148 LYS
Chi-restraints excluded: chain C residue  188 THR
Chi-restraints excluded: chain a residue  108 LEU
Chi-restraints excluded: chain a residue  156 ASP
Chi-restraints excluded: chain a residue  186 SER
Chi-restraints excluded: chain a residue  228 VAL
Chi-restraints excluded: chain a residue  229 LEU
Chi-restraints excluded: chain a residue  256 GLN
Chi-restraints excluded: chain a residue  268 VAL
Chi-restraints excluded: chain b residue  312 SER
Chi-restraints excluded: chain b residue  340 GLU
Chi-restraints excluded: chain b residue  349 SER
Chi-restraints excluded: chain b residue  368 THR
Chi-restraints excluded: chain b residue  373 LEU
Chi-restraints excluded: chain c residue   19 ILE
Chi-restraints excluded: chain c residue   46 SER
Chi-restraints excluded: chain c residue  123 ASN
Chi-restraints excluded: chain c residue  188 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 4 optimal weight:    0.2980
   chunk 67 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9990
   chunk 14 optimal weight:    0.5980
   chunk 16 optimal weight:    0.8980
   chunk 75 optimal weight:    2.9990
   chunk 33 optimal weight:    5.9990
   chunk 32 optimal weight:    8.9990
   chunk 50 optimal weight:    0.6980
   chunk 15 optimal weight:    0.9990
   chunk 2 optimal weight:    2.9990
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
A 262 ASN
b 310 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4260 r_free = 0.4260 target = 0.194943 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.124524 restraints weight = 7354.095|
|-----------------------------------------------------------------------------|
r_work (start): 0.3498 rms_B_bonded: 3.34
r_work: 0.3305 rms_B_bonded: 3.86 restraints_weight: 0.5000
r_work (final): 0.3305
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7366
moved from start:          0.2934

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   6856  Z= 0.203
  Angle     :  0.637   8.300   9230  Z= 0.331
  Chirality :  0.043   0.148   1016
  Planarity :  0.003   0.033   1192
  Dihedral  :  4.832  44.698    892
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 11.08
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  6.90 %
    Favored  : 92.98 %
  Rotamer:
    Outliers :  5.13 %
    Allowed  : 28.42 %
    Favored  : 66.45 %
  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: -1.31 (0.28), residues: 812
  helix:  1.00 (0.39), residues: 154
  sheet: -0.70 (0.41), residues: 162
  loop : -1.60 (0.26), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP b 335 
 HIS   0.003   0.001   HIS A 148 
 PHE   0.010   0.001   PHE c  13 
 TYR   0.020   0.001   TYR c  37 
 ARG   0.003   0.000   ARG C  49 

