Starting phenix.real_space_refine
on Mon Jan 13 19:40:38 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8r9x_19015/01_2025/8r9x_19015.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8r9x_19015/01_2025/8r9x_19015.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8r9x_19015/01_2025/8r9x_19015.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8r9x_19015/01_2025/8r9x_19015.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8r9x_19015/01_2025/8r9x_19015.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8r9x_19015/01_2025/8r9x_19015.cif"
  }
  resolution = 3.1
  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=   0.015
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      18      5.16       5
     C    2381      2.51       5
     N     612      2.21       5
     O     771      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 3782
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 1844
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 235, 1844
          Classifications: {'peptide': 235}
          Link IDs: {'PTRANS': 9, 'TRANS': 225}
    Chain: "H"
      Number of atoms: 929
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 121, 920
          Classifications: {'peptide': 121}
          Link IDs: {'PTRANS': 3, 'TRANS': 117}
      Conformer: "B"
        Number of residues, atoms: 121, 920
          Classifications: {'peptide': 121}
          Link IDs: {'PTRANS': 3, 'TRANS': 117}
          bond proxies already assigned to first conformer: 930
    Chain: "L"
      Number of atoms: 812
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 105, 812
          Classifications: {'peptide': 105}
          Link IDs: {'PTRANS': 5, 'TRANS': 99}
    Chain: "B"
      Number of atoms: 38
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 38
          Unusual residues: {'FUC': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "D"
      Number of atoms: 61
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 61
          Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 5
    Chain: "E"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 42
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 42
          Unusual residues: {'NAG': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
  Time building chain proxies: 4.19, per 1000 atoms: 1.11
  Number of scatterers: 3782
  At special positions: 0
  Unit cell: (97.09, 68.474, 70.518, 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      18     16.00
     O     771      8.00
     N     612      7.00
     C    2381      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  93 " - pdb=" SG  CYS A 116 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 157 " - pdb=" SG  CYS A 181 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 260 " - pdb=" SG  CYS A 270 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  88 " 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
  Links applied
    ALPHA1-3
      " BMA D   3 " - " MAN D   4 "
    ALPHA1-6
      " BMA D   3 " - " MAN D   5 "
    BETA1-4
      " NAG B   1 " - " NAG B   2 "
      " NAG C   1 " - " NAG C   2 "
      " NAG D   1 " - " NAG D   2 "
      " NAG D   2 " - " BMA D   3 "
      " NAG E   1 " - " NAG E   2 "
    BETA1-6
      " NAG B   1 " - " FUC B   3 "
       ~> Even though FUC is an alpha isomer, a beta linkage is required...
    NAG-ASN
      " NAG A1101 " - " ASN A 162 "
      " NAG A1102 " - " ASN A 169 "
      " NAG A1103 " - " ASN A 251 "
      " NAG B   1 " - " ASN A  99 "
      " NAG C   1 " - " ASN A 184 "
      " NAG D   1 " - " ASN A 241 "
      " NAG E   1 " - " ASN A  74 "
  Time building additional restraints: 1.38
  Conformation dependent library (CDL) restraints added in 551.0 milliseconds
  

  912 Ramachandran restraints generated.
    456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  854

  Finding SS restraints...
    Secondary structure from input PDB file:
      6 helices and 9 sheets defined
      8.9% alpha, 36.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.44
  Creating SS restraints...
    Processing helix  chain 'A' and resid 65 through 69
      removed outlier: 3.790A  pdb=" N   LEU A  68 " --> pdb=" O   ASN A  65 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 117 through 124
      removed outlier: 3.650A  pdb=" N   MET A 120 " --> pdb=" O   GLY A 117 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   VAL A 121 " --> pdb=" O   GLY A 118 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   LYS A 122 " --> pdb=" O   ALA A 119 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 162 through 169
    Processing helix  chain 'A' and resid 263 through 272
    Processing helix  chain 'H' and resid 28 through 32
    Processing helix  chain 'H' and resid 87 through 91
      removed outlier: 3.711A  pdb=" N   THR H  91 " --> pdb=" O   ALA H  88 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 80 through 88
      removed outlier: 3.600A  pdb=" N   GLY A  81 " --> pdb=" O   LEU A 249 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   GLN A 256 " --> pdb=" O   THR A 248 " (cutoff:3.500A)
      removed outlier: 6.468A  pdb=" N   THR A 250 " --> pdb=" O   ILE A 254 " (cutoff:3.500A)
      removed outlier: 5.234A  pdb=" N   ILE A 254 " --> pdb=" O   THR A 250 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 95 through 96
      removed outlier: 4.618A  pdb=" N   GLN A 205 " --> pdb=" O   TYR A 201 " (cutoff:3.500A)
      removed outlier: 7.085A  pdb=" N   PHE A 206 " --> pdb=" O   LEU A 213 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 101 through 105
      removed outlier: 7.251A  pdb=" N   ILE A 141 " --> pdb=" O   CYS A 157 " (cutoff:3.500A)
      removed outlier: 5.627A  pdb=" N   CYS A 157 " --> pdb=" O   ILE A 141 " (cutoff:3.500A)
      removed outlier: 6.791A  pdb=" N   CYS A 181 " --> pdb=" O   LEU A 188 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 7
    Processing sheet with id=AA5, first strand: chain 'H' and resid 11 through 12
      removed outlier: 6.918A  pdb=" N   MET H  34 " --> pdb=" O   ILE H  50 " (cutoff:3.500A)
      removed outlier: 4.691A  pdb=" N   ILE H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 6.696A  pdb=" N   TRP H  36 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'H' and resid 11 through 12
      removed outlier: 3.663A  pdb=" N   TYR H 111 " --> pdb=" O   LYS H  98 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'L' and resid 4 through 5
    Processing sheet with id=AA8, first strand: chain 'L' and resid 10 through 12
      removed outlier: 6.346A  pdb=" N   LEU L  11 " --> pdb=" O   GLU L 104 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'L' and resid 53 through 54
      removed outlier: 5.767A  pdb=" N   LEU L  46 " --> pdb=" O   GLN L  37 " (cutoff:3.500A)
      removed outlier: 6.632A  pdb=" N   GLN L  37 " --> pdb=" O   LEU L  46 " (cutoff:3.500A)

