Starting phenix.real_space_refine
on Thu Jul 24 09:52:35 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9jbh_61314/07_2025/9jbh_61314.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9jbh_61314/07_2025/9jbh_61314.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.73
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9jbh_61314/07_2025/9jbh_61314.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9jbh_61314/07_2025/9jbh_61314.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9jbh_61314/07_2025/9jbh_61314.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9jbh_61314/07_2025/9jbh_61314.cif"
  }
  resolution = 2.73
  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=   0.040
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: 5
    Type Number    sf(0)   Gaussians
     P      10      5.49       5
     S      30      5.16       5
     C    3898      2.51       5
     N     812      2.21       5
     O     974      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 5724
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 2609
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 334, 2609
          Classifications: {'peptide': 334}
          Link IDs: {'PTRANS': 15, 'TRANS': 318}
    Chain: "B"
      Number of atoms: 2609
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 334, 2609
          Classifications: {'peptide': 334}
          Link IDs: {'PTRANS': 15, 'TRANS': 318}
    Chain: "A"
      Number of atoms: 253
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 253
          Unusual residues: {'3PE': 3, 'CDL': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
    Chain: "B"
      Number of atoms: 253
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 253
          Unusual residues: {'3PE': 3, 'CDL': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
  Time building chain proxies: 6.20, per 1000 atoms: 1.08
  Number of scatterers: 5724
  At special positions: 0
  Unit cell: (75.952, 105.848, 71.912, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      30     16.00
     P      10     15.00
     O     974      8.00
     N     812      7.00
     C    3898      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: 1.83
  Conformation dependent library (CDL) restraints added in 893.7 milliseconds
  

  1328 Ramachandran restraints generated.
    664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1256

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 0 sheets defined
      84.7% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.56
  Creating SS restraints...
    Processing helix  chain 'A' and resid 38 through 62
      removed outlier: 4.043A  pdb=" N   PHE A  43 " --> pdb=" O   ILE A  39 " (cutoff:3.500A)
      Proline residue:  A  44  - end of helix
    Processing helix  chain 'A' and resid 66 through 80
      removed outlier: 3.808A  pdb=" N   LYS A  71 " --> pdb=" O   SER A  67 " (cutoff:3.500A)
      removed outlier: 4.297A  pdb=" N   GLY A  72 " --> pdb=" O   THR A  68 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   LEU A  73 " --> pdb=" O   GLN A  69 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 80 through 93
      removed outlier: 3.506A  pdb=" N   VAL A  92 " --> pdb=" O   LYS A  88 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   LEU A  93 " --> pdb=" O   ASN A  89 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 99 through 125
      removed outlier: 3.828A  pdb=" N   LEU A 103 " --> pdb=" O   ASP A  99 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 130 through 141
      Proline residue:  A 138  - end of helix
    Processing helix  chain 'A' and resid 149 through 158
      removed outlier: 3.736A  pdb=" N   ILE A 153 " --> pdb=" O   LEU A 149 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 162 through 167
    Processing helix  chain 'A' and resid 168 through 196
      removed outlier: 3.636A  pdb=" N   ALA A 173 " --> pdb=" O   ILE A 169 " (cutoff:3.500A)
      Proline residue:  A 174  - end of helix
      removed outlier: 3.941A  pdb=" N   ASN A 181 " --> pdb=" O   LEU A 177 " (cutoff:3.500A)
      Proline residue:  A 182  - end of helix
    Processing helix  chain 'A' and resid 202 through 217
      removed outlier: 3.713A  pdb=" N   VAL A 214 " --> pdb=" O   GLY A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 217 through 233
      removed outlier: 3.556A  pdb=" N   PHE A 221 " --> pdb=" O   ASN A 217 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 238 through 250
      removed outlier: 4.194A  pdb=" N   ASN A 243 " --> pdb=" O   VAL A 239 " (cutoff:3.500A)
      removed outlier: 5.010A  pdb=" N   PHE A 244 " --> pdb=" O   TYR A 240 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 251 through 264
    Processing helix  chain 'A' and resid 272 through 288
    Processing helix  chain 'A' and resid 288 through 302
    Processing helix  chain 'A' and resid 306 through 320
      removed outlier: 3.659A  pdb=" N   HIS A 310 " --> pdb=" O   SER A 306 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 326 through 337
      removed outlier: 4.001A  pdb=" N   ALA A 330 " --> pdb=" O   ALA A 326 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 341 through 367
      removed outlier: 3.696A  pdb=" N   ALA A 355 " --> pdb=" O   THR A 351 " (cutoff:3.500A)
      Proline residue:  A 356  - end of helix
    Processing helix  chain 'B' and resid 41 through 62
    Processing helix  chain 'B' and resid 66 through 80
      removed outlier: 3.786A  pdb=" N   LYS B  71 " --> pdb=" O   SER B  67 " (cutoff:3.500A)
      removed outlier: 4.264A  pdb=" N   GLY B  72 " --> pdb=" O   THR B  68 " (cutoff:3.500A)
      removed outlier: 3.946A  pdb=" N   LEU B  73 " --> pdb=" O   GLN B  69 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 80 through 93
      removed outlier: 3.506A  pdb=" N   LEU B  93 " --> pdb=" O   ASN B  89 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 99 through 125
      removed outlier: 3.847A  pdb=" N   LEU B 103 " --> pdb=" O   ASP B  99 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 126 through 128
      No H-bonds generated for 'chain 'B' and resid 126 through 128'
    Processing helix  chain 'B' and resid 129 through 141
      Proline residue:  B 138  - end of helix
    Processing helix  chain 'B' and resid 149 through 158
      removed outlier: 3.708A  pdb=" N   ILE B 153 " --> pdb=" O   LEU B 149 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 162 through 167
    Processing helix  chain 'B' and resid 168 through 195
      removed outlier: 3.591A  pdb=" N   ALA B 173 " --> pdb=" O   ILE B 169 " (cutoff:3.500A)
      Proline residue:  B 174  - end of helix
      removed outlier: 4.062A  pdb=" N   ASN B 181 " --> pdb=" O   LEU B 177 " (cutoff:3.500A)
      Proline residue:  B 182  - end of helix
    Processing helix  chain 'B' and resid 202 through 217
      removed outlier: 3.685A  pdb=" N   VAL B 214 " --> pdb=" O   GLY B 210 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 217 through 233
      removed outlier: 3.843A  pdb=" N   VAL B 223 " --> pdb=" O   ILE B 219 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 238 through 249
      removed outlier: 4.142A  pdb=" N   ASN B 243 " --> pdb=" O   VAL B 239 " (cutoff:3.500A)
      removed outlier: 4.731A  pdb=" N   PHE B 244 " --> pdb=" O   TYR B 240 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 251 through 264
      removed outlier: 3.643A  pdb=" N   SER B 255 " --> pdb=" O   SER B 251 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 272 through 288
    Processing helix  chain 'B' and resid 288 through 301
    Processing helix  chain 'B' and resid 306 through 320
      removed outlier: 3.716A  pdb=" N   HIS B 310 " --> pdb=" O   SER B 306 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 326 through 337
      removed outlier: 3.916A  pdb=" N   ALA B 330 " --> pdb=" O   ALA B 326 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 341 through 367
      removed outlier: 3.590A  pdb=" N   SER B 345 " --> pdb=" O   GLU B 341 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   ALA B 355 " --> pdb=" O   THR B 351 " (cutoff:3.500A)
      Proline residue:  B 356  - end of helix

