Starting phenix.real_space_refine
on Wed Feb 12 02:08:52 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9cgx_45588/02_2025/9cgx_45588.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9cgx_45588/02_2025/9cgx_45588.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.97
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9cgx_45588/02_2025/9cgx_45588.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9cgx_45588/02_2025/9cgx_45588.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9cgx_45588/02_2025/9cgx_45588.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9cgx_45588/02_2025/9cgx_45588.cif"
  }
  resolution = 2.97
  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=   0.001
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
     S       6      5.16       5
     C    2142      2.51       5
     N     630      2.21       5
     O     642      1.98       5
     H    3540      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 6960
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1160
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 74, 1160
          Classifications: {'peptide': 74}
          Link IDs: {'PTRANS': 3, 'TRANS': 70}
    Chain: "B"
      Number of atoms: 1160
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 74, 1160
          Classifications: {'peptide': 74}
          Link IDs: {'PTRANS': 3, 'TRANS': 70}
    Chain: "C"
      Number of atoms: 1160
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 74, 1160
          Classifications: {'peptide': 74}
          Link IDs: {'PTRANS': 3, 'TRANS': 70}
    Chain: "D"
      Number of atoms: 1160
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 74, 1160
          Classifications: {'peptide': 74}
          Link IDs: {'PTRANS': 3, 'TRANS': 70}
    Chain: "E"
      Number of atoms: 1160
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 74, 1160
          Classifications: {'peptide': 74}
          Link IDs: {'PTRANS': 3, 'TRANS': 70}
    Chain: "F"
      Number of atoms: 1160
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 74, 1160
          Classifications: {'peptide': 74}
          Link IDs: {'PTRANS': 3, 'TRANS': 70}
  Time building chain proxies: 4.78, per 1000 atoms: 0.69
  Number of scatterers: 6960
  At special positions: 0
  Unit cell: (149.46, 76.32, 33.92, 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       6     16.00
     O     642      8.00
     N     630      7.00
     C    2142      6.00
     H    3540      1.00
    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: 1.70
  Conformation dependent library (CDL) restraints added in 621.3 milliseconds
  

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  780

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 20 sheets defined
      0.0% alpha, 44.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.71
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 308 through 310
      removed outlier: 6.762A  pdb=" N   ILE A 308 " --> pdb=" O   VAL C 309 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 313 through 314
    Processing sheet with id=AA3, first strand: chain 'A' and resid 317 through 322
    Processing sheet with id=AA4, first strand: chain 'A' and resid 328 through 330
    Processing sheet with id=AA5, first strand: chain 'A' and resid 336 through 340
      removed outlier: 6.649A  pdb=" N   VAL A 337 " --> pdb=" O   GLU C 338 " (cutoff:3.500A)
      removed outlier: 7.974A  pdb=" N   LYS C 340 " --> pdb=" O   VAL A 337 " (cutoff:3.500A)
      removed outlier: 6.480A  pdb=" N   VAL A 339 " --> pdb=" O   LYS C 340 " (cutoff:3.500A)
      removed outlier: 6.636A  pdb=" N   VAL C 337 " --> pdb=" O   GLU E 338 " (cutoff:3.500A)
      removed outlier: 8.059A  pdb=" N   LYS E 340 " --> pdb=" O   VAL C 337 " (cutoff:3.500A)
      removed outlier: 6.660A  pdb=" N   VAL C 339 " --> pdb=" O   LYS E 340 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'A' and resid 343 through 344
    Processing sheet with id=AA7, first strand: chain 'A' and resid 351 through 356
      removed outlier: 6.844A  pdb=" N   SER A 356 " --> pdb=" O   GLY C 355 " (cutoff:3.500A)
      removed outlier: 6.880A  pdb=" N   SER C 356 " --> pdb=" O   GLY E 355 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 359 through 362
    Processing sheet with id=AA9, first strand: chain 'A' and resid 369 through 371
      removed outlier: 6.444A  pdb=" N   LYS A 370 " --> pdb=" O   ILE C 371 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 374 through 378
    Processing sheet with id=AB2, first strand: chain 'B' and resid 308 through 310
      removed outlier: 6.680A  pdb=" N   ILE B 308 " --> pdb=" O   VAL D 309 " (cutoff:3.500A)
      removed outlier: 6.602A  pdb=" N   ILE D 308 " --> pdb=" O   VAL F 309 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB2
    Processing sheet with id=AB3, first strand: chain 'B' and resid 313 through 314
    Processing sheet with id=AB4, first strand: chain 'B' and resid 317 through 322
    Processing sheet with id=AB5, first strand: chain 'B' and resid 329 through 330
    Processing sheet with id=AB6, first strand: chain 'B' and resid 336 through 340
      removed outlier: 6.545A  pdb=" N   VAL B 337 " --> pdb=" O   GLU D 338 " (cutoff:3.500A)
      removed outlier: 8.041A  pdb=" N   LYS D 340 " --> pdb=" O   VAL B 337 " (cutoff:3.500A)
      removed outlier: 6.564A  pdb=" N   VAL B 339 " --> pdb=" O   LYS D 340 " (cutoff:3.500A)
      removed outlier: 6.544A  pdb=" N   VAL D 337 " --> pdb=" O   GLU F 338 " (cutoff:3.500A)
      removed outlier: 7.955A  pdb=" N   LYS F 340 " --> pdb=" O   VAL D 337 " (cutoff:3.500A)
      removed outlier: 6.493A  pdb=" N   VAL D 339 " --> pdb=" O   LYS F 340 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB6
    Processing sheet with id=AB7, first strand: chain 'B' and resid 343 through 347
      removed outlier: 6.325A  pdb=" N   LEU B 344 " --> pdb=" O   ASP D 345 " (cutoff:3.500A)
      removed outlier: 7.822A  pdb=" N   LYS D 347 " --> pdb=" O   LEU B 344 " (cutoff:3.500A)
      removed outlier: 6.471A  pdb=" N   PHE B 346 " --> pdb=" O   LYS D 347 " (cutoff:3.500A)
      removed outlier: 6.446A  pdb=" N   LEU D 344 " --> pdb=" O   ASP F 345 " (cutoff:3.500A)
      removed outlier: 7.921A  pdb=" N   LYS F 347 " --> pdb=" O   LEU D 344 " (cutoff:3.500A)
      removed outlier: 6.517A  pdb=" N   PHE D 346 " --> pdb=" O   LYS F 347 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB7
    Processing sheet with id=AB8, first strand: chain 'B' and resid 351 through 356
      removed outlier: 6.819A  pdb=" N   SER B 356 " --> pdb=" O   GLY D 355 " (cutoff:3.500A)
      removed outlier: 6.889A  pdb=" N   SER D 356 " --> pdb=" O   GLY F 355 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'B' and resid 359 through 362
    Processing sheet with id=AC1, first strand: chain 'B' and resid 369 through 371
    Processing sheet with id=AC2, first strand: chain 'B' and resid 369 through 371