    127 hydrogen bonds defined for protein.
    318 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.94

  Time building geometry restraints manager: 1.50 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: 1174
        1.34 -     1.46: 912
        1.46 -     1.57: 1756
        1.57 -     1.69: 0
        1.69 -     1.81: 24
  Bond restraints: 3866
  Sorted by residual:
  bond pdb=" C1  NAG C   1 "
       pdb=" O5  NAG C   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.438 -0.032 2.00e-02 2.50e+03 2.59e+00
  bond pdb=" CA  SER A  43 "
       pdb=" CB  SER A  43 "
    ideal  model  delta    sigma   weight residual
    1.530  1.498  0.032 2.00e-02 2.50e+03 2.53e+00
  bond pdb=" C1  NAG A1102 "
       pdb=" O5  NAG A1102 "
    ideal  model  delta    sigma   weight residual
    1.406  1.436 -0.030 2.00e-02 2.50e+03 2.30e+00
  bond pdb=" C1  NAG B   2 "
       pdb=" O5  NAG B   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.436 -0.030 2.00e-02 2.50e+03 2.25e+00
  bond pdb=" N   SER A  43 "
       pdb=" CA  SER A  43 "
    ideal  model  delta    sigma   weight residual
    1.458  1.485 -0.027 1.90e-02 2.77e+03 1.97e+00
  ... (remaining 3861 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.63: 5111
        1.63 -     3.26: 129
        3.26 -     4.89: 20
        4.89 -     6.52: 8
        6.52 -     8.15: 1
  Bond angle restraints: 5269
  Sorted by residual:
  angle pdb=" N   LEU A  58 "
        pdb=" CA  LEU A  58 "
        pdb=" C   LEU A  58 "
      ideal   model   delta    sigma   weight residual
     109.81  115.70   -5.89 2.21e+00 2.05e-01 7.09e+00
  angle pdb=" CA  LEU A 106 "
        pdb=" CB  LEU A 106 "
        pdb=" CG  LEU A 106 "
      ideal   model   delta    sigma   weight residual
     116.30  124.45   -8.15 3.50e+00 8.16e-02 5.42e+00
  angle pdb=" C1  BMA D   3 "
        pdb=" O5  BMA D   3 "
        pdb=" C5  BMA D   3 "
      ideal   model   delta    sigma   weight residual
     118.82  112.31    6.51 3.00e+00 1.11e-01 4.71e+00
  angle pdb=" C3  BMA D   3 "
        pdb=" C2  BMA D   3 "
        pdb=" O2  BMA D   3 "
      ideal   model   delta    sigma   weight residual
     112.95  106.48    6.47 3.00e+00 1.11e-01 4.65e+00
  angle pdb=" C3  MAN D   4 "
        pdb=" C2  MAN D   4 "
        pdb=" O2  MAN D   4 "
      ideal   model   delta    sigma   weight residual
     111.77  105.37    6.40 3.00e+00 1.11e-01 4.56e+00
  ... (remaining 5264 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.65: 2226
       21.65 -    43.30: 196
       43.30 -    64.94: 23
       64.94 -    86.59: 11
       86.59 -   108.24: 5
  Dihedral angle restraints: 2461
    sinusoidal: 1118
      harmonic: 1343
  Sorted by residual:
  dihedral pdb=" CA  LEU A  58 "
           pdb=" C   LEU A  58 "
           pdb=" N   PRO A  59 "
           pdb=" CA  PRO A  59 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.41   29.59     0      5.00e+00 4.00e-02 3.50e+01
  dihedral pdb=" CA  PHE A 182 "
           pdb=" C   PHE A 182 "
           pdb=" N   THR A 183 "
           pdb=" CA  THR A 183 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.24   20.76     0      5.00e+00 4.00e-02 1.72e+01
  dihedral pdb=" O4  BMA D   3 "
           pdb=" C4  BMA D   3 "
           pdb=" C5  BMA D   3 "
           pdb=" O5  BMA D   3 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -71.29 -179.53  108.24     1      3.00e+01 1.11e-03 1.40e+01
  ... (remaining 2458 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 494
       0.044 -    0.089: 104
       0.089 -    0.133: 46
       0.133 -    0.177: 2
       0.177 -    0.221: 1
  Chirality restraints: 647
  Sorted by residual:
  chirality pdb=" C5  BMA D   3 "
            pdb=" C4  BMA D   3 "
            pdb=" C6  BMA D   3 "
            pdb=" O5  BMA D   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.50    0.22 2.00e-01 2.50e+01 1.23e+00
  chirality pdb=" C1  NAG D   1 "
            pdb=" ND2 ASN A 241 "
            pdb=" C2  NAG D   1 "
            pdb=" O5  NAG D   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.23   -0.17 2.00e-01 2.50e+01 6.99e-01
  chirality pdb=" C3  FUC B   3 "
            pdb=" C2  FUC B   3 "
            pdb=" C4  FUC B   3 "
            pdb=" O3  FUC B   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.45   -2.59    0.13 2.00e-01 2.50e+01 4.47e-01
  ... (remaining 644 not shown)