    368 hydrogen bonds defined for protein.
    1086 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: 1.48

  Time building geometry restraints manager: 1.96 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.19 -     1.31: 806
        1.31 -     1.44: 1489
        1.44 -     1.56: 3477
        1.56 -     1.68: 22
        1.68 -     1.81: 50
  Bond restraints: 5844
  Sorted by residual:
  bond pdb=" C   PRO B 138 "
       pdb=" O   PRO B 138 "
    ideal  model  delta    sigma   weight residual
    1.237  1.186  0.051 1.16e-02 7.43e+03 1.94e+01
  bond pdb=" C   PRO A 138 "
       pdb=" O   PRO A 138 "
    ideal  model  delta    sigma   weight residual
    1.238  1.187  0.050 1.24e-02 6.50e+03 1.64e+01
  bond pdb=" N   PHE A 137 "
       pdb=" CA  PHE A 137 "
    ideal  model  delta    sigma   weight residual
    1.459  1.490 -0.031 1.04e-02 9.25e+03 8.86e+00
  bond pdb=" C   ASN A 202 "
       pdb=" O   ASN A 202 "
    ideal  model  delta    sigma   weight residual
    1.233  1.196  0.037 1.30e-02 5.92e+03 8.02e+00
  bond pdb=" N   ILE A 139 "
       pdb=" CA  ILE A 139 "
    ideal  model  delta    sigma   weight residual
    1.460  1.493 -0.033 1.19e-02 7.06e+03 7.59e+00
  ... (remaining 5839 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.99: 7641
        1.99 -     3.97: 150
        3.97 -     5.96: 29
        5.96 -     7.94: 3
        7.94 -     9.93: 1
  Bond angle restraints: 7824
  Sorted by residual:
  angle pdb=" CA  ASN A 202 "
        pdb=" C   ASN A 202 "
        pdb=" O   ASN A 202 "
      ideal   model   delta    sigma   weight residual
     121.65  116.07    5.58 1.17e+00 7.31e-01 2.27e+01
  angle pdb=" CA  PRO B 127 "
        pdb=" N   PRO B 127 "
        pdb=" CD  PRO B 127 "
      ideal   model   delta    sigma   weight residual
     112.00  106.20    5.80 1.40e+00 5.10e-01 1.72e+01
  angle pdb=" CA  SER A 200 "
        pdb=" C   SER A 200 "
        pdb=" O   SER A 200 "
      ideal   model   delta    sigma   weight residual
     121.66  117.00    4.66 1.17e+00 7.31e-01 1.59e+01
  angle pdb=" CA  ASN A 202 "
        pdb=" C   ASN A 202 "
        pdb=" N   LYS A 203 "
      ideal   model   delta    sigma   weight residual
     115.67  120.32   -4.65 1.23e+00 6.61e-01 1.43e+01
  angle pdb=" CA  LYS B 303 "
        pdb=" CB  LYS B 303 "
        pdb=" CG  LYS B 303 "
      ideal   model   delta    sigma   weight residual
     114.10  121.04   -6.94 2.00e+00 2.50e-01 1.20e+01
  ... (remaining 7819 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    32.74: 3393
       32.74 -    65.48: 220
       65.48 -    98.23: 11
       98.23 -   130.97: 0
      130.97 -   163.71: 2
  Dihedral angle restraints: 3626
    sinusoidal: 1678
      harmonic: 1948
  Sorted by residual:
  dihedral pdb=" O21 3PE A 404 "
           pdb=" C2  3PE A 404 "
           pdb=" C3  3PE A 404 "
           pdb=" O31 3PE A 404 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.47 -103.24  163.71     1      3.00e+01 1.11e-03 2.09e+01
  dihedral pdb=" O21 3PE B 404 "
           pdb=" C2  3PE B 404 "
           pdb=" C3  3PE B 404 "
           pdb=" O31 3PE B 404 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.47 -102.81  163.28     1      3.00e+01 1.11e-03 2.09e+01
  dihedral pdb=" CB  GLU B 339 "
           pdb=" CG  GLU B 339 "
           pdb=" CD  GLU B 339 "
           pdb=" OE1 GLU B 339 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -88.31   88.31     1      3.00e+01 1.11e-03 1.04e+01
  ... (remaining 3623 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 628
       0.042 -    0.083: 196
       0.083 -    0.124: 50
       0.124 -    0.166: 5
       0.166 -    0.207: 3
  Chirality restraints: 882
  Sorted by residual:
  chirality pdb=" CA  ILE A 139 "
            pdb=" N   ILE A 139 "
            pdb=" C   ILE A 139 "
            pdb=" CB  ILE A 139 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.64   -0.21 2.00e-01 2.50e+01 1.08e+00
  chirality pdb=" CA  ILE B 139 "
            pdb=" N   ILE B 139 "
            pdb=" C   ILE B 139 "
            pdb=" CB  ILE B 139 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.63   -0.20 2.00e-01 2.50e+01 9.60e-01
  chirality pdb=" CA  LEU B 107 "
            pdb=" N   LEU B 107 "
            pdb=" C   LEU B 107 "
            pdb=" CB  LEU B 107 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 6.97e-01
  ... (remaining 879 not shown)