    90 hydrogen bonds defined for protein.
    267 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: 2.44

  Time building geometry restraints manager: 1.95 seconds

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

  Histogram of bond lengths:
        0.95 -     1.12: 3534
        1.12 -     1.29: 576
        1.29 -     1.47: 1061
        1.47 -     1.64: 1837
        1.64 -     1.81: 6
  Bond restraints: 7014
  Sorted by residual:
  bond pdb=" N   VAL B 363 "
       pdb=" H   VAL B 363 "
    ideal  model  delta    sigma   weight residual
    0.860  1.010 -0.150 2.00e-02 2.50e+03 5.65e+01
  bond pdb=" N   GLY A 366 "
       pdb=" H   GLY A 366 "
    ideal  model  delta    sigma   weight residual
    0.860  1.010 -0.150 2.00e-02 2.50e+03 5.65e+01
  bond pdb=" N   VAL B 339 "
       pdb=" H   VAL B 339 "
    ideal  model  delta    sigma   weight residual
    0.860  1.010 -0.150 2.00e-02 2.50e+03 5.65e+01
  bond pdb=" N   LYS D 347 "
       pdb=" H   LYS D 347 "
    ideal  model  delta    sigma   weight residual
    0.860  1.010 -0.150 2.00e-02 2.50e+03 5.65e+01
  bond pdb=" N   SER E 324 "
       pdb=" H   SER E 324 "
    ideal  model  delta    sigma   weight residual
    0.860  1.010 -0.150 2.00e-02 2.50e+03 5.65e+01
  ... (remaining 7009 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.54: 10618
        2.54 -     5.07: 1645
        5.07 -     7.61: 487
        7.61 -    10.14: 24
       10.14 -    12.68: 6
  Bond angle restraints: 12780
  Sorted by residual:
  angle pdb=" CA  PHE E 346 "
        pdb=" CB  PHE E 346 "
        pdb=" CG  PHE E 346 "
      ideal   model   delta    sigma   weight residual
     113.80  121.32   -7.52 1.00e+00 1.00e+00 5.66e+01
  angle pdb=" CA  ASP A 358 "
        pdb=" CB  ASP A 358 "
        pdb=" CG  ASP A 358 "
      ideal   model   delta    sigma   weight residual
     112.60  118.57   -5.97 1.00e+00 1.00e+00 3.57e+01
  angle pdb=" CA  ASP B 358 "
        pdb=" CB  ASP B 358 "
        pdb=" CG  ASP B 358 "
      ideal   model   delta    sigma   weight residual
     112.60  118.55   -5.95 1.00e+00 1.00e+00 3.54e+01
  angle pdb=" CA  ASP B 345 "
        pdb=" CB  ASP B 345 "
        pdb=" CG  ASP B 345 "
      ideal   model   delta    sigma   weight residual
     112.60  118.51   -5.91 1.00e+00 1.00e+00 3.49e+01
  angle pdb=" CA  ASP C 345 "
        pdb=" CB  ASP C 345 "
        pdb=" CG  ASP C 345 "
      ideal   model   delta    sigma   weight residual
     112.60  118.35   -5.75 1.00e+00 1.00e+00 3.30e+01
  ... (remaining 12775 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.63: 2851
       17.63 -    35.25: 204
       35.25 -    52.88: 85
       52.88 -    70.50: 84
       70.50 -    88.13: 4
  Dihedral angle restraints: 3228
    sinusoidal: 1848
      harmonic: 1380
  Sorted by residual:
  dihedral pdb=" CA  LEU B 325 "
           pdb=" C   LEU B 325 "
           pdb=" N   GLY B 326 "
           pdb=" CA  GLY B 326 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.78  -29.22     0      5.00e+00 4.00e-02 3.41e+01
  dihedral pdb=" CA  LEU E 325 "
           pdb=" C   LEU E 325 "
           pdb=" N   GLY E 326 "
           pdb=" CA  GLY E 326 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.80  -29.20     0      5.00e+00 4.00e-02 3.41e+01
  dihedral pdb=" CA  LEU D 325 "
           pdb=" C   LEU D 325 "
           pdb=" N   GLY D 326 "
           pdb=" CA  GLY D 326 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.89  -29.11     0      5.00e+00 4.00e-02 3.39e+01
  ... (remaining 3225 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.056: 230
       0.056 -    0.113: 169
       0.113 -    0.169: 73
       0.169 -    0.225: 34
       0.225 -    0.282: 10
  Chirality restraints: 516
  Sorted by residual:
  chirality pdb=" CA  ARG C 379 "
            pdb=" N   ARG C 379 "
            pdb=" C   ARG C 379 "
            pdb=" CB  ARG C 379 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.23    0.28 2.00e-01 2.50e+01 1.98e+00
  chirality pdb=" CA  ARG F 349 "
            pdb=" N   ARG F 349 "
            pdb=" C   ARG F 349 "
            pdb=" CB  ARG F 349 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.65e+00
  chirality pdb=" CA  ARG D 379 "
            pdb=" N   ARG D 379 "
            pdb=" C   ARG D 379 "
            pdb=" CB  ARG D 379 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.64e+00
  ... (remaining 513 not shown)