  Planarity restraints: 655
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A  58 "   -0.033 5.00e-02 4.00e+02   5.03e-02 4.05e+00
        pdb=" N   PRO A  59 "    0.087 5.00e-02 4.00e+02
        pdb=" CA  PRO A  59 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO A  59 "   -0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL L   3 "    0.005 2.00e-02 2.50e+03   1.01e-02 1.03e+00
        pdb=" C   VAL L   3 "   -0.018 2.00e-02 2.50e+03
        pdb=" O   VAL L   3 "    0.007 2.00e-02 2.50e+03
        pdb=" N   MET L   4 "    0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA L  43 "   -0.015 5.00e-02 4.00e+02   2.28e-02 8.34e-01
        pdb=" N   PRO L  44 "    0.039 5.00e-02 4.00e+02
        pdb=" CA  PRO L  44 "   -0.012 5.00e-02 4.00e+02
        pdb=" CD  PRO L  44 "   -0.013 5.00e-02 4.00e+02
  ... (remaining 652 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.80: 1005
        2.80 -     3.33: 3150
        3.33 -     3.85: 6103
        3.85 -     4.38: 7321
        4.38 -     4.90: 13218
  Nonbonded interactions: 30797
  Sorted by model distance:
  nonbonded pdb=" NH1 ARG A  48 "
            pdb=" OD2 ASP A 134 "
     model   vdw
     2.277 3.120
  nonbonded pdb=" O   THR L  20 "
            pdb=" OG1 THR L  20 "
     model   vdw
     2.292 3.040
  nonbonded pdb=" NH1 ARG L  61 "
            pdb=" OE1 GLN L  79 "
     model   vdw
     2.307 3.120
  nonbonded pdb=" O   ASP L  82 "
            pdb=" OH  TYR L  86 "
     model   vdw
     2.362 3.040
  nonbonded pdb=" O   ASN A 251 "
            pdb=" OG1 THR A 252 "
     model   vdw
     2.379 3.040
  ... (remaining 30792 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'C'
  selection = chain 'E'
}

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=0.38 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:             2.190
  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:          0.150
  Check model and map are aligned:         0.020
  Set scattering table:                    0.050
  Process input model:                     15.480
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  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:2.860
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.830
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8629
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      :  0.004   0.032   3866  Z= 0.253
  Angle     :  0.650   8.147   5269  Z= 0.298
  Chirality :  0.044   0.221    647
  Planarity :  0.003   0.050    648
  Dihedral  : 16.479 108.236   1592
  Min Nonbonded Distance : 2.277

Molprobity Statistics.
  All-atom Clashscore : 5.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 20.95 %
    Favored  : 79.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.47 (0.41), residues: 456
  helix: -0.35 (1.07), residues: 25
  sheet: -0.02 (0.41), residues: 176
  loop : -0.44 (0.41), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP H 112 
 HIS   0.003   0.001   HIS A 168 
 PHE   0.011   0.001   PHE A 237 
 TYR   0.009   0.001   TYR A 222 
 ARG   0.002   0.000   ARG H  19 

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

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

  912 Ramachandran restraints generated.
    456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  912 Ramachandran restraints generated.
    456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.399 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 85
  average time/residue: 0.2353
  time to fit residues: 23.1954
Evaluate side-chains
  74 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 74
  time to evaluate  : 0.450 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 37 optimal weight:    4.9990
   chunk 34 optimal weight:    0.4980
   chunk 18 optimal weight:    2.9990
   chunk 11 optimal weight:    1.9990
   chunk 23 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9980
   chunk 13 optimal weight:    0.9980
   chunk 21 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9980
   chunk 40 optimal weight:    0.0970
   chunk 22 optimal weight:    0.6980
   overall best weight:    0.6578

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

Flipped N/Q/H residues before XYZ refinement:
A 271 GLN
H 114 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3048 r_free = 0.3048 target = 0.074552 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2707 r_free = 0.2707 target = 0.057489 restraints weight = 20990.994|
|-----------------------------------------------------------------------------|
r_work (start): 0.2689 rms_B_bonded: 4.92
r_work: 0.2514 rms_B_bonded: 4.68 restraints_weight: 0.5000
r_work (final): 0.2514
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2540
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2540 r_free = 0.2540    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2540 r_free = 0.2540    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2540
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8338
moved from start:          0.1489

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3866  Z= 0.201
  Angle     :  0.626   7.748   5269  Z= 0.319
  Chirality :  0.043   0.179    647
  Planarity :  0.004   0.048    648
  Dihedral  :  9.983  82.589    815
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 5.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 21.20 %
    Favored  : 75.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.28 (0.40), residues: 456
  helix:  0.31 (1.17), residues: 25
  sheet:  0.17 (0.41), residues: 163
  loop : -0.40 (0.39), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP H  47 
 HIS   0.002   0.001   HIS A 236 
 PHE   0.012   0.001   PHE A 237 
 TYR   0.014   0.001   TYR H  80 
 ARG   0.007   0.001   ARG L  42 