  Planarity restraints: 908
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER B 126 "    0.082 5.00e-02 4.00e+02   1.21e-01 2.35e+01
        pdb=" N   PRO B 127 "   -0.209 5.00e-02 4.00e+02
        pdb=" CA  PRO B 127 "    0.064 5.00e-02 4.00e+02
        pdb=" CD  PRO B 127 "    0.064 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 126 "    0.042 5.00e-02 4.00e+02   6.39e-02 6.52e+00
        pdb=" N   PRO A 127 "   -0.110 5.00e-02 4.00e+02
        pdb=" CA  PRO A 127 "    0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO A 127 "    0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN A 337 "   -0.010 2.00e-02 2.50e+03   1.93e-02 3.71e+00
        pdb=" C   ASN A 337 "    0.033 2.00e-02 2.50e+03
        pdb=" O   ASN A 337 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   MET A 338 "   -0.011 2.00e-02 2.50e+03
  ... (remaining 905 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1159
        2.78 -     3.31: 5629
        3.31 -     3.84: 9757
        3.84 -     4.37: 12022
        4.37 -     4.90: 20189
  Nonbonded interactions: 48756
  Sorted by model distance:
  nonbonded pdb=" O   VAL B 172 "
            pdb=" OG  SER B 176 "
     model   vdw
     2.248 3.040
  nonbonded pdb=" O   VAL B  91 "
            pdb=" ND2 ASN B 230 "
     model   vdw
     2.321 3.120
  nonbonded pdb=" O   VAL A  91 "
            pdb=" ND2 ASN A 230 "
     model   vdw
     2.348 3.120
  nonbonded pdb=" O   VAL A 340 "
            pdb=" OG1 THR A 344 "
     model   vdw
     2.362 3.040
  nonbonded pdb=" O   SER A 101 "
            pdb=" OG  SER A 105 "
     model   vdw
     2.366 3.040
  ... (remaining 48751 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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:             3.950
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.050
  Set scattering table:                    0.050
  Process input model:                     20.640
  Find NCS groups from input model:        0.200
  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:             0.010
  Load rotamer database and sin/cos tables:13.700
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.860
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7644
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   0.094   5844  Z= 0.205
  Angle     :  0.684   9.929   7824  Z= 0.401
  Chirality :  0.043   0.207    882
  Planarity :  0.007   0.121    908
  Dihedral  : 19.284 163.710   2370
  Min Nonbonded Distance : 2.248

Molprobity Statistics.
  All-atom Clashscore : 9.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.90 %
    Favored  : 99.10 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 20.93 %
    Favored  : 77.51 %
  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:  0.77 (0.33), residues: 664
  helix:  0.93 (0.24), residues: 500
  sheet:  None (None), residues: 0
  loop : -0.59 (0.50), residues: 164

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 363 
 HIS   0.007   0.003   HIS A 310 
 PHE   0.018   0.001   PHE B 102 
 TYR   0.009   0.001   TYR B 316 
 ARG   0.006   0.001   ARG B  79 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15565 (  368)
  hydrogen bonds       : angle       6.22503 ( 1086)
  covalent geometry    : bond        0.00362 ( 5844)
  covalent geometry    : angle       0.68450 ( 7824)

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

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

  1328 Ramachandran restraints generated.
    664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1328 Ramachandran restraints generated.
    664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 94
  time to evaluate  : 0.549 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  293 LEU cc_start: 0.8168 (mp) cc_final: 0.7927 (mt)
REVERT: B  293 LEU cc_start: 0.8205 (mp) cc_final: 0.7885 (mt)
  outliers start: 9
  outliers final: 7
  residues processed: 102
  average time/residue: 0.9196
  time to fit residues: 99.3488
Evaluate side-chains
  92 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 85
  time to evaluate  : 0.603 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain A residue  351 THR
Chi-restraints excluded: chain B residue   92 VAL
Chi-restraints excluded: chain B residue  177 LEU
Chi-restraints excluded: chain B residue  180 LEU
Chi-restraints excluded: chain B residue  223 VAL
Chi-restraints excluded: chain B residue  351 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 55 optimal weight:    1.9990
   chunk 50 optimal weight:    2.9990
   chunk 27 optimal weight:    5.9990
   chunk 17 optimal weight:    0.6980
   chunk 33 optimal weight:    2.9990
   chunk 26 optimal weight:    0.5980
   chunk 51 optimal weight:    0.9990
   chunk 20 optimal weight:    0.6980
   chunk 31 optimal weight:    0.9980
   chunk 38 optimal weight:    0.6980
   chunk 59 optimal weight:    0.8980
   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 = 0.4199 r_free = 0.4199 target = 0.190218 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.160517 restraints weight = 5958.626|
|-----------------------------------------------------------------------------|
r_work (start): 0.3873 rms_B_bonded: 1.42
r_work: 0.3687 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.3541 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.3541
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7842
moved from start:          0.1289

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.067   5844  Z= 0.170
  Angle     :  0.638   7.696   7824  Z= 0.312
  Chirality :  0.044   0.179    882
  Planarity :  0.006   0.070    908
  Dihedral  : 18.209 134.676   1199
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 10.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.36 %
    Favored  : 98.64 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 17.65 %
    Favored  : 78.72 %
  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:  0.85 (0.33), residues: 664
  helix:  0.84 (0.23), residues: 512
  sheet:  None (None), residues: 0
  loop : -0.05 (0.53), residues: 152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 363 
 HIS   0.003   0.001   HIS A 310 
 PHE   0.029   0.002   PHE B 221 
 TYR   0.011   0.002   TYR A 170 
 ARG   0.004   0.001   ARG B  79 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04836 (  368)
  hydrogen bonds       : angle       5.08604 ( 1086)
  covalent geometry    : bond        0.00414 ( 5844)
  covalent geometry    : angle       0.63821 ( 7824)

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

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

  1328 Ramachandran restraints generated.
    664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1328 Ramachandran restraints generated.
    664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 88
  time to evaluate  : 0.621 
Fit side-chains
   revert: symmetry clash
REVERT: A  194 LYS cc_start: 0.7990 (mtpt) cc_final: 0.7484 (ptpp)
REVERT: A  295 ARG cc_start: 0.7545 (mtp180) cc_final: 0.7335 (ttm-80)
REVERT: B  338 MET cc_start: 0.6614 (OUTLIER) cc_final: 0.6155 (ptp)
  outliers start: 21
  outliers final: 10
  residues processed: 99
  average time/residue: 1.1200
  time to fit residues: 116.3652
Evaluate side-chains
  88 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 77
  time to evaluate  : 0.595 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  126 SER
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  253 SER
Chi-restraints excluded: chain A residue  288 LEU
Chi-restraints excluded: chain B residue  120 LEU
Chi-restraints excluded: chain B residue  129 SER
Chi-restraints excluded: chain B residue  180 LEU
Chi-restraints excluded: chain B residue  223 VAL
Chi-restraints excluded: chain B residue  239 VAL
Chi-restraints excluded: chain B residue  338 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 65 optimal weight:    0.5980
   chunk 19 optimal weight:    0.9990
   chunk 46 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9990
   chunk 11 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9990
   chunk 23 optimal weight:    0.5980
   chunk 43 optimal weight:    0.6980
   chunk 49 optimal weight:    0.0970
   chunk 42 optimal weight:    0.2980
   chunk 48 optimal weight:    0.6980
   overall best weight:    0.4578