  Planarity restraints: 1014
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE E 346 "   -0.168 2.00e-02 2.50e+03   1.18e-01 4.15e+02
        pdb=" CG  PHE E 346 "    0.167 2.00e-02 2.50e+03
        pdb=" CD1 PHE E 346 "   -0.030 2.00e-02 2.50e+03
        pdb=" CD2 PHE E 346 "    0.147 2.00e-02 2.50e+03
        pdb=" CE1 PHE E 346 "    0.064 2.00e-02 2.50e+03
        pdb=" CE2 PHE E 346 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ  PHE E 346 "    0.030 2.00e-02 2.50e+03
        pdb=" HD1 PHE E 346 "   -0.134 2.00e-02 2.50e+03
        pdb=" HD2 PHE E 346 "    0.107 2.00e-02 2.50e+03
        pdb=" HE1 PHE E 346 "    0.083 2.00e-02 2.50e+03
        pdb=" HE2 PHE E 346 "   -0.208 2.00e-02 2.50e+03
        pdb=" HZ  PHE E 346 "   -0.054 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 346 "   -0.101 2.00e-02 2.50e+03   5.35e-02 8.57e+01
        pdb=" CG  PHE B 346 "   -0.042 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 346 "    0.023 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 346 "    0.021 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 346 "   -0.011 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 346 "    0.028 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 346 "   -0.027 2.00e-02 2.50e+03
        pdb=" HD1 PHE B 346 "    0.107 2.00e-02 2.50e+03
        pdb=" HD2 PHE B 346 "    0.033 2.00e-02 2.50e+03
        pdb=" HE1 PHE B 346 "   -0.007 2.00e-02 2.50e+03
        pdb=" HE2 PHE B 346 "    0.046 2.00e-02 2.50e+03
        pdb=" HZ  PHE B 346 "   -0.071 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS D 330 "   -0.106 2.00e-02 2.50e+03   5.93e-02 7.91e+01
        pdb=" CG  HIS D 330 "    0.069 2.00e-02 2.50e+03
        pdb=" ND1 HIS D 330 "    0.039 2.00e-02 2.50e+03
        pdb=" CD2 HIS D 330 "    0.066 2.00e-02 2.50e+03
        pdb=" CE1 HIS D 330 "    0.021 2.00e-02 2.50e+03
        pdb=" NE2 HIS D 330 "    0.037 2.00e-02 2.50e+03
        pdb=" HD2 HIS D 330 "   -0.003 2.00e-02 2.50e+03
        pdb=" HE1 HIS D 330 "   -0.047 2.00e-02 2.50e+03
        pdb=" HE2 HIS D 330 "   -0.077 2.00e-02 2.50e+03
  ... (remaining 1011 not shown)

  Histogram of nonbonded interaction distances:
        1.56 -     2.17: 517
        2.17 -     2.77: 11836
        2.77 -     3.38: 18315
        3.38 -     3.99: 24527
        3.99 -     4.60: 34690
  Nonbonded interactions: 89885
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP C 314 "
            pdb=" HG  SER C 316 "
     model   vdw
     1.556 2.450
  nonbonded pdb=" OD1 ASP F 314 "
            pdb=" HG  SER F 316 "
     model   vdw
     1.568 2.450
  nonbonded pdb=" OD1 ASP B 314 "
            pdb=" HG  SER B 316 "
     model   vdw
     1.585 2.450
  nonbonded pdb=" OD1 ASP D 314 "
            pdb=" HG  SER D 316 "
     model   vdw
     1.593 2.450
  nonbonded pdb=" OD1 ASP E 314 "
            pdb=" HG  SER E 316 "
     model   vdw
     1.605 2.450
  ... (remaining 89880 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
}

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:             3.900
  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:             0.110
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     19.560
  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:             0.000
  Load rotamer database and sin/cos tables:13.230
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.380
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6155
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      :  0.011   0.037   3474  Z= 0.722
  Angle     :  2.027  12.677   4644  Z= 1.311
  Chirality :  0.094   0.282    516
  Planarity :  0.012   0.098    594
  Dihedral  : 13.192  88.128   1344
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 0.00
  Ramachandran Plot:
    Outliers :  2.78 %
    Allowed  :  4.86 %
    Favored  : 92.36 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  :  3.08 %
    Favored  : 94.10 %
  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: -2.56 (0.32), residues: 432
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.94 (0.24), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.016   0.004   HIS E 362 
 PHE   0.164   0.019   PHE E 346 
 TYR   0.060   0.020   TYR E 310 
 ARG   0.010   0.002   ARG F 349 

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

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

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 129
  time to evaluate  : 0.560 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  311 LYS cc_start: 0.8129 (tttt) cc_final: 0.7598 (ttmm)
REVERT: A  331 LYS cc_start: 0.8052 (mttt) cc_final: 0.7781 (mttp)
REVERT: A  338 GLU cc_start: 0.7369 (tt0) cc_final: 0.6876 (mm-30)
REVERT: A  342 GLU cc_start: 0.7462 (mt-10) cc_final: 0.6872 (mp0)
REVERT: A  369 LYS cc_start: 0.7903 (mttt) cc_final: 0.7614 (mmtp)
REVERT: B  321 LYS cc_start: 0.8203 (ttmt) cc_final: 0.7873 (mtpt)
REVERT: B  338 GLU cc_start: 0.7849 (tt0) cc_final: 0.7341 (mp0)
REVERT: B  342 GLU cc_start: 0.7027 (mt-10) cc_final: 0.6638 (mp0)
REVERT: B  348 ASP cc_start: 0.7879 (t0) cc_final: 0.7648 (t0)
REVERT: B  351 GLN cc_start: 0.7893 (mt0) cc_final: 0.7691 (mt0)
REVERT: B  373 THR cc_start: 0.7127 (m) cc_final: 0.6817 (p)
REVERT: B  379 ARG cc_start: 0.6423 (ttt180) cc_final: 0.5833 (ttp-110)
REVERT: C  315 LEU cc_start: 0.8292 (mt) cc_final: 0.8069 (mm)
REVERT: C  321 LYS cc_start: 0.7320 (mtmt) cc_final: 0.7071 (mtpt)
REVERT: C  338 GLU cc_start: 0.7060 (tt0) cc_final: 0.6805 (tt0)
REVERT: C  340 LYS cc_start: 0.7668 (mtmt) cc_final: 0.7024 (tptp)
REVERT: C  345 ASP cc_start: 0.7836 (m-30) cc_final: 0.7597 (m-30)
REVERT: C  349 ARG cc_start: 0.6841 (mtm180) cc_final: 0.6505 (mtp85)
REVERT: C  369 LYS cc_start: 0.7169 (mttt) cc_final: 0.6521 (mtpt)
REVERT: D  315 LEU cc_start: 0.8368 (mt) cc_final: 0.7936 (mm)
REVERT: D  317 LYS cc_start: 0.6758 (mttp) cc_final: 0.6283 (ttmt)
REVERT: D  321 LYS cc_start: 0.7159 (ttmt) cc_final: 0.6203 (tmtt)
REVERT: D  338 GLU cc_start: 0.7010 (tt0) cc_final: 0.6116 (mt-10)
REVERT: D  340 LYS cc_start: 0.6788 (mttt) cc_final: 0.6460 (mtpt)
REVERT: E  311 LYS cc_start: 0.7346 (tttt) cc_final: 0.6449 (tppt)
REVERT: E  317 LYS cc_start: 0.6759 (mttt) cc_final: 0.6460 (ttpt)
REVERT: E  321 LYS cc_start: 0.7212 (mtmt) cc_final: 0.6021 (mmtm)
REVERT: E  327 ASN cc_start: 0.7408 (t0) cc_final: 0.7195 (t0)
REVERT: E  343 LYS cc_start: 0.7732 (mttt) cc_final: 0.6382 (mmpt)
REVERT: E  353 LYS cc_start: 0.7912 (tttt) cc_final: 0.7571 (tttm)
REVERT: E  370 LYS cc_start: 0.7962 (tttt) cc_final: 0.5911 (mttt)
REVERT: F  311 LYS cc_start: 0.7423 (tttt) cc_final: 0.6566 (tppt)
REVERT: F  327 ASN cc_start: 0.7434 (m-40) cc_final: 0.7180 (m-40)
REVERT: F  331 LYS cc_start: 0.7292 (mttt) cc_final: 0.5391 (tmtt)
REVERT: F  338 GLU cc_start: 0.7201 (tt0) cc_final: 0.6440 (mp0)
REVERT: F  343 LYS cc_start: 0.7277 (mptt) cc_final: 0.6524 (mmtm)
REVERT: F  358 ASP cc_start: 0.7483 (m-30) cc_final: 0.7216 (m-30)
  outliers start: 11
  outliers final: 3
  residues processed: 138
  average time/residue: 2.9623
  time to fit residues: 418.0644
Evaluate side-chains
  104 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 101
  time to evaluate  : 0.596 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  361 THR
Chi-restraints excluded: chain D residue  361 THR
Chi-restraints excluded: chain F residue  361 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 35 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9980
   chunk 17 optimal weight:    0.8980
   chunk 10 optimal weight:    0.6980
   chunk 21 optimal weight:    0.7980
   chunk 32 optimal weight:    0.5980
   chunk 12 optimal weight:    0.8980
   chunk 20 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9990
   chunk 11 optimal weight:    0.7980
   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 307 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4330 r_free = 0.4330 target = 0.154411 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4010 r_free = 0.4010 target = 0.128434 restraints weight = 11059.795|
|-----------------------------------------------------------------------------|
r_work (start): 0.4032 rms_B_bonded: 2.06
r_work: 0.3934 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.3830 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.3830
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7506
moved from start:          0.3575