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

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

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  244 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 205
  time to evaluate  : 0.746 
Fit side-chains
   revert: symmetry clash
REVERT: A  227 ASP cc_start: 0.8123 (t70) cc_final: 0.7711 (t0)
REVERT: B  314 ARG cc_start: 0.7349 (OUTLIER) cc_final: 0.6050 (ttp80)
REVERT: B  373 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8321 (mm)
REVERT: C  122 MET cc_start: 0.7594 (mmt) cc_final: 0.7123 (tpt)
REVERT: a  123 GLU cc_start: 0.8585 (pm20) cc_final: 0.8341 (pm20)
REVERT: a  157 PHE cc_start: 0.8291 (m-80) cc_final: 0.7986 (m-80)
REVERT: a  223 GLU cc_start: 0.8453 (mm-30) cc_final: 0.8102 (pm20)
REVERT: a  227 ASP cc_start: 0.8175 (t70) cc_final: 0.7868 (t0)
REVERT: b  373 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8536 (mm)
REVERT: c   87 MET cc_start: 0.5375 (pmm) cc_final: 0.4389 (ppp)
REVERT: c  165 LYS cc_start: 0.7433 (tptt) cc_final: 0.7009 (ptmm)
  outliers start: 39
  outliers final: 31
  residues processed: 219
  average time/residue: 0.2001
  time to fit residues: 56.7693
Evaluate side-chains
  236 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 202
  time to evaluate  : 0.703 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  186 SER
Chi-restraints excluded: chain A residue  197 HIS
Chi-restraints excluded: chain A residue  228 VAL
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  234 ILE
Chi-restraints excluded: chain A residue  236 GLN
Chi-restraints excluded: chain A residue  244 LEU
Chi-restraints excluded: chain A residue  248 ASP
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain B residue  340 GLU
Chi-restraints excluded: chain B residue  349 SER
Chi-restraints excluded: chain B residue  373 LEU
Chi-restraints excluded: chain C residue   46 SER
Chi-restraints excluded: chain C residue   52 ASN
Chi-restraints excluded: chain C residue  116 ILE
Chi-restraints excluded: chain C residue  119 PHE
Chi-restraints excluded: chain C residue  148 LYS
Chi-restraints excluded: chain C residue  188 THR
Chi-restraints excluded: chain a residue  108 LEU
Chi-restraints excluded: chain a residue  156 ASP
Chi-restraints excluded: chain a residue  186 SER
Chi-restraints excluded: chain a residue  228 VAL
Chi-restraints excluded: chain a residue  229 LEU
Chi-restraints excluded: chain a residue  268 VAL
Chi-restraints excluded: chain b residue  312 SER
Chi-restraints excluded: chain b residue  340 GLU
Chi-restraints excluded: chain b residue  349 SER
Chi-restraints excluded: chain b residue  368 THR
Chi-restraints excluded: chain b residue  373 LEU
Chi-restraints excluded: chain c residue   19 ILE
Chi-restraints excluded: chain c residue   38 PHE
Chi-restraints excluded: chain c residue   46 SER
Chi-restraints excluded: chain c residue   52 ASN
Chi-restraints excluded: chain c residue  188 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 64 optimal weight:    6.9990
   chunk 1 optimal weight:    0.5980
   chunk 21 optimal weight:    0.6980
   chunk 3 optimal weight:    0.8980
   chunk 35 optimal weight:    8.9990
   chunk 22 optimal weight:    0.0970
   chunk 73 optimal weight:    0.7980
   chunk 31 optimal weight:    0.7980
   chunk 9 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 2 optimal weight:    2.9990
   overall best weight:    0.5978

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

Flipped N/Q/H residues before XYZ refinement:
A 262 ASN
b 310 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4275 r_free = 0.4275 target = 0.196337 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.125361 restraints weight = 7455.198|
|-----------------------------------------------------------------------------|
r_work (start): 0.3513 rms_B_bonded: 3.37
r_work: 0.3325 rms_B_bonded: 3.87 restraints_weight: 0.5000
r_work (final): 0.3325
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7359
moved from start:          0.3035

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6856  Z= 0.193
  Angle     :  0.641   9.754   9230  Z= 0.330
  Chirality :  0.043   0.147   1016
  Planarity :  0.003   0.032   1192
  Dihedral  :  4.743  44.259    892
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 10.85
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  6.16 %
    Favored  : 93.72 %
  Rotamer:
    Outliers :  4.74 %
    Allowed  : 28.95 %
    Favored  : 66.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.22 (0.28), residues: 812
  helix:  1.15 (0.39), residues: 154
  sheet: -0.65 (0.41), residues: 162
  loop : -1.58 (0.26), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP b 335 
 HIS   0.003   0.001   HIS A 148 
 PHE   0.010   0.001   PHE C  13 
 TYR   0.029   0.001   TYR c  37 
 ARG   0.002   0.000   ARG C  49 