-------------------------------------------------------------------------------
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 = 0.4219 r_free = 0.4219 target = 0.192476 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.162623 restraints weight = 5970.428|
|-----------------------------------------------------------------------------|
r_work (start): 0.3892 rms_B_bonded: 1.44
r_work: 0.3709 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.3564 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.3564
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7808
moved from start:          0.1416

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   5844  Z= 0.135
  Angle     :  0.589   6.163   7824  Z= 0.288
  Chirality :  0.042   0.174    882
  Planarity :  0.005   0.058    908
  Dihedral  : 17.615 119.471   1193
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 9.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.75 %
    Favored  : 99.25 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 18.17 %
    Favored  : 78.72 %
  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:  1.08 (0.33), residues: 664
  helix:  1.03 (0.23), residues: 510
  sheet:  None (None), residues: 0
  loop : -0.05 (0.50), residues: 154

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 363 
 HIS   0.004   0.002   HIS A 310 
 PHE   0.026   0.002   PHE B 221 
 TYR   0.009   0.001   TYR A 170 
 ARG   0.002   0.000   ARG B  79 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04225 (  368)
  hydrogen bonds       : angle       4.84119 ( 1086)
  covalent geometry    : bond        0.00321 ( 5844)
  covalent geometry    : angle       0.58899 ( 7824)

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

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

  1328 Ramachandran restraints generated.
    664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1328 Ramachandran restraints generated.
    664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 93
  time to evaluate  : 0.607 
Fit side-chains
   revert: symmetry clash
REVERT: A  194 LYS cc_start: 0.7914 (mtpt) cc_final: 0.7633 (ptpp)
REVERT: A  205 LYS cc_start: 0.7090 (OUTLIER) cc_final: 0.6740 (ttmm)
REVERT: B  194 LYS cc_start: 0.8229 (ptmt) cc_final: 0.7940 (ptmm)
REVERT: B  205 LYS cc_start: 0.7231 (OUTLIER) cc_final: 0.6912 (ttmm)
REVERT: B  295 ARG cc_start: 0.7395 (mtp180) cc_final: 0.7148 (ttm-80)
REVERT: B  337 ASN cc_start: 0.8527 (t0) cc_final: 0.8292 (t0)
REVERT: B  338 MET cc_start: 0.6408 (OUTLIER) cc_final: 0.5984 (ptp)
  outliers start: 18
  outliers final: 8
  residues processed: 102
  average time/residue: 0.9906
  time to fit residues: 106.6708
Evaluate side-chains
  92 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 81
  time to evaluate  : 0.568 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  205 LYS
Chi-restraints excluded: chain A residue  288 LEU
Chi-restraints excluded: chain A residue  338 MET
Chi-restraints excluded: chain B residue   92 VAL
Chi-restraints excluded: chain B residue  120 LEU
Chi-restraints excluded: chain B residue  129 SER
Chi-restraints excluded: chain B residue  205 LYS
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain B residue  288 LEU
Chi-restraints excluded: chain B residue  338 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 17 optimal weight:    0.8980
   chunk 39 optimal weight:    3.9990
   chunk 19 optimal weight:    0.7980
   chunk 8 optimal weight:    0.8980
   chunk 11 optimal weight:    0.7980
   chunk 25 optimal weight:    0.0980
   chunk 27 optimal weight:    8.9990
   chunk 38 optimal weight:    0.9990
   chunk 49 optimal weight:    0.0070
   chunk 26 optimal weight:    0.8980
   chunk 35 optimal weight:    1.9990
   overall best weight:    0.5198

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

Flipped N/Q/H residues before XYZ refinement:
B 230 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4211 r_free = 0.4211 target = 0.191510 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.161196 restraints weight = 6117.473|
|-----------------------------------------------------------------------------|
r_work (start): 0.3885 rms_B_bonded: 1.48
r_work: 0.3700 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work: 0.3553 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.3553
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7820
moved from start:          0.1639

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058   5844  Z= 0.142
  Angle     :  0.601   7.663   7824  Z= 0.292
  Chirality :  0.043   0.157    882
  Planarity :  0.005   0.057    908
  Dihedral  : 17.481 117.062   1190
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 9.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.20 %
    Favored  : 98.80 %
  Rotamer:
    Outliers :  3.81 %
    Allowed  : 19.20 %
    Favored  : 76.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.05 (0.32), residues: 664
  helix:  1.00 (0.23), residues: 512
  sheet:  None (None), residues: 0
  loop : -0.07 (0.50), residues: 152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 363 
 HIS   0.001   0.001   HIS A 310 
 PHE   0.028   0.002   PHE B 221 
 TYR   0.009   0.001   TYR B 170 
 ARG   0.004   0.000   ARG A 130 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04218 (  368)
  hydrogen bonds       : angle       4.83778 ( 1086)
  covalent geometry    : bond        0.00341 ( 5844)
  covalent geometry    : angle       0.60141 ( 7824)

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

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

  1328 Ramachandran restraints generated.
    664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1328 Ramachandran restraints generated.
    664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 84
  time to evaluate  : 0.544 
Fit side-chains
   revert: symmetry clash
REVERT: A  194 LYS cc_start: 0.7907 (mtpt) cc_final: 0.7698 (ptpp)
REVERT: A  217 ASN cc_start: 0.7300 (OUTLIER) cc_final: 0.6999 (t0)
REVERT: A  347 MET cc_start: 0.7836 (OUTLIER) cc_final: 0.7325 (ttm)
REVERT: B  129 SER cc_start: 0.8381 (OUTLIER) cc_final: 0.8038 (m)
REVERT: B  194 LYS cc_start: 0.8257 (ptmt) cc_final: 0.7983 (ptmm)
REVERT: B  205 LYS cc_start: 0.7327 (OUTLIER) cc_final: 0.6982 (ttmm)
REVERT: B  272 LYS cc_start: 0.8124 (OUTLIER) cc_final: 0.7736 (mttt)
REVERT: B  338 MET cc_start: 0.6325 (OUTLIER) cc_final: 0.5675 (ptp)
REVERT: B  347 MET cc_start: 0.7859 (OUTLIER) cc_final: 0.7446 (ttm)
  outliers start: 22
  outliers final: 11
  residues processed: 95
  average time/residue: 1.1550
  time to fit residues: 114.9783
Evaluate side-chains
  98 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 80
  time to evaluate  : 0.609 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  217 ASN
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  253 SER
Chi-restraints excluded: chain A residue  288 LEU
Chi-restraints excluded: chain A residue  338 MET
Chi-restraints excluded: chain A residue  347 MET
Chi-restraints excluded: chain B residue   92 VAL
Chi-restraints excluded: chain B residue  120 LEU
Chi-restraints excluded: chain B residue  129 SER
Chi-restraints excluded: chain B residue  205 LYS
Chi-restraints excluded: chain B residue  223 VAL
Chi-restraints excluded: chain B residue  239 VAL
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain B residue  272 LYS
Chi-restraints excluded: chain B residue  288 LEU
Chi-restraints excluded: chain B residue  338 MET
Chi-restraints excluded: chain B residue  347 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 6 optimal weight:    4.9990
   chunk 9 optimal weight:    3.9990
   chunk 54 optimal weight:    1.9990
   chunk 50 optimal weight:    0.6980
   chunk 49 optimal weight:    0.0370
   chunk 11 optimal weight:    0.8980
   chunk 27 optimal weight:    0.7980
   chunk 65 optimal weight:    2.9990
   chunk 46 optimal weight:    0.5980
   chunk 16 optimal weight:    0.9980
   chunk 62 optimal weight:    0.7980
   overall best weight:    0.5858