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   3474  Z= 0.244
  Angle     :  0.771   6.999   4644  Z= 0.393
  Chirality :  0.054   0.141    516
  Planarity :  0.004   0.024    594
  Dihedral  :  8.000  24.518    459
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 3.74
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  7.18 %
    Favored  : 92.59 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 11.54 %
    Favored  : 86.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.35 (0.33), residues: 432
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.78 (0.25), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS A 362 
 PHE   0.018   0.002   PHE E 346 
 TYR   0.012   0.002   TYR C 310 
 ARG   0.004   0.001   ARG E 349 

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

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

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 101
  time to evaluate  : 0.592 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  338 GLU cc_start: 0.8155 (tt0) cc_final: 0.7613 (mp0)
REVERT: A  342 GLU cc_start: 0.7685 (mt-10) cc_final: 0.7339 (mp0)
REVERT: A  351 GLN cc_start: 0.8261 (OUTLIER) cc_final: 0.7919 (mt0)
REVERT: A  379 ARG cc_start: 0.6048 (ttt180) cc_final: 0.4886 (ttp80)
REVERT: B  338 GLU cc_start: 0.8422 (tt0) cc_final: 0.7871 (mp0)
REVERT: B  342 GLU cc_start: 0.7504 (mt-10) cc_final: 0.6907 (mp0)
REVERT: B  343 LYS cc_start: 0.7982 (mptt) cc_final: 0.7559 (mppt)
REVERT: B  348 ASP cc_start: 0.8059 (t0) cc_final: 0.7666 (t0)
REVERT: B  351 GLN cc_start: 0.8284 (mt0) cc_final: 0.8037 (mt0)
REVERT: B  379 ARG cc_start: 0.6550 (ttt180) cc_final: 0.5591 (ttp-110)
REVERT: C  321 LYS cc_start: 0.8009 (mtmt) cc_final: 0.7802 (mtpt)
REVERT: C  338 GLU cc_start: 0.8197 (tt0) cc_final: 0.7669 (tm-30)
REVERT: C  340 LYS cc_start: 0.8561 (mtmt) cc_final: 0.7844 (tptp)
REVERT: C  349 ARG cc_start: 0.7531 (mtm180) cc_final: 0.6993 (mtp85)
REVERT: D  317 LYS cc_start: 0.7520 (mttp) cc_final: 0.7051 (ptmt)
REVERT: D  321 LYS cc_start: 0.7860 (ttmt) cc_final: 0.6953 (tmmt)
REVERT: D  340 LYS cc_start: 0.7977 (mttt) cc_final: 0.7699 (mtpt)
REVERT: D  342 GLU cc_start: 0.7631 (mm-30) cc_final: 0.6893 (mm-30)
REVERT: D  343 LYS cc_start: 0.7983 (mptp) cc_final: 0.7702 (mmtt)
REVERT: D  348 ASP cc_start: 0.8120 (t70) cc_final: 0.7875 (t70)
REVERT: E  311 LYS cc_start: 0.7420 (tttt) cc_final: 0.6519 (tppt)
REVERT: E  317 LYS cc_start: 0.7175 (mttt) cc_final: 0.6940 (ptmt)
REVERT: E  321 LYS cc_start: 0.7936 (mtmt) cc_final: 0.7714 (mttp)
REVERT: E  338 GLU cc_start: 0.7778 (tt0) cc_final: 0.7578 (tt0)
REVERT: F  311 LYS cc_start: 0.7715 (tttt) cc_final: 0.6705 (tppt)
REVERT: F  331 LYS cc_start: 0.8695 (mttt) cc_final: 0.6987 (tmtt)
REVERT: F  343 LYS cc_start: 0.7616 (mptt) cc_final: 0.7307 (mmtm)
REVERT: F  348 ASP cc_start: 0.7876 (t0) cc_final: 0.7488 (t0)
  outliers start: 6
  outliers final: 2
  residues processed: 104
  average time/residue: 3.0442
  time to fit residues: 324.0075
Evaluate side-chains
  91 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 88
  time to evaluate  : 0.644 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  341 SER
Chi-restraints excluded: chain A residue  351 GLN
Chi-restraints excluded: chain B residue  341 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 25 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9990
   chunk 37 optimal weight:    0.2980
   chunk 28 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9980
   chunk 4 optimal weight:    0.8980
   chunk 20 optimal weight:    1.9990
   chunk 26 optimal weight:    0.3980
   chunk 0 optimal weight:    2.9990
   chunk 6 optimal weight:    0.6980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4333 r_free = 0.4333 target = 0.156435 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4018 r_free = 0.4018 target = 0.130606 restraints weight = 10850.487|
|-----------------------------------------------------------------------------|
r_work (start): 0.4028 rms_B_bonded: 1.93
r_work: 0.3936 rms_B_bonded: 2.11 restraints_weight: 0.5000
r_work: 0.3834 rms_B_bonded: 3.56 restraints_weight: 0.2500
r_work (final): 0.3834
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7605
moved from start:          0.4727