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

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

  912 Ramachandran restraints generated.
    456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  912 Ramachandran restraints generated.
    456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 78
  time to evaluate  : 0.443 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   54 ASP cc_start: 0.8856 (t0) cc_final: 0.8615 (t0)
REVERT: A  139 ASP cc_start: 0.9250 (t0) cc_final: 0.9014 (m-30)
REVERT: A  197 ASP cc_start: 0.9017 (t0) cc_final: 0.8773 (t0)
REVERT: H    1 GLU cc_start: 0.8188 (tp30) cc_final: 0.7744 (tp30)
REVERT: L   79 GLN cc_start: 0.8876 (mt0) cc_final: 0.8657 (mt0)
  outliers start: 12
  outliers final: 5
  residues processed: 86
  average time/residue: 0.2180
  time to fit residues: 22.0334
Evaluate side-chains
  80 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 75
  time to evaluate  : 0.454 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  219 THR
Chi-restraints excluded: chain A residue  265 VAL
Chi-restraints excluded: chain H residue  117 LEU
Chi-restraints excluded: chain L residue    2 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 11 optimal weight:    1.9990
   chunk 42 optimal weight:    4.9990
   chunk 18 optimal weight:    2.9990
   chunk 20 optimal weight:    3.9990
   chunk 21 optimal weight:    0.9990
   chunk 14 optimal weight:    0.7980
   chunk 34 optimal weight:    0.8980
   chunk 25 optimal weight:    3.9990
   chunk 27 optimal weight:    0.0670
   chunk 13 optimal weight:    0.6980
   chunk 15 optimal weight:    0.5980
   overall best weight:    0.6118

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.074586 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2731 r_free = 0.2731 target = 0.058499 restraints weight = 15101.830|
|-----------------------------------------------------------------------------|
r_work (start): 0.2709 rms_B_bonded: 4.26
r_work: 0.2553 rms_B_bonded: 4.19 restraints_weight: 0.5000
r_work (final): 0.2553
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2560
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2560 r_free = 0.2560    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2560 r_free = 0.2560    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2560
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8333
moved from start:          0.1779

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   3866  Z= 0.187
  Angle     :  0.581   7.975   5269  Z= 0.296
  Chirality :  0.042   0.207    647
  Planarity :  0.004   0.046    648
  Dihedral  :  9.235  78.092    815
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 4.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 21.20 %
    Favored  : 76.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.23 (0.40), residues: 456
  helix:  0.54 (1.20), residues: 25
  sheet:  0.31 (0.41), residues: 158
  loop : -0.46 (0.38), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP H 112 
 HIS   0.002   0.001   HIS A 236 
 PHE   0.010   0.001   PHE A 206 
 TYR   0.013   0.001   TYR A 222 
 ARG   0.006   0.001   ARG L  18 

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

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

  912 Ramachandran restraints generated.
    456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  912 Ramachandran restraints generated.
    456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 75
  time to evaluate  : 0.433 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   54 ASP cc_start: 0.8888 (t0) cc_final: 0.8592 (t0)
REVERT: A  120 MET cc_start: 0.8532 (tpp) cc_final: 0.8158 (tpp)
REVERT: A  139 ASP cc_start: 0.9154 (t0) cc_final: 0.8927 (m-30)
REVERT: A  197 ASP cc_start: 0.9102 (t0) cc_final: 0.8760 (t0)
REVERT: H    1 GLU cc_start: 0.8214 (tp30) cc_final: 0.7760 (tp30)
REVERT: H    3 ARG cc_start: 0.8155 (mmm-85) cc_final: 0.7660 (mmm-85)
REVERT: L   11 LEU cc_start: 0.8401 (tt) cc_final: 0.8059 (tt)
REVERT: L   79 GLN cc_start: 0.8929 (mt0) cc_final: 0.8632 (mt0)
  outliers start: 9
  outliers final: 7
  residues processed: 83
  average time/residue: 0.2245
  time to fit residues: 21.8644
Evaluate side-chains
  80 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 73
  time to evaluate  : 0.428 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  135 LEU
Chi-restraints excluded: chain A residue  171 THR
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  190 ILE
Chi-restraints excluded: chain A residue  219 THR
Chi-restraints excluded: chain A residue  265 VAL
Chi-restraints excluded: chain H residue  117 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 6 optimal weight:    0.0670
   chunk 25 optimal weight:    3.9990
   chunk 7 optimal weight:    0.0870
   chunk 34 optimal weight:    0.7980
   chunk 23 optimal weight:    0.8980
   chunk 29 optimal weight:    3.9990
   chunk 12 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9990
   chunk 24 optimal weight:    2.9990
   chunk 0 optimal weight:    3.9990
   chunk 9 optimal weight:    2.9990
   overall best weight:    0.5698

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.074918 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2723 r_free = 0.2723 target = 0.058001 restraints weight = 21556.557|
|-----------------------------------------------------------------------------|
r_work (start): 0.2717 rms_B_bonded: 5.03
r_work: 0.2539 rms_B_bonded: 4.80 restraints_weight: 0.5000
r_work (final): 0.2539
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2538
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2538 r_free = 0.2538    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2538 r_free = 0.2538    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2538
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8293
moved from start:          0.1979

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3866  Z= 0.175
  Angle     :  0.586   7.940   5269  Z= 0.297
  Chirality :  0.042   0.228    647
  Planarity :  0.003   0.044    648
  Dihedral  :  8.550  73.372    815
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 4.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 22.44 %
    Favored  : 74.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.08 (0.40), residues: 456
  helix:  0.60 (1.20), residues: 25
  sheet:  0.42 (0.41), residues: 168
  loop : -0.39 (0.40), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP H  47 
 HIS   0.002   0.001   HIS A 236 
 PHE   0.010   0.001   PHE A 237 
 TYR   0.013   0.001   TYR A 222 
 ARG   0.004   0.001   ARG H  87 