-------------------------------------------------------------------------------
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 = 0.4207 r_free = 0.4207 target = 0.191100 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.160697 restraints weight = 5977.295|
|-----------------------------------------------------------------------------|
r_work (start): 0.3876 rms_B_bonded: 1.46
r_work: 0.3691 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.3544 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.3544
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7833
moved from start:          0.1760

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062   5844  Z= 0.147
  Angle     :  0.604   6.938   7824  Z= 0.294
  Chirality :  0.043   0.161    882
  Planarity :  0.005   0.056    908
  Dihedral  : 17.381 113.578   1190
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 9.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.75 %
    Favored  : 99.25 %
  Rotamer:
    Outliers :  5.02 %
    Allowed  : 18.34 %
    Favored  : 76.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.98 (0.32), residues: 664
  helix:  0.96 (0.23), residues: 512
  sheet:  None (None), residues: 0
  loop : -0.10 (0.50), residues: 152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 363 
 HIS   0.001   0.000   HIS B 310 
 PHE   0.030   0.002   PHE B 221 
 TYR   0.009   0.002   TYR B 170 
 ARG   0.005   0.000   ARG B  79 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04277 (  368)
  hydrogen bonds       : angle       4.81362 ( 1086)
  covalent geometry    : bond        0.00357 ( 5844)
  covalent geometry    : angle       0.60425 ( 7824)

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

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

  1328 Ramachandran restraints generated.
    664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1328 Ramachandran restraints generated.
    664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 82
  time to evaluate  : 0.563 
Fit side-chains
   revert: symmetry clash
REVERT: A  217 ASN cc_start: 0.7311 (OUTLIER) cc_final: 0.7024 (t0)
REVERT: A  347 MET cc_start: 0.7874 (OUTLIER) cc_final: 0.7347 (ttm)
REVERT: B  129 SER cc_start: 0.8401 (OUTLIER) cc_final: 0.8061 (m)
REVERT: B  194 LYS cc_start: 0.8271 (ptmt) cc_final: 0.8028 (ptmm)
REVERT: B  205 LYS cc_start: 0.7312 (OUTLIER) cc_final: 0.6960 (ttmm)
REVERT: B  272 LYS cc_start: 0.8116 (OUTLIER) cc_final: 0.7713 (mttt)
REVERT: B  338 MET cc_start: 0.6234 (OUTLIER) cc_final: 0.5599 (ptp)
REVERT: B  347 MET cc_start: 0.7844 (OUTLIER) cc_final: 0.7401 (ttm)
  outliers start: 29
  outliers final: 14
  residues processed: 95
  average time/residue: 1.2289
  time to fit residues: 122.6916
Evaluate side-chains
  100 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 79
  time to evaluate  : 0.560 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  217 ASN
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  253 SER
Chi-restraints excluded: chain A residue  288 LEU
Chi-restraints excluded: chain A residue  338 MET
Chi-restraints excluded: chain A residue  347 MET
Chi-restraints excluded: chain B residue   92 VAL
Chi-restraints excluded: chain B residue  120 LEU
Chi-restraints excluded: chain B residue  129 SER
Chi-restraints excluded: chain B residue  180 LEU
Chi-restraints excluded: chain B residue  205 LYS
Chi-restraints excluded: chain B residue  223 VAL
Chi-restraints excluded: chain B residue  239 VAL
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain B residue  272 LYS
Chi-restraints excluded: chain B residue  288 LEU
Chi-restraints excluded: chain B residue  295 ARG
Chi-restraints excluded: chain B residue  338 MET
Chi-restraints excluded: chain B residue  347 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 33 optimal weight:    1.9990
   chunk 46 optimal weight:    0.5980
   chunk 55 optimal weight:    1.9990
   chunk 6 optimal weight:    3.9990
   chunk 21 optimal weight:    0.9980
   chunk 22 optimal weight:    0.2980
   chunk 43 optimal weight:    0.5980
   chunk 52 optimal weight:    1.9990
   chunk 9 optimal weight:    2.9990
   chunk 58 optimal weight:    0.5980
   chunk 5 optimal weight:    0.6980
   overall best weight:    0.5580

-------------------------------------------------------------------------------
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 = 0.4206 r_free = 0.4206 target = 0.190969 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.160554 restraints weight = 6012.539|
|-----------------------------------------------------------------------------|
r_work (start): 0.3876 rms_B_bonded: 1.47
r_work: 0.3692 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.3545 rms_B_bonded: 4.94 restraints_weight: 0.2500
r_work (final): 0.3545
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7831
moved from start:          0.1872

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061   5844  Z= 0.143
  Angle     :  0.605   8.466   7824  Z= 0.294
  Chirality :  0.043   0.161    882
  Planarity :  0.005   0.055    908
  Dihedral  : 17.156 110.194   1190
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 9.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.05 %
    Favored  : 98.95 %
  Rotamer:
    Outliers :  4.33 %
    Allowed  : 19.55 %
    Favored  : 76.12 %
  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:  1.05 (0.32), residues: 664
  helix:  1.01 (0.23), residues: 512
  sheet:  None (None), residues: 0
  loop : -0.09 (0.50), residues: 152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 363 
 HIS   0.001   0.000   HIS B 310 
 PHE   0.029   0.002   PHE B 221 
 TYR   0.009   0.001   TYR B 170 
 ARG   0.005   0.000   ARG B  79 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04203 (  368)
  hydrogen bonds       : angle       4.80272 ( 1086)
  covalent geometry    : bond        0.00345 ( 5844)
  covalent geometry    : angle       0.60530 ( 7824)