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019   3474  Z= 0.196
  Angle     :  0.623   4.473   4644  Z= 0.318
  Chirality :  0.052   0.138    516
  Planarity :  0.003   0.025    594
  Dihedral  :  7.192  21.133    456
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 3.02
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  6.94 %
    Favored  : 92.82 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 16.41 %
    Favored  : 82.05 %
  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: -2.36 (0.34), residues: 432
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.79 (0.26), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS E 362 
 PHE   0.012   0.002   PHE E 346 
 TYR   0.011   0.002   TYR C 310 
 ARG   0.002   0.000   ARG B 349 

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

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

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 83
  time to evaluate  : 0.665 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  338 GLU cc_start: 0.8193 (tt0) cc_final: 0.7666 (mp0)
REVERT: A  342 GLU cc_start: 0.7690 (mt-10) cc_final: 0.7271 (mp0)
REVERT: A  351 GLN cc_start: 0.8200 (OUTLIER) cc_final: 0.7977 (mt0)
REVERT: A  369 LYS cc_start: 0.8070 (OUTLIER) cc_final: 0.7620 (mttm)
REVERT: A  379 ARG cc_start: 0.5987 (ttt180) cc_final: 0.3518 (mmp-170)
REVERT: B  342 GLU cc_start: 0.7546 (mt-10) cc_final: 0.7004 (mp0)
REVERT: B  343 LYS cc_start: 0.8064 (mptt) cc_final: 0.7676 (mppt)
REVERT: B  351 GLN cc_start: 0.8238 (mt0) cc_final: 0.8017 (mt0)
REVERT: B  379 ARG cc_start: 0.6356 (ttt180) cc_final: 0.5504 (ttp-110)
REVERT: C  349 ARG cc_start: 0.7708 (mtm180) cc_final: 0.7094 (mtp85)
REVERT: D  317 LYS cc_start: 0.7545 (mttp) cc_final: 0.7083 (ptmt)
REVERT: D  340 LYS cc_start: 0.8056 (mttt) cc_final: 0.7757 (mtpt)
REVERT: D  342 GLU cc_start: 0.7755 (mm-30) cc_final: 0.7240 (mt-10)
REVERT: D  343 LYS cc_start: 0.8077 (mptp) cc_final: 0.7798 (mmtt)
REVERT: E  311 LYS cc_start: 0.7553 (tttt) cc_final: 0.6599 (tppt)
REVERT: F  311 LYS cc_start: 0.7733 (tttt) cc_final: 0.6993 (tppt)
REVERT: F  331 LYS cc_start: 0.8768 (mttt) cc_final: 0.7086 (tmtt)
REVERT: F  348 ASP cc_start: 0.8050 (t0) cc_final: 0.7844 (t0)
  outliers start: 6
  outliers final: 1
  residues processed: 85
  average time/residue: 3.2604
  time to fit residues: 283.1583
Evaluate side-chains
  78 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 75
  time to evaluate  : 0.584 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  351 GLN
Chi-restraints excluded: chain A residue  369 LYS
Chi-restraints excluded: chain B residue  325 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 40 optimal weight:    0.6980
   chunk 24 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9990
   chunk 4 optimal weight:    1.9990
   chunk 38 optimal weight:    0.6980
   chunk 37 optimal weight:    0.9990
   chunk 32 optimal weight:    0.4980
   chunk 14 optimal weight:    2.9990
   chunk 21 optimal weight:    3.9990
   chunk 1 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9990
   overall best weight:    0.7784

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

Flipped N/Q/H residues before XYZ refinement:
D 307 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4263 r_free = 0.4263 target = 0.150348 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.124032 restraints weight = 11156.010|
|-----------------------------------------------------------------------------|
r_work (start): 0.3956 rms_B_bonded: 1.98
r_work: 0.3868 rms_B_bonded: 2.14 restraints_weight: 0.5000
r_work: 0.3769 rms_B_bonded: 3.61 restraints_weight: 0.2500
r_work (final): 0.3769
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7619
moved from start:          0.5516

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   3474  Z= 0.220
  Angle     :  0.596   4.550   4644  Z= 0.301
  Chirality :  0.051   0.133    516
  Planarity :  0.003   0.026    594
  Dihedral  :  6.926  20.519    456
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 3.02
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  8.10 %
    Favored  : 91.67 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 17.18 %
    Favored  : 80.77 %
  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: -2.51 (0.33), residues: 432
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.91 (0.25), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS A 329 
 PHE   0.010   0.002   PHE E 346 
 TYR   0.010   0.002   TYR C 310 
 ARG   0.004   0.000   ARG F 349 

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

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

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 85
  time to evaluate  : 0.594 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  342 GLU cc_start: 0.7619 (mt-10) cc_final: 0.7197 (mp0)
REVERT: A  369 LYS cc_start: 0.8190 (OUTLIER) cc_final: 0.7782 (mttm)
REVERT: A  379 ARG cc_start: 0.5955 (ttt180) cc_final: 0.3585 (mmp-170)
REVERT: B  311 LYS cc_start: 0.7942 (tttt) cc_final: 0.7178 (tmmt)
REVERT: B  331 LYS cc_start: 0.8891 (mttt) cc_final: 0.8636 (mtpt)
REVERT: B  340 LYS cc_start: 0.8563 (mttt) cc_final: 0.8331 (mttt)
REVERT: B  342 GLU cc_start: 0.7677 (mt-10) cc_final: 0.7062 (mp0)
REVERT: B  343 LYS cc_start: 0.8060 (mptt) cc_final: 0.7636 (mppt)
REVERT: B  351 GLN cc_start: 0.8261 (mt0) cc_final: 0.8032 (mt0)
REVERT: B  379 ARG cc_start: 0.6508 (ttt180) cc_final: 0.5667 (ttp-110)
REVERT: C  349 ARG cc_start: 0.7805 (mtm180) cc_final: 0.7249 (mtp180)
REVERT: D  317 LYS cc_start: 0.7492 (mttp) cc_final: 0.6982 (ptmt)
REVERT: D  340 LYS cc_start: 0.8027 (mttt) cc_final: 0.7622 (mtpt)
REVERT: D  342 GLU cc_start: 0.7732 (mm-30) cc_final: 0.7207 (mt-10)
REVERT: D  343 LYS cc_start: 0.8162 (mptp) cc_final: 0.7844 (mmtt)
REVERT: E  311 LYS cc_start: 0.7621 (tttt) cc_final: 0.6775 (tptt)
REVERT: F  331 LYS cc_start: 0.8778 (mttt) cc_final: 0.7086 (tmtt)
REVERT: F  343 LYS cc_start: 0.7957 (mptt) cc_final: 0.7516 (mppt)
REVERT: F  353 LYS cc_start: 0.8601 (tttm) cc_final: 0.8396 (tttm)
  outliers start: 8
  outliers final: 1
  residues processed: 90
  average time/residue: 3.1457
  time to fit residues: 289.6554
Evaluate side-chains
  73 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 71
  time to evaluate  : 0.555 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  369 LYS
Chi-restraints excluded: chain B residue  325 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 29 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   chunk 19 optimal weight:    0.4980
   chunk 1 optimal weight:    0.9990
   chunk 26 optimal weight:    1.9990
   chunk 4 optimal weight:    0.6980
   chunk 31 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 39 optimal weight:    0.6980
   chunk 7 optimal weight:    2.9990
   overall best weight:    0.9784