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

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

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  245 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 209
  time to evaluate  : 0.780 
Fit side-chains
   revert: symmetry clash
REVERT: A  199 SER cc_start: 0.9132 (m) cc_final: 0.8778 (t)
REVERT: A  227 ASP cc_start: 0.8078 (t70) cc_final: 0.7717 (t0)
REVERT: B  373 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8314 (mm)
REVERT: C  122 MET cc_start: 0.7544 (mmt) cc_final: 0.7163 (tpt)
REVERT: a  123 GLU cc_start: 0.8552 (pm20) cc_final: 0.8321 (pm20)
REVERT: a  157 PHE cc_start: 0.8257 (m-80) cc_final: 0.7965 (m-80)
REVERT: a  223 GLU cc_start: 0.8458 (mm-30) cc_final: 0.8083 (mp0)
REVERT: a  227 ASP cc_start: 0.8166 (t70) cc_final: 0.7939 (t0)
REVERT: c   87 MET cc_start: 0.5382 (pmm) cc_final: 0.4490 (ppp)
  outliers start: 36
  outliers final: 31
  residues processed: 222
  average time/residue: 0.2019
  time to fit residues: 58.2255
Evaluate side-chains
  237 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 205
  time to evaluate  : 0.775 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  186 SER
Chi-restraints excluded: chain A residue  197 HIS
Chi-restraints excluded: chain A residue  228 VAL
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  236 GLN
Chi-restraints excluded: chain A residue  244 LEU
Chi-restraints excluded: chain A residue  248 ASP
Chi-restraints excluded: chain B residue  339 LEU
Chi-restraints excluded: chain B residue  340 GLU
Chi-restraints excluded: chain B residue  349 SER
Chi-restraints excluded: chain B residue  373 LEU
Chi-restraints excluded: chain C residue   46 SER
Chi-restraints excluded: chain C residue   52 ASN
Chi-restraints excluded: chain C residue  116 ILE
Chi-restraints excluded: chain C residue  119 PHE
Chi-restraints excluded: chain C residue  148 LYS
Chi-restraints excluded: chain C residue  188 THR
Chi-restraints excluded: chain a residue  108 LEU
Chi-restraints excluded: chain a residue  156 ASP
Chi-restraints excluded: chain a residue  186 SER
Chi-restraints excluded: chain a residue  228 VAL
Chi-restraints excluded: chain a residue  229 LEU
Chi-restraints excluded: chain a residue  268 VAL
Chi-restraints excluded: chain b residue  312 SER
Chi-restraints excluded: chain b residue  340 GLU
Chi-restraints excluded: chain b residue  349 SER
Chi-restraints excluded: chain b residue  368 THR
Chi-restraints excluded: chain c residue   19 ILE
Chi-restraints excluded: chain c residue   38 PHE
Chi-restraints excluded: chain c residue   46 SER
Chi-restraints excluded: chain c residue   52 ASN
Chi-restraints excluded: chain c residue  188 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 22 optimal weight:    0.0570
   chunk 69 optimal weight:    2.9990
   chunk 20 optimal weight:    3.9990
   chunk 39 optimal weight:    4.9990
   chunk 43 optimal weight:    0.9980
   chunk 53 optimal weight:    0.8980
   chunk 28 optimal weight:    0.9990
   chunk 36 optimal weight:    9.9990
   chunk 41 optimal weight:    7.9990
   chunk 52 optimal weight:    2.9990
   chunk 44 optimal weight:    0.8980
   overall best weight:    0.7700

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

Flipped N/Q/H residues before XYZ refinement:
A 262 ASN
b 310 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4263 r_free = 0.4263 target = 0.195003 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.124776 restraints weight = 7340.250|
|-----------------------------------------------------------------------------|
r_work (start): 0.3505 rms_B_bonded: 3.29
r_work: 0.3317 rms_B_bonded: 3.81 restraints_weight: 0.5000
r_work (final): 0.3317
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7374
moved from start:          0.3080

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6856  Z= 0.209
  Angle     :  0.642   9.382   9230  Z= 0.331
  Chirality :  0.043   0.148   1016
  Planarity :  0.003   0.034   1192
  Dihedral  :  4.750  44.756    892
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 11.38
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  6.65 %
    Favored  : 93.23 %
  Rotamer:
    Outliers :  4.61 %
    Allowed  : 29.47 %
    Favored  : 65.92 %
  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: -1.20 (0.28), residues: 812
  helix:  1.11 (0.39), residues: 154
  sheet: -0.59 (0.42), residues: 162
  loop : -1.56 (0.26), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP b 335 
 HIS   0.003   0.001   HIS A 148 
 PHE   0.009   0.001   PHE c  13 
 TYR   0.032   0.001   TYR c  37 
 ARG   0.002   0.000   ARG A 269 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4524.88 seconds
wall clock time: 78 minutes 0.21 seconds (4680.21 seconds total)