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

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

  912 Ramachandran restraints generated.
    456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  912 Ramachandran restraints generated.
    456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 75
  time to evaluate  : 0.434 
Fit side-chains
   revert: symmetry clash
REVERT: A   54 ASP cc_start: 0.8925 (t0) cc_final: 0.8597 (t0)
REVERT: A  120 MET cc_start: 0.8525 (tpp) cc_final: 0.8146 (tpp)
REVERT: A  151 GLU cc_start: 0.8239 (pm20) cc_final: 0.7977 (pm20)
REVERT: A  197 ASP cc_start: 0.9186 (t0) cc_final: 0.8764 (t0)
REVERT: H    1 GLU cc_start: 0.8307 (tp30) cc_final: 0.7877 (tp30)
REVERT: H    3 ARG cc_start: 0.8191 (mmm-85) cc_final: 0.7716 (mmm-85)
REVERT: H   76 LYS cc_start: 0.9548 (mtpp) cc_final: 0.9318 (mtmm)
REVERT: H   87 ARG cc_start: 0.8391 (ptp-170) cc_final: 0.7717 (ptp-170)
REVERT: L   79 GLN cc_start: 0.8947 (mt0) cc_final: 0.8637 (mt0)
  outliers start: 11
  outliers final: 8
  residues processed: 82
  average time/residue: 0.2351
  time to fit residues: 22.5438
Evaluate side-chains
  81 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 73
  time to evaluate  : 0.437 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  116 CYS
Chi-restraints excluded: chain A residue  135 LEU
Chi-restraints excluded: chain A residue  171 THR
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  219 THR
Chi-restraints excluded: chain A residue  265 VAL
Chi-restraints excluded: chain H residue  117 LEU
Chi-restraints excluded: chain L residue    2 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 28 optimal weight:    1.9990
   chunk 39 optimal weight:    0.5980
   chunk 42 optimal weight:    0.9980
   chunk 22 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9980
   chunk 16 optimal weight:    2.9990
   chunk 27 optimal weight:    4.9990
   chunk 25 optimal weight:    3.9990
   chunk 1 optimal weight:    0.8980
   chunk 38 optimal weight:    0.6980
   chunk 44 optimal weight:    0.7980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
H 114 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3046 r_free = 0.3046 target = 0.073974 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2711 r_free = 0.2711 target = 0.057015 restraints weight = 21433.972|
|-----------------------------------------------------------------------------|
r_work (start): 0.2709 rms_B_bonded: 4.95
r_work: 0.2536 rms_B_bonded: 4.66 restraints_weight: 0.5000
r_work (final): 0.2536
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2546
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2546 r_free = 0.2546    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2546 r_free = 0.2546    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2546
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8371
moved from start:          0.2127

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   3866  Z= 0.212
  Angle     :  0.596   7.815   5269  Z= 0.300
  Chirality :  0.042   0.233    647
  Planarity :  0.004   0.044    648
  Dihedral  :  8.333  71.464    815
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 5.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 22.19 %
    Favored  : 75.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.12 (0.40), residues: 456
  helix:  0.61 (1.20), residues: 25
  sheet:  0.45 (0.42), residues: 158
  loop : -0.43 (0.38), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP H  47 
 HIS   0.001   0.001   HIS A 236 
 PHE   0.010   0.001   PHE A 237 
 TYR   0.013   0.001   TYR H  59 
 ARG   0.007   0.001   ARG A  48 

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

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

  912 Ramachandran restraints generated.
    456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  912 Ramachandran restraints generated.
    456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 74
  time to evaluate  : 0.470 
Fit side-chains
   revert: symmetry clash
REVERT: A   48 ARG cc_start: 0.9487 (mtm110) cc_final: 0.8723 (ttp80)
REVERT: A   54 ASP cc_start: 0.8978 (t0) cc_final: 0.8654 (t0)
REVERT: A  120 MET cc_start: 0.8602 (tpp) cc_final: 0.8261 (tpp)
REVERT: A  197 ASP cc_start: 0.9232 (t0) cc_final: 0.8828 (t0)
REVERT: H    1 GLU cc_start: 0.8406 (tp30) cc_final: 0.8143 (tp30)
REVERT: H   87 ARG cc_start: 0.8421 (OUTLIER) cc_final: 0.8045 (ptt-90)
REVERT: L   79 GLN cc_start: 0.8931 (mt0) cc_final: 0.8276 (mm110)
  outliers start: 11
  outliers final: 8
  residues processed: 82
  average time/residue: 0.2305
  time to fit residues: 22.1214
Evaluate side-chains
  82 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 73
  time to evaluate  : 0.416 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  116 CYS
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  135 LEU
Chi-restraints excluded: chain A residue  171 THR
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  190 ILE
Chi-restraints excluded: chain A residue  219 THR
Chi-restraints excluded: chain H residue   87 ARG
Chi-restraints excluded: chain H residue  117 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 28 optimal weight:    2.9990
   chunk 43 optimal weight:    0.2980
   chunk 42 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9980
   chunk 23 optimal weight:    0.0170
   chunk 11 optimal weight:    0.7980
   chunk 18 optimal weight:    3.9990
   chunk 38 optimal weight:    0.8980
   chunk 12 optimal weight:    0.7980
   chunk 44 optimal weight:    1.9990
   overall best weight:    0.5618

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.075090 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2732 r_free = 0.2732 target = 0.058232 restraints weight = 19536.285|
|-----------------------------------------------------------------------------|
r_work (start): 0.2710 rms_B_bonded: 4.88
r_work: 0.2536 rms_B_bonded: 4.67 restraints_weight: 0.5000
r_work (final): 0.2536
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2546
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2546 r_free = 0.2546    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2546 r_free = 0.2546    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2546
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8310
moved from start:          0.2279