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

Flipped N/Q/H residues before XYZ refinement:
D 307 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4232 r_free = 0.4232 target = 0.148179 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.121573 restraints weight = 11182.076|
|-----------------------------------------------------------------------------|
r_work (start): 0.3917 rms_B_bonded: 1.93
r_work: 0.3833 rms_B_bonded: 2.08 restraints_weight: 0.5000
r_work: 0.3735 rms_B_bonded: 3.50 restraints_weight: 0.2500
r_work (final): 0.3735
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7657
moved from start:          0.5945

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024   3474  Z= 0.265
  Angle     :  0.605   4.837   4644  Z= 0.307
  Chirality :  0.051   0.139    516
  Planarity :  0.003   0.027    594
  Dihedral  :  6.926  20.770    456
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 3.16
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  8.10 %
    Favored  : 91.67 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 17.69 %
    Favored  : 80.00 %
  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: -2.61 (0.33), residues: 432
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.98 (0.25), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS A 329 
 PHE   0.010   0.002   PHE D 346 
 TYR   0.011   0.002   TYR C 310 
 ARG   0.002   0.000   ARG E 349 

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

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

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 77
  time to evaluate  : 0.610 
Fit side-chains
   revert: symmetry clash
REVERT: A  311 LYS cc_start: 0.8120 (tttt) cc_final: 0.7792 (ttmm)
REVERT: A  331 LYS cc_start: 0.8903 (OUTLIER) cc_final: 0.8509 (mttm)
REVERT: A  342 GLU cc_start: 0.7620 (mt-10) cc_final: 0.7139 (mp0)
REVERT: A  369 LYS cc_start: 0.8309 (OUTLIER) cc_final: 0.7923 (mttm)
REVERT: A  379 ARG cc_start: 0.6249 (ttt180) cc_final: 0.3765 (mmp-170)
REVERT: B  311 LYS cc_start: 0.7845 (tttt) cc_final: 0.7138 (tmmt)
REVERT: B  331 LYS cc_start: 0.8933 (mttt) cc_final: 0.8683 (mtpt)
REVERT: B  340 LYS cc_start: 0.8502 (mttt) cc_final: 0.8257 (mttt)
REVERT: B  342 GLU cc_start: 0.7655 (mt-10) cc_final: 0.7057 (mp0)
REVERT: B  343 LYS cc_start: 0.8098 (mptt) cc_final: 0.7687 (mppt)
REVERT: B  351 GLN cc_start: 0.8331 (mt0) cc_final: 0.8078 (mt0)
REVERT: B  379 ARG cc_start: 0.6564 (ttt180) cc_final: 0.5681 (ttp-110)
REVERT: C  342 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7355 (mt-10)
REVERT: D  317 LYS cc_start: 0.7543 (mttp) cc_final: 0.6951 (ttmt)
REVERT: D  340 LYS cc_start: 0.8067 (mttt) cc_final: 0.7609 (mtpt)
REVERT: D  342 GLU cc_start: 0.7765 (mm-30) cc_final: 0.7226 (mt-10)
REVERT: D  343 LYS cc_start: 0.8135 (mptp) cc_final: 0.7790 (mmtt)
REVERT: E  311 LYS cc_start: 0.7584 (tttt) cc_final: 0.7259 (ttpp)
REVERT: F  311 LYS cc_start: 0.8403 (tttp) cc_final: 0.7359 (tppt)
REVERT: F  321 LYS cc_start: 0.8103 (OUTLIER) cc_final: 0.7896 (mttp)
REVERT: F  343 LYS cc_start: 0.8082 (mptt) cc_final: 0.7674 (mppt)
REVERT: F  370 LYS cc_start: 0.8380 (tttt) cc_final: 0.6732 (mttt)
  outliers start: 9
  outliers final: 2
  residues processed: 80
  average time/residue: 3.0700
  time to fit residues: 251.3290
Evaluate side-chains
  77 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 71
  time to evaluate  : 0.572 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  331 LYS
Chi-restraints excluded: chain A residue  356 SER
Chi-restraints excluded: chain A residue  369 LYS
Chi-restraints excluded: chain B residue  325 LEU
Chi-restraints excluded: chain C residue  342 GLU
Chi-restraints excluded: chain F residue  321 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 29 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 19 optimal weight:    0.5980
   chunk 14 optimal weight:    2.9990
   chunk 8 optimal weight:    2.9990
   chunk 12 optimal weight:    0.4980
   chunk 20 optimal weight:    0.9980
   chunk 34 optimal weight:    0.8980
   chunk 27 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   chunk 5 optimal weight:    0.8980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4283 r_free = 0.4283 target = 0.153613 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.127950 restraints weight = 10890.021|
|-----------------------------------------------------------------------------|
r_work (start): 0.3930 rms_B_bonded: 1.90
r_work: 0.3842 rms_B_bonded: 2.06 restraints_weight: 0.5000
r_work: 0.3744 rms_B_bonded: 3.48 restraints_weight: 0.2500
r_work (final): 0.3744
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7642
moved from start:          0.6145

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   3474  Z= 0.213
  Angle     :  0.563   4.499   4644  Z= 0.286
  Chirality :  0.051   0.138    516
  Planarity :  0.003   0.027    594
  Dihedral  :  6.730  19.566    456
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 3.74
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  7.87 %
    Favored  : 91.90 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 18.72 %
    Favored  : 80.00 %
  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: -2.66 (0.33), residues: 432
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.02 (0.25), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS C 374 
 PHE   0.006   0.001   PHE E 346 
 TYR   0.008   0.002   TYR D 310 
 ARG   0.002   0.000   ARG F 349 