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

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

  1328 Ramachandran restraints generated.
    664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1328 Ramachandran restraints generated.
    664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 82
  time to evaluate  : 0.956 
Fit side-chains
   revert: symmetry clash
REVERT: A  194 LYS cc_start: 0.7924 (mtpt) cc_final: 0.7716 (ptpp)
REVERT: A  217 ASN cc_start: 0.7281 (OUTLIER) cc_final: 0.7026 (t0)
REVERT: A  264 MET cc_start: 0.8028 (mtm) cc_final: 0.7726 (mtt)
REVERT: A  347 MET cc_start: 0.7871 (OUTLIER) cc_final: 0.7345 (ttm)
REVERT: B  129 SER cc_start: 0.8371 (OUTLIER) cc_final: 0.8029 (m)
REVERT: B  194 LYS cc_start: 0.8276 (ptmt) cc_final: 0.8063 (ptmm)
REVERT: B  205 LYS cc_start: 0.7280 (OUTLIER) cc_final: 0.6932 (ttmm)
REVERT: B  272 LYS cc_start: 0.8144 (OUTLIER) cc_final: 0.7727 (mttt)
REVERT: B  338 MET cc_start: 0.6201 (OUTLIER) cc_final: 0.5670 (ptp)
REVERT: B  347 MET cc_start: 0.7823 (OUTLIER) cc_final: 0.7390 (ttm)
  outliers start: 25
  outliers final: 14
  residues processed: 95
  average time/residue: 2.0317
  time to fit residues: 203.3876
Evaluate side-chains
  99 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 78
  time to evaluate  : 0.496 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  217 ASN
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  253 SER
Chi-restraints excluded: chain A residue  288 LEU
Chi-restraints excluded: chain A residue  338 MET
Chi-restraints excluded: chain A residue  347 MET
Chi-restraints excluded: chain B residue   92 VAL
Chi-restraints excluded: chain B residue  120 LEU
Chi-restraints excluded: chain B residue  129 SER
Chi-restraints excluded: chain B residue  180 LEU
Chi-restraints excluded: chain B residue  205 LYS
Chi-restraints excluded: chain B residue  223 VAL
Chi-restraints excluded: chain B residue  239 VAL
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain B residue  272 LYS
Chi-restraints excluded: chain B residue  288 LEU
Chi-restraints excluded: chain B residue  295 ARG
Chi-restraints excluded: chain B residue  338 MET
Chi-restraints excluded: chain B residue  347 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 31 optimal weight:    0.0770
   chunk 46 optimal weight:    0.9990
   chunk 62 optimal weight:    0.5980
   chunk 29 optimal weight:    0.2980
   chunk 9 optimal weight:    2.9990
   chunk 60 optimal weight:    4.9990
   chunk 26 optimal weight:    3.9990
   chunk 11 optimal weight:    0.8980
   chunk 63 optimal weight:    0.5980
   chunk 14 optimal weight:    0.4980
   chunk 21 optimal weight:    0.6980
   overall best weight:    0.4138

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

Flipped N/Q/H residues before XYZ refinement:
B 143 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4224 r_free = 0.4224 target = 0.192787 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.162676 restraints weight = 6028.322|
|-----------------------------------------------------------------------------|
r_work (start): 0.3898 rms_B_bonded: 1.46
r_work: 0.3714 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work: 0.3568 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.3568
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7803
moved from start:          0.1921

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   5844  Z= 0.129
  Angle     :  0.593   8.396   7824  Z= 0.288
  Chirality :  0.042   0.161    882
  Planarity :  0.005   0.055    908
  Dihedral  : 16.735 106.279   1190
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 9.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.90 %
    Favored  : 99.10 %
  Rotamer:
    Outliers :  4.50 %
    Allowed  : 19.03 %
    Favored  : 76.47 %
  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 (0.32), residues: 664
  helix:  1.14 (0.23), residues: 518
  sheet:  None (None), residues: 0
  loop : -0.11 (0.51), residues: 146

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 363 
 HIS   0.001   0.001   HIS A 310 
 PHE   0.028   0.002   PHE B 221 
 TYR   0.008   0.001   TYR A 170 
 ARG   0.006   0.001   ARG B  79 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03944 (  368)
  hydrogen bonds       : angle       4.68361 ( 1086)
  covalent geometry    : bond        0.00309 ( 5844)
  covalent geometry    : angle       0.59315 ( 7824)

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

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

  1328 Ramachandran restraints generated.
    664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1328 Ramachandran restraints generated.
    664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 84
  time to evaluate  : 0.583 
Fit side-chains
REVERT: A  347 MET cc_start: 0.7804 (OUTLIER) cc_final: 0.7298 (ttm)
REVERT: B  129 SER cc_start: 0.8330 (OUTLIER) cc_final: 0.7982 (m)
REVERT: B  143 GLN cc_start: 0.6840 (OUTLIER) cc_final: 0.6001 (tp-100)
REVERT: B  167 GLN cc_start: 0.7628 (OUTLIER) cc_final: 0.7402 (pt0)
REVERT: B  205 LYS cc_start: 0.7262 (OUTLIER) cc_final: 0.6938 (ttmm)
REVERT: B  272 LYS cc_start: 0.8128 (OUTLIER) cc_final: 0.7711 (mttt)
REVERT: B  338 MET cc_start: 0.6123 (OUTLIER) cc_final: 0.5576 (ptp)
  outliers start: 26
  outliers final: 12
  residues processed: 97
  average time/residue: 1.0836
  time to fit residues: 110.5334
Evaluate side-chains
  100 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 81
  time to evaluate  : 0.565 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  253 SER
Chi-restraints excluded: chain A residue  288 LEU
Chi-restraints excluded: chain A residue  338 MET
Chi-restraints excluded: chain A residue  347 MET
Chi-restraints excluded: chain B residue   92 VAL
Chi-restraints excluded: chain B residue  120 LEU
Chi-restraints excluded: chain B residue  129 SER
Chi-restraints excluded: chain B residue  143 GLN
Chi-restraints excluded: chain B residue  167 GLN
Chi-restraints excluded: chain B residue  205 LYS
Chi-restraints excluded: chain B residue  223 VAL
Chi-restraints excluded: chain B residue  239 VAL
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain B residue  272 LYS
Chi-restraints excluded: chain B residue  288 LEU
Chi-restraints excluded: chain B residue  295 ARG
Chi-restraints excluded: chain B residue  338 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 45 optimal weight:    0.9990
   chunk 41 optimal weight:    0.8980
   chunk 12 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 0 optimal weight:    1.9990
   chunk 3 optimal weight:    0.6980
   chunk 24 optimal weight:    1.9990
   chunk 15 optimal weight:    0.8980
   chunk 5 optimal weight:    0.6980
   chunk 51 optimal weight:    0.5980
   chunk 59 optimal weight:    0.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
B 143 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4199 r_free = 0.4199 target = 0.190078 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.159637 restraints weight = 5937.198|
|-----------------------------------------------------------------------------|
r_work (start): 0.3863 rms_B_bonded: 1.45
r_work: 0.3677 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.3529 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.3529
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7853
moved from start:          0.2103