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   3866  Z= 0.169
  Angle     :  0.577   7.942   5269  Z= 0.293
  Chirality :  0.042   0.239    647
  Planarity :  0.003   0.044    648
  Dihedral  :  7.996  68.657    815
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 4.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 22.69 %
    Favored  : 74.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.06 (0.40), residues: 456
  helix:  0.55 (1.19), residues: 25
  sheet:  0.51 (0.42), residues: 158
  loop : -0.39 (0.39), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP H 112 
 HIS   0.002   0.001   HIS A 236 
 PHE   0.010   0.001   PHE A 237 
 TYR   0.013   0.001   TYR H  59 
 ARG   0.008   0.001   ARG L  18 

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

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

  912 Ramachandran restraints generated.
    456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  912 Ramachandran restraints generated.
    456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 76
  time to evaluate  : 0.421 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   48 ARG cc_start: 0.9430 (mtm110) cc_final: 0.8629 (ttp80)
REVERT: A   54 ASP cc_start: 0.8940 (t0) cc_final: 0.8588 (t0)
REVERT: A  106 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8562 (pp)
REVERT: A  120 MET cc_start: 0.8541 (tpp) cc_final: 0.8188 (tpp)
REVERT: A  197 ASP cc_start: 0.9271 (t0) cc_final: 0.8855 (t0)
REVERT: H   73 ASP cc_start: 0.8081 (t0) cc_final: 0.7514 (t0)
REVERT: H   87 ARG cc_start: 0.8368 (ptp-170) cc_final: 0.8118 (ptt-90)
REVERT: H   90 ASP cc_start: 0.8746 (m-30) cc_final: 0.8451 (m-30)
REVERT: L   79 GLN cc_start: 0.8920 (mt0) cc_final: 0.8598 (mt0)
  outliers start: 10
  outliers final: 9
  residues processed: 83
  average time/residue: 0.2266
  time to fit residues: 22.0333
Evaluate side-chains
  84 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 74
  time to evaluate  : 0.416 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  116 CYS
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  135 LEU
Chi-restraints excluded: chain A residue  171 THR
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  190 ILE
Chi-restraints excluded: chain A residue  219 THR
Chi-restraints excluded: chain A residue  265 VAL
Chi-restraints excluded: chain H residue  117 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 41 optimal weight:    7.9990
   chunk 10 optimal weight:    0.9980
   chunk 24 optimal weight:    4.9990
   chunk 40 optimal weight:    2.9990
   chunk 9 optimal weight:    1.9990
   chunk 4 optimal weight:    0.8980
   chunk 29 optimal weight:    2.9990
   chunk 36 optimal weight:    0.5980
   chunk 30 optimal weight:    1.9990
   chunk 32 optimal weight:    0.7980
   chunk 13 optimal weight:    0.8980
   overall best weight:    0.8380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.072740 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.2752 r_free = 0.2752 target = 0.057137 restraints weight = 19829.546|
|-----------------------------------------------------------------------------|
r_work (start): 0.2727 rms_B_bonded: 4.58
r_work: 0.2563 rms_B_bonded: 4.42 restraints_weight: 0.5000
r_work (final): 0.2563
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2572
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2572 r_free = 0.2572    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2571 r_free = 0.2571    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2571
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8570
moved from start:          0.2308

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   3866  Z= 0.220
  Angle     :  0.595   7.467   5269  Z= 0.303
  Chirality :  0.042   0.245    647
  Planarity :  0.004   0.045    648
  Dihedral  :  7.879  67.291    815
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 5.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.18 %
    Favored  : 95.82 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 22.44 %
    Favored  : 74.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.10 (0.40), residues: 456
  helix:  0.54 (1.19), residues: 25
  sheet:  0.47 (0.42), residues: 159
  loop : -0.41 (0.39), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP L  35 
 HIS   0.002   0.001   HIS A 236 
 PHE   0.021   0.001   PHE A 173 
 TYR   0.013   0.001   TYR A 222 
 ARG   0.008   0.001   ARG L  18 

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

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

  912 Ramachandran restraints generated.
    456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  912 Ramachandran restraints generated.
    456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 76
  time to evaluate  : 0.388 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   48 ARG cc_start: 0.9423 (mtm110) cc_final: 0.8672 (ttp80)
REVERT: A   54 ASP cc_start: 0.8974 (t0) cc_final: 0.8644 (t0)
REVERT: A  120 MET cc_start: 0.8728 (tpp) cc_final: 0.8426 (tpp)
REVERT: A  197 ASP cc_start: 0.9202 (t0) cc_final: 0.8948 (t0)
REVERT: H    3 ARG cc_start: 0.8434 (mmm-85) cc_final: 0.8194 (mmm-85)
REVERT: H   73 ASP cc_start: 0.8376 (t0) cc_final: 0.8089 (t0)
REVERT: L   11 LEU cc_start: 0.8683 (tp) cc_final: 0.8386 (tt)
REVERT: L   79 GLN cc_start: 0.8817 (mt0) cc_final: 0.8229 (mm110)
  outliers start: 12
  outliers final: 10
  residues processed: 84
  average time/residue: 0.2283
  time to fit residues: 22.3494
Evaluate side-chains
  84 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 74
  time to evaluate  : 0.394 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  116 CYS
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  135 LEU
Chi-restraints excluded: chain A residue  171 THR
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  190 ILE
Chi-restraints excluded: chain A residue  219 THR
Chi-restraints excluded: chain A residue  265 VAL
Chi-restraints excluded: chain H residue  117 LEU
Chi-restraints excluded: chain L residue    2 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 13 optimal weight:    0.6980
   chunk 32 optimal weight:    0.8980
   chunk 11 optimal weight:    1.9990
   chunk 44 optimal weight:    2.9990
   chunk 0 optimal weight:    2.9990
   chunk 1 optimal weight:    0.8980
   chunk 8 optimal weight:    3.9990
   chunk 25 optimal weight:    0.7980
   chunk 37 optimal weight:    1.9990
   chunk 20 optimal weight:    2.9990
   chunk 17 optimal weight:    0.2980
   overall best weight:    0.7180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.073055 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2755 r_free = 0.2755 target = 0.057401 restraints weight = 21848.600|
|-----------------------------------------------------------------------------|
r_work (start): 0.2732 rms_B_bonded: 4.72
r_work: 0.2564 rms_B_bonded: 4.57 restraints_weight: 0.5000
r_work (final): 0.2564
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2575
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2575 r_free = 0.2575    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2575 r_free = 0.2575    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2575
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8522
moved from start:          0.2423