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

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

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 75
  time to evaluate  : 0.459 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  311 LYS cc_start: 0.8101 (tttt) cc_final: 0.7772 (ttmm)
REVERT: A  342 GLU cc_start: 0.7589 (mt-10) cc_final: 0.7111 (mp0)
REVERT: A  369 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.7917 (mttm)
REVERT: A  379 ARG cc_start: 0.6124 (ttt180) cc_final: 0.3740 (mmp-170)
REVERT: B  311 LYS cc_start: 0.7848 (tttt) cc_final: 0.7149 (tmmt)
REVERT: B  331 LYS cc_start: 0.8910 (mttt) cc_final: 0.8665 (mtpt)
REVERT: B  340 LYS cc_start: 0.8482 (mttt) cc_final: 0.8223 (mttt)
REVERT: B  342 GLU cc_start: 0.7658 (mt-10) cc_final: 0.7066 (mp0)
REVERT: B  343 LYS cc_start: 0.8108 (mptt) cc_final: 0.7695 (mppt)
REVERT: B  351 GLN cc_start: 0.8327 (mt0) cc_final: 0.8062 (mt0)
REVERT: B  379 ARG cc_start: 0.6540 (ttt180) cc_final: 0.5643 (ttp-110)
REVERT: C  342 GLU cc_start: 0.7746 (mt-10) cc_final: 0.7327 (mt-10)
REVERT: D  317 LYS cc_start: 0.7457 (mttp) cc_final: 0.6934 (ttmt)
REVERT: D  340 LYS cc_start: 0.8150 (mttt) cc_final: 0.7638 (mtpt)
REVERT: D  342 GLU cc_start: 0.7723 (mm-30) cc_final: 0.7229 (mt-10)
REVERT: D  343 LYS cc_start: 0.8146 (mptp) cc_final: 0.7804 (mmtt)
REVERT: F  311 LYS cc_start: 0.8342 (tttp) cc_final: 0.7388 (tppt)
REVERT: F  321 LYS cc_start: 0.8083 (OUTLIER) cc_final: 0.7879 (mttp)
REVERT: F  343 LYS cc_start: 0.8066 (mptt) cc_final: 0.7682 (mppt)
REVERT: F  370 LYS cc_start: 0.8399 (tttt) cc_final: 0.6713 (mttt)
  outliers start: 5
  outliers final: 2
  residues processed: 76
  average time/residue: 2.9944
  time to fit residues: 233.0596
Evaluate side-chains
  78 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 74
  time to evaluate  : 0.460 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  356 SER
Chi-restraints excluded: chain A residue  369 LYS
Chi-restraints excluded: chain B residue  325 LEU
Chi-restraints excluded: chain F residue  321 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 2 optimal weight:    0.9990
   chunk 12 optimal weight:    0.0670
   chunk 9 optimal weight:    0.6980
   chunk 35 optimal weight:    1.9990
   chunk 33 optimal weight:    0.1980
   chunk 21 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9990
   chunk 26 optimal weight:    0.3980
   chunk 1 optimal weight:    1.9990
   chunk 34 optimal weight:    0.7980
   chunk 37 optimal weight:    0.6980
   overall best weight:    0.4118

-------------------------------------------------------------------------------
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 = 0.4325 r_free = 0.4325 target = 0.157334 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.132254 restraints weight = 10598.789|
|-----------------------------------------------------------------------------|
r_work (start): 0.3972 rms_B_bonded: 1.87
r_work: 0.3889 rms_B_bonded: 2.03 restraints_weight: 0.5000
r_work: 0.3794 rms_B_bonded: 3.44 restraints_weight: 0.2500
r_work (final): 0.3794
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7588
moved from start:          0.6298

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   3474  Z= 0.148
  Angle     :  0.526   4.180   4644  Z= 0.268
  Chirality :  0.051   0.138    516
  Planarity :  0.003   0.028    594
  Dihedral  :  6.359  18.369    456
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 3.16
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  7.64 %
    Favored  : 92.13 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 19.49 %
    Favored  : 79.23 %
  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: -2.67 (0.33), residues: 432
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.03 (0.25), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS F 362 
 PHE   0.007   0.001   PHE E 346 
 TYR   0.006   0.001   TYR C 310 
 ARG   0.002   0.000   ARG D 349 

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

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

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 72
  time to evaluate  : 0.567 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  342 GLU cc_start: 0.7519 (mt-10) cc_final: 0.7071 (mp0)
REVERT: A  369 LYS cc_start: 0.8184 (OUTLIER) cc_final: 0.7713 (mttm)
REVERT: A  379 ARG cc_start: 0.5976 (ttt180) cc_final: 0.3636 (mmp-170)
REVERT: B  311 LYS cc_start: 0.7724 (tttt) cc_final: 0.7018 (tmmt)
REVERT: B  331 LYS cc_start: 0.8876 (mttt) cc_final: 0.8636 (mtpt)
REVERT: B  342 GLU cc_start: 0.7606 (mt-10) cc_final: 0.7036 (mp0)
REVERT: B  343 LYS cc_start: 0.8068 (mptt) cc_final: 0.7667 (mppt)
REVERT: B  351 GLN cc_start: 0.8323 (mt0) cc_final: 0.8058 (mt0)
REVERT: B  379 ARG cc_start: 0.6438 (ttt180) cc_final: 0.5261 (mpp80)
REVERT: C  342 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7327 (mt-10)
REVERT: D  317 LYS cc_start: 0.7415 (mttp) cc_final: 0.6912 (ttmt)
REVERT: D  340 LYS cc_start: 0.8142 (mttt) cc_final: 0.7618 (mtpt)
REVERT: D  342 GLU cc_start: 0.7671 (mm-30) cc_final: 0.7216 (mt-10)
REVERT: D  343 LYS cc_start: 0.8096 (mptp) cc_final: 0.7807 (mmtt)
REVERT: E  314 ASP cc_start: 0.8200 (t0) cc_final: 0.7932 (t0)
REVERT: F  311 LYS cc_start: 0.8309 (tttp) cc_final: 0.7324 (tppt)
REVERT: F  343 LYS cc_start: 0.7988 (mptt) cc_final: 0.7609 (mppt)
  outliers start: 5
  outliers final: 2
  residues processed: 74
  average time/residue: 2.8779
  time to fit residues: 218.3394
Evaluate side-chains
  73 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 69
  time to evaluate  : 0.585 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  356 SER
Chi-restraints excluded: chain A residue  369 LYS
Chi-restraints excluded: chain B residue  325 LEU
Chi-restraints excluded: chain C residue  342 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 9 optimal weight:    1.9990
   chunk 23 optimal weight:    0.5980
   chunk 10 optimal weight:    0.7980
   chunk 39 optimal weight:    0.1980
   chunk 4 optimal weight:    0.7980
   chunk 2 optimal weight:    0.9990
   chunk 12 optimal weight:    0.5980
   chunk 36 optimal weight:    1.9990
   chunk 18 optimal weight:    0.6980
   chunk 20 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9990
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
E 351 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4310 r_free = 0.4310 target = 0.156052 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.130707 restraints weight = 10844.695|
|-----------------------------------------------------------------------------|
r_work (start): 0.3950 rms_B_bonded: 1.89
r_work: 0.3863 rms_B_bonded: 2.06 restraints_weight: 0.5000
r_work: 0.3767 rms_B_bonded: 3.48 restraints_weight: 0.2500
r_work (final): 0.3767
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7619
moved from start:          0.6384