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.071   5844  Z= 0.169
  Angle     :  0.645   8.863   7824  Z= 0.313
  Chirality :  0.044   0.175    882
  Planarity :  0.005   0.053    908
  Dihedral  : 16.893 106.139   1190
  Min Nonbonded Distance : 2.382

Molprobity Statistics.
  All-atom Clashscore : 10.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.36 %
    Favored  : 98.64 %
  Rotamer:
    Outliers :  3.98 %
    Allowed  : 19.72 %
    Favored  : 76.30 %
  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:  0.91 (0.32), residues: 664
  helix:  0.93 (0.23), residues: 510
  sheet:  None (None), residues: 0
  loop : -0.19 (0.49), residues: 154

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 363 
 HIS   0.001   0.001   HIS A 310 
 PHE   0.031   0.002   PHE B 221 
 TYR   0.010   0.002   TYR A 158 
 ARG   0.006   0.001   ARG B  79 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04395 (  368)
  hydrogen bonds       : angle       4.83957 ( 1086)
  covalent geometry    : bond        0.00417 ( 5844)
  covalent geometry    : angle       0.64480 ( 7824)

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

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

  1328 Ramachandran restraints generated.
    664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1328 Ramachandran restraints generated.
    664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 87
  time to evaluate  : 0.605 
Fit side-chains
   revert: symmetry clash
REVERT: A  264 MET cc_start: 0.8076 (mtm) cc_final: 0.7821 (mtt)
REVERT: A  347 MET cc_start: 0.7901 (OUTLIER) cc_final: 0.7339 (ttm)
REVERT: B  129 SER cc_start: 0.8366 (OUTLIER) cc_final: 0.8028 (m)
REVERT: B  143 GLN cc_start: 0.7008 (OUTLIER) cc_final: 0.6666 (tt0)
REVERT: B  205 LYS cc_start: 0.7241 (OUTLIER) cc_final: 0.6906 (ttmm)
REVERT: B  272 LYS cc_start: 0.8133 (OUTLIER) cc_final: 0.7709 (mttt)
REVERT: B  338 MET cc_start: 0.6228 (OUTLIER) cc_final: 0.5589 (ptp)
  outliers start: 23
  outliers final: 13
  residues processed: 99
  average time/residue: 1.1166
  time to fit residues: 116.0287
Evaluate side-chains
  99 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 80
  time to evaluate  : 0.624 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  144 SER
Chi-restraints excluded: chain A residue  253 SER
Chi-restraints excluded: chain A residue  288 LEU
Chi-restraints excluded: chain A residue  338 MET
Chi-restraints excluded: chain A residue  347 MET
Chi-restraints excluded: chain B residue   92 VAL
Chi-restraints excluded: chain B residue  120 LEU
Chi-restraints excluded: chain B residue  129 SER
Chi-restraints excluded: chain B residue  143 GLN
Chi-restraints excluded: chain B residue  205 LYS
Chi-restraints excluded: chain B residue  223 VAL
Chi-restraints excluded: chain B residue  239 VAL
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain B residue  272 LYS
Chi-restraints excluded: chain B residue  288 LEU
Chi-restraints excluded: chain B residue  295 ARG
Chi-restraints excluded: chain B residue  338 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 18 optimal weight:    0.0980
   chunk 28 optimal weight:    0.9980
   chunk 35 optimal weight:    1.9990
   chunk 27 optimal weight:    0.8980
   chunk 57 optimal weight:    0.7980
   chunk 5 optimal weight:    0.5980
   chunk 45 optimal weight:    0.6980
   chunk 2 optimal weight:    1.9990
   chunk 63 optimal weight:    0.7980
   chunk 17 optimal weight:    0.2980
   chunk 41 optimal weight:    0.9990
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
A 202 ASN
B 143 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4214 r_free = 0.4214 target = 0.191555 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.161092 restraints weight = 6081.203|
|-----------------------------------------------------------------------------|
r_work (start): 0.3879 rms_B_bonded: 1.47
r_work: 0.3695 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.3548 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.3548
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7828
moved from start:          0.2072

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058   5844  Z= 0.139
  Angle     :  0.603   6.460   7824  Z= 0.299
  Chirality :  0.043   0.170    882
  Planarity :  0.005   0.052    908
  Dihedral  : 16.555 103.710   1190
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 9.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.90 %
    Favored  : 99.10 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 20.59 %
    Favored  : 76.12 %
  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:  1.08 (0.32), residues: 664
  helix:  1.06 (0.23), residues: 510
  sheet:  None (None), residues: 0
  loop : -0.16 (0.50), residues: 154

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 363 
 HIS   0.001   0.001   HIS A 310 
 PHE   0.028   0.002   PHE B 221 
 TYR   0.008   0.001   TYR B 170 
 ARG   0.006   0.001   ARG B  79 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04100 (  368)
  hydrogen bonds       : angle       4.72185 ( 1086)
  covalent geometry    : bond        0.00336 ( 5844)
  covalent geometry    : angle       0.60283 ( 7824)