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3866  Z= 0.197
  Angle     :  0.589   7.839   5269  Z= 0.300
  Chirality :  0.043   0.247    647
  Planarity :  0.004   0.047    648
  Dihedral  :  7.675  65.448    815
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 4.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 22.19 %
    Favored  : 75.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.01 (0.40), residues: 456
  helix:  0.57 (1.19), residues: 25
  sheet:  0.56 (0.42), residues: 163
  loop : -0.39 (0.39), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP H 112 
 HIS   0.001   0.000   HIS A 236 
 PHE   0.019   0.001   PHE A 173 
 TYR   0.016   0.001   TYR H  59 
 ARG   0.008   0.001   ARG L  18 

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

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

  912 Ramachandran restraints generated.
    456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  912 Ramachandran restraints generated.
    456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 74
  time to evaluate  : 0.485 
Fit side-chains
   revert: symmetry clash
REVERT: A   54 ASP cc_start: 0.8980 (t0) cc_final: 0.8639 (t0)
REVERT: A  120 MET cc_start: 0.8704 (tpp) cc_final: 0.8410 (tpp)
REVERT: A  197 ASP cc_start: 0.9243 (t0) cc_final: 0.8969 (t0)
REVERT: H    3 ARG cc_start: 0.8365 (mmm-85) cc_final: 0.8103 (mmm-85)
REVERT: H   73 ASP cc_start: 0.8309 (t0) cc_final: 0.7786 (t0)
REVERT: H   76 LYS cc_start: 0.9570 (mtpp) cc_final: 0.9257 (mtmm)
REVERT: L   11 LEU cc_start: 0.8627 (tp) cc_final: 0.8311 (tt)
REVERT: L   79 GLN cc_start: 0.8845 (mt0) cc_final: 0.8233 (mm110)
  outliers start: 11
  outliers final: 10
  residues processed: 82
  average time/residue: 0.2341
  time to fit residues: 22.5089
Evaluate side-chains
  85 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 75
  time to evaluate  : 0.424 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  116 CYS
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  135 LEU
Chi-restraints excluded: chain A residue  171 THR
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  190 ILE
Chi-restraints excluded: chain A residue  219 THR
Chi-restraints excluded: chain A residue  265 VAL
Chi-restraints excluded: chain H residue  117 LEU
Chi-restraints excluded: chain L residue    2 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 23 optimal weight:    0.0980
   chunk 22 optimal weight:    1.9990
   chunk 39 optimal weight:    3.9990
   chunk 43 optimal weight:    3.9990
   chunk 15 optimal weight:    0.5980
   chunk 32 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9980
   chunk 27 optimal weight:    0.8980
   chunk 44 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9980
   chunk 34 optimal weight:    0.6980
   overall best weight:    0.6580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3075 r_free = 0.3075 target = 0.073821 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.2811 r_free = 0.2811 target = 0.060053 restraints weight = 8652.217|
|-----------------------------------------------------------------------------|
r_work (start): 0.2782 rms_B_bonded: 3.19
r_work: 0.2658 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.2658
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2661
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2661 r_free = 0.2661    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2661 r_free = 0.2661    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2661
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8476
moved from start:          0.2489

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   3866  Z= 0.190
  Angle     :  0.605   7.788   5269  Z= 0.305
  Chirality :  0.043   0.250    647
  Planarity :  0.004   0.045    648
  Dihedral  :  7.516  63.925    815
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 5.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 22.94 %
    Favored  : 74.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.01 (0.41), residues: 456
  helix:  0.57 (1.19), residues: 25
  sheet:  0.56 (0.41), residues: 163
  loop : -0.36 (0.40), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.000   TRP H 112 
 HIS   0.001   0.000   HIS A 236 
 PHE   0.019   0.001   PHE A 173 
 TYR   0.015   0.001   TYR H  59 
 ARG   0.008   0.001   ARG L  18 

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

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

  912 Ramachandran restraints generated.
    456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  912 Ramachandran restraints generated.
    456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 73
  time to evaluate  : 0.443 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   48 ARG cc_start: 0.9343 (mtm110) cc_final: 0.8668 (ttp80)
REVERT: A   54 ASP cc_start: 0.8905 (t0) cc_final: 0.8584 (t0)
REVERT: A  120 MET cc_start: 0.8598 (tpp) cc_final: 0.8308 (tpp)
REVERT: A  197 ASP cc_start: 0.9130 (t0) cc_final: 0.8875 (t0)
REVERT: H    3 ARG cc_start: 0.8302 (mmm-85) cc_final: 0.8037 (mmm-85)
REVERT: H   73 ASP cc_start: 0.8280 (t0) cc_final: 0.7980 (t0)
REVERT: L   11 LEU cc_start: 0.8668 (tp) cc_final: 0.8366 (tt)
REVERT: L   79 GLN cc_start: 0.8794 (mt0) cc_final: 0.8203 (mm110)
  outliers start: 10
  outliers final: 10
  residues processed: 80
  average time/residue: 0.2372
  time to fit residues: 22.2273
Evaluate side-chains
  82 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 72
  time to evaluate  : 0.410 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  116 CYS
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  135 LEU
Chi-restraints excluded: chain A residue  171 THR
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  190 ILE
Chi-restraints excluded: chain A residue  219 THR
Chi-restraints excluded: chain A residue  265 VAL
Chi-restraints excluded: chain H residue  117 LEU
Chi-restraints excluded: chain L residue    2 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 38 optimal weight:    2.9990
   chunk 3 optimal weight:    5.9990
   chunk 11 optimal weight:    2.9990
   chunk 33 optimal weight:    0.6980
   chunk 4 optimal weight:    0.5980
   chunk 16 optimal weight:    0.6980
   chunk 5 optimal weight:    0.9980
   chunk 20 optimal weight:    0.7980
   chunk 41 optimal weight:    6.9990
   chunk 31 optimal weight:    0.7980
   chunk 7 optimal weight:    3.9990
   overall best weight:    0.7180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.073156 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2775 r_free = 0.2775 target = 0.058511 restraints weight = 12204.555|
|-----------------------------------------------------------------------------|
r_work (start): 0.2760 rms_B_bonded: 3.71
r_work: 0.2620 rms_B_bonded: 3.74 restraints_weight: 0.5000
r_work (final): 0.2620
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2632
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2632 r_free = 0.2632    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2632 r_free = 0.2632    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2632
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8471
moved from start:          0.2543

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   3866  Z= 0.200
  Angle     :  0.603   7.887   5269  Z= 0.306
  Chirality :  0.043   0.250    647
  Planarity :  0.004   0.044    648
  Dihedral  :  7.422  63.031    815
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 5.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 22.69 %
    Favored  : 74.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.05 (0.41), residues: 456
  helix:  0.58 (1.19), residues: 25
  sheet:  0.63 (0.42), residues: 163
  loop : -0.36 (0.40), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP H 112 
 HIS   0.002   0.000   HIS A 236 
 PHE   0.019   0.001   PHE A 173 
 TYR   0.014   0.001   TYR H  80 
 ARG   0.009   0.001   ARG L  18 

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

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

  912 Ramachandran restraints generated.
    456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  912 Ramachandran restraints generated.
    456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 74
  time to evaluate  : 0.478 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   48 ARG cc_start: 0.9341 (mtm110) cc_final: 0.8633 (ttp80)
REVERT: A   54 ASP cc_start: 0.8934 (t0) cc_final: 0.8598 (t0)
REVERT: A  120 MET cc_start: 0.8620 (tpp) cc_final: 0.8314 (tpp)
REVERT: A  197 ASP cc_start: 0.9161 (t0) cc_final: 0.8880 (t0)
REVERT: H    3 ARG cc_start: 0.8313 (mmm-85) cc_final: 0.8055 (mmm-85)
REVERT: H   73 ASP cc_start: 0.8260 (t0) cc_final: 0.7942 (t0)
REVERT: L   11 LEU cc_start: 0.8632 (tp) cc_final: 0.8304 (tt)
REVERT: L   79 GLN cc_start: 0.8827 (mt0) cc_final: 0.8207 (mm110)
  outliers start: 10
  outliers final: 10
  residues processed: 81
  average time/residue: 0.2347
  time to fit residues: 22.1405
Evaluate side-chains
  83 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 73
  time to evaluate  : 0.441 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  116 CYS
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  135 LEU
Chi-restraints excluded: chain A residue  171 THR
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  190 ILE
Chi-restraints excluded: chain A residue  219 THR
Chi-restraints excluded: chain A residue  265 VAL
Chi-restraints excluded: chain H residue  117 LEU
Chi-restraints excluded: chain L residue    2 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 43 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 39 optimal weight:    2.9990
   chunk 38 optimal weight:    0.8980
   chunk 18 optimal weight:    3.9990
   chunk 4 optimal weight:    0.9980
   chunk 15 optimal weight:    0.8980
   chunk 35 optimal weight:    0.8980
   chunk 3 optimal weight:    5.9990
   chunk 33 optimal weight:    0.6980
   chunk 0 optimal weight:    3.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
A 100 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.073239 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 22)----------------|
| r_work = 0.2765 r_free = 0.2765 target = 0.057771 restraints weight = 21879.996|
|-----------------------------------------------------------------------------|
r_work (start): 0.2730 rms_B_bonded: 4.72
r_work: 0.2563 rms_B_bonded: 4.52 restraints_weight: 0.5000
r_work (final): 0.2563
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2572
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2572 r_free = 0.2572    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2572 r_free = 0.2572    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2572
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8550
moved from start:          0.2539

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   3866  Z= 0.228
  Angle     :  0.612   7.666   5269  Z= 0.311
  Chirality :  0.043   0.250    647
  Planarity :  0.004   0.044    648
  Dihedral  :  7.400  62.587    815
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 5.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 22.44 %
    Favored  : 75.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.04 (0.41), residues: 456
  helix:  0.58 (1.19), residues: 25
  sheet:  0.67 (0.42), residues: 163
  loop : -0.40 (0.40), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP H 112 
 HIS   0.002   0.001   HIS A 236 
 PHE   0.019   0.001   PHE A 173 
 TYR   0.013   0.001   TYR A 222 
 ARG   0.009   0.001   ARG L  18 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2433.34 seconds
wall clock time: 44 minutes 27.00 seconds (2667.00 seconds total)