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

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

  1328 Ramachandran restraints generated.
    664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1328 Ramachandran restraints generated.
    664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 79
  time to evaluate  : 0.621 
Fit side-chains
   revert: symmetry clash
REVERT: A  264 MET cc_start: 0.8051 (mtm) cc_final: 0.7786 (mtp)
REVERT: A  347 MET cc_start: 0.7849 (OUTLIER) cc_final: 0.7333 (ttm)
REVERT: B  129 SER cc_start: 0.8335 (OUTLIER) cc_final: 0.7987 (m)
REVERT: B  143 GLN cc_start: 0.7003 (OUTLIER) cc_final: 0.6203 (tp-100)
REVERT: B  205 LYS cc_start: 0.7229 (OUTLIER) cc_final: 0.6899 (ttmm)
REVERT: B  272 LYS cc_start: 0.8139 (OUTLIER) cc_final: 0.7724 (mttt)
REVERT: B  338 MET cc_start: 0.6187 (OUTLIER) cc_final: 0.5576 (ptp)
  outliers start: 19
  outliers final: 13
  residues processed: 90
  average time/residue: 1.1358
  time to fit residues: 107.4112
Evaluate side-chains
  97 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 78
  time to evaluate  : 0.586 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  144 SER
Chi-restraints excluded: chain A residue  253 SER
Chi-restraints excluded: chain A residue  288 LEU
Chi-restraints excluded: chain A residue  338 MET
Chi-restraints excluded: chain A residue  347 MET
Chi-restraints excluded: chain B residue   92 VAL
Chi-restraints excluded: chain B residue  120 LEU
Chi-restraints excluded: chain B residue  129 SER
Chi-restraints excluded: chain B residue  143 GLN
Chi-restraints excluded: chain B residue  205 LYS
Chi-restraints excluded: chain B residue  223 VAL
Chi-restraints excluded: chain B residue  239 VAL
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain B residue  272 LYS
Chi-restraints excluded: chain B residue  288 LEU
Chi-restraints excluded: chain B residue  295 ARG
Chi-restraints excluded: chain B residue  338 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 59 optimal weight:    0.0980
   chunk 5 optimal weight:    0.7980
   chunk 23 optimal weight:    0.0070
   chunk 62 optimal weight:    0.4980
   chunk 34 optimal weight:    0.5980
   chunk 60 optimal weight:    0.7980
   chunk 9 optimal weight:    2.9990
   chunk 35 optimal weight:    0.1980
   chunk 58 optimal weight:    0.0370
   chunk 33 optimal weight:    0.8980
   chunk 57 optimal weight:    0.5980
   overall best weight:    0.1676

-------------------------------------------------------------------------------
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 = 0.4263 r_free = 0.4263 target = 0.196798 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.167289 restraints weight = 6068.723|
|-----------------------------------------------------------------------------|
r_work (start): 0.3947 rms_B_bonded: 1.46
r_work: 0.3765 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work (final): 0.3765
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7613
moved from start:          0.2199

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   5844  Z= 0.111
  Angle     :  0.580   8.005   7824  Z= 0.283
  Chirality :  0.041   0.166    882
  Planarity :  0.005   0.053    908
  Dihedral  : 15.851  98.387   1190
  Min Nonbonded Distance : 2.400

Molprobity Statistics.
  All-atom Clashscore : 9.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.05 %
    Favored  : 98.95 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 21.28 %
    Favored  : 76.12 %
  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:  1.49 (0.33), residues: 664
  helix:  1.31 (0.23), residues: 520
  sheet:  None (None), residues: 0
  loop :  0.04 (0.51), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 100 
 HIS   0.001   0.001   HIS A 310 
 PHE   0.023   0.001   PHE B 221 
 TYR   0.007   0.001   TYR B 165 
 ARG   0.006   0.001   ARG B  79 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03587 (  368)
  hydrogen bonds       : angle       4.50897 ( 1086)
  covalent geometry    : bond        0.00251 ( 5844)
  covalent geometry    : angle       0.58038 ( 7824)

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

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

  1328 Ramachandran restraints generated.
    664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1328 Ramachandran restraints generated.
    664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 88
  time to evaluate  : 0.557 
Fit side-chains
REVERT: A  264 MET cc_start: 0.7799 (mtm) cc_final: 0.7533 (mtp)
REVERT: B  155 GLU cc_start: 0.6813 (tp30) cc_final: 0.6383 (tp30)
REVERT: B  272 LYS cc_start: 0.8145 (OUTLIER) cc_final: 0.7842 (mttt)
REVERT: B  338 MET cc_start: 0.5897 (OUTLIER) cc_final: 0.5565 (ptp)
  outliers start: 15
  outliers final: 11
  residues processed: 98
  average time/residue: 1.0292
  time to fit residues: 106.2256
Evaluate side-chains
  95 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 82
  time to evaluate  : 0.625 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  253 SER
Chi-restraints excluded: chain A residue  288 LEU
Chi-restraints excluded: chain A residue  338 MET
Chi-restraints excluded: chain B residue  120 LEU
Chi-restraints excluded: chain B residue  223 VAL
Chi-restraints excluded: chain B residue  239 VAL
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain B residue  272 LYS
Chi-restraints excluded: chain B residue  288 LEU
Chi-restraints excluded: chain B residue  295 ARG
Chi-restraints excluded: chain B residue  338 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 14 optimal weight:    0.9980
   chunk 6 optimal weight:    3.9990
   chunk 24 optimal weight:    1.9990
   chunk 4 optimal weight:    0.6980
   chunk 61 optimal weight:    0.9990
   chunk 40 optimal weight:    0.1980
   chunk 64 optimal weight:    0.2980
   chunk 0 optimal weight:    3.9990
   chunk 1 optimal weight:    0.6980
   chunk 56 optimal weight:    0.0970
   chunk 13 optimal weight:    0.7980
   overall best weight:    0.3978

-------------------------------------------------------------------------------
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 = 0.4237 r_free = 0.4237 target = 0.193763 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.163750 restraints weight = 6075.282|
|-----------------------------------------------------------------------------|
r_work (start): 0.3914 rms_B_bonded: 1.46
r_work: 0.3731 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work: 0.3582 rms_B_bonded: 4.99 restraints_weight: 0.2500
r_work (final): 0.3582
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7795
moved from start:          0.2257

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   5844  Z= 0.129
  Angle     :  0.613  10.327   7824  Z= 0.299
  Chirality :  0.043   0.167    882
  Planarity :  0.005   0.051    908
  Dihedral  : 15.735  96.989   1190
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 10.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.20 %
    Favored  : 98.80 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 21.45 %
    Favored  : 75.78 %
  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 (0.32), residues: 664
  helix:  1.22 (0.23), residues: 518
  sheet:  None (None), residues: 0
  loop : -0.09 (0.51), residues: 146

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 363 
 HIS   0.009   0.003   HIS A 310 
 PHE   0.026   0.002   PHE B 221 
 TYR   0.009   0.001   TYR B 151 
 ARG   0.007   0.001   ARG B 130 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03934 (  368)
  hydrogen bonds       : angle       4.59198 ( 1086)
  covalent geometry    : bond        0.00306 ( 5844)
  covalent geometry    : angle       0.61313 ( 7824)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4712.57 seconds
wall clock time: 82 minutes 11.61 seconds (4931.61 seconds total)