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019   3474  Z= 0.174
  Angle     :  0.528   4.181   4644  Z= 0.269
  Chirality :  0.050   0.135    516
  Planarity :  0.003   0.029    594
  Dihedral  :  6.380  18.727    456
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 3.60
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  8.33 %
    Favored  : 91.44 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 20.00 %
    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: -2.70 (0.33), residues: 432
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.05 (0.25), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS C 374 
 PHE   0.005   0.001   PHE E 346 
 TYR   0.006   0.002   TYR A 310 
 ARG   0.001   0.000   ARG E 379 

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

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

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 77
  time to evaluate  : 0.630 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  331 LYS cc_start: 0.8889 (OUTLIER) cc_final: 0.8483 (mttm)
REVERT: A  342 GLU cc_start: 0.7562 (mt-10) cc_final: 0.7081 (mp0)
REVERT: A  369 LYS cc_start: 0.8285 (OUTLIER) cc_final: 0.7819 (mttm)
REVERT: A  379 ARG cc_start: 0.5847 (ttt180) cc_final: 0.3600 (mmp-170)
REVERT: B  311 LYS cc_start: 0.7718 (tttt) cc_final: 0.7032 (tmmt)
REVERT: B  331 LYS cc_start: 0.8888 (mttt) cc_final: 0.8654 (mtpt)
REVERT: B  342 GLU cc_start: 0.7642 (mt-10) cc_final: 0.7046 (mp0)
REVERT: B  343 LYS cc_start: 0.8087 (mptt) cc_final: 0.7683 (mppt)
REVERT: B  351 GLN cc_start: 0.8311 (mt0) cc_final: 0.8052 (mt0)
REVERT: B  379 ARG cc_start: 0.6399 (ttt180) cc_final: 0.5279 (mpp80)
REVERT: C  342 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.7337 (mt-10)
REVERT: D  317 LYS cc_start: 0.7433 (mttp) cc_final: 0.6935 (ttmt)
REVERT: D  340 LYS cc_start: 0.8173 (mttt) cc_final: 0.7632 (mtpt)
REVERT: D  342 GLU cc_start: 0.7696 (mm-30) cc_final: 0.7238 (mt-10)
REVERT: D  343 LYS cc_start: 0.8105 (mptp) cc_final: 0.7806 (mmtt)
REVERT: E  314 ASP cc_start: 0.8234 (t0) cc_final: 0.7952 (t0)
REVERT: F  311 LYS cc_start: 0.8268 (tttp) cc_final: 0.7300 (tppt)
REVERT: F  343 LYS cc_start: 0.8060 (mptt) cc_final: 0.7657 (mppt)
REVERT: F  370 LYS cc_start: 0.8381 (tttt) cc_final: 0.6735 (mttt)
  outliers start: 5
  outliers final: 2
  residues processed: 77
  average time/residue: 2.8364
  time to fit residues: 224.8375
Evaluate side-chains
  79 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 74
  time to evaluate  : 0.592 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  331 LYS
Chi-restraints excluded: chain A residue  356 SER
Chi-restraints excluded: chain A residue  369 LYS
Chi-restraints excluded: chain B residue  325 LEU
Chi-restraints excluded: chain C residue  342 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 16 optimal weight:    0.9980
   chunk 10 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   chunk 7 optimal weight:    2.9990
   chunk 28 optimal weight:    0.3980
   chunk 39 optimal weight:    0.5980
   chunk 6 optimal weight:    0.8980
   chunk 2 optimal weight:    0.3980
   chunk 30 optimal weight:    0.9980
   chunk 36 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
E 351 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4306 r_free = 0.4306 target = 0.155356 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.130144 restraints weight = 10849.181|
|-----------------------------------------------------------------------------|
r_work (start): 0.3948 rms_B_bonded: 1.87
r_work: 0.3862 rms_B_bonded: 2.03 restraints_weight: 0.5000
r_work: 0.3764 rms_B_bonded: 3.43 restraints_weight: 0.2500
r_work (final): 0.3764
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7622
moved from start:          0.6532

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3474  Z= 0.188
  Angle     :  0.531   4.342   4644  Z= 0.270
  Chirality :  0.050   0.136    516
  Planarity :  0.003   0.028    594
  Dihedral  :  6.384  18.698    456
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 3.45
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  8.10 %
    Favored  : 91.67 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 21.54 %
    Favored  : 77.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.77 (0.33), residues: 432
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.10 (0.25), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS C 374 
 PHE   0.005   0.001   PHE E 378 
 TYR   0.007   0.002   TYR C 310 
 ARG   0.001   0.000   ARG D 349 

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

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

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 74
  time to evaluate  : 0.561 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  331 LYS cc_start: 0.8870 (OUTLIER) cc_final: 0.8469 (mttm)
REVERT: A  342 GLU cc_start: 0.7584 (mt-10) cc_final: 0.7114 (mp0)
REVERT: A  369 LYS cc_start: 0.8364 (OUTLIER) cc_final: 0.7913 (mttm)
REVERT: B  311 LYS cc_start: 0.7792 (tttt) cc_final: 0.7076 (tmmt)
REVERT: B  331 LYS cc_start: 0.8898 (mttt) cc_final: 0.8662 (mtpt)
REVERT: B  342 GLU cc_start: 0.7650 (mt-10) cc_final: 0.7082 (mp0)
REVERT: B  343 LYS cc_start: 0.8112 (mptt) cc_final: 0.7703 (mppt)
REVERT: B  351 GLN cc_start: 0.8316 (mt0) cc_final: 0.8044 (mt0)
REVERT: B  379 ARG cc_start: 0.6446 (ttt180) cc_final: 0.5323 (mpp80)
REVERT: C  342 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.7313 (mt-10)
REVERT: D  317 LYS cc_start: 0.7285 (mttp) cc_final: 0.6757 (ttmt)
REVERT: D  340 LYS cc_start: 0.8165 (mttt) cc_final: 0.7619 (mtpt)
REVERT: D  342 GLU cc_start: 0.7711 (mm-30) cc_final: 0.7241 (mt-10)
REVERT: D  343 LYS cc_start: 0.8099 (mptp) cc_final: 0.7775 (mmtt)
REVERT: E  314 ASP cc_start: 0.8272 (t0) cc_final: 0.7976 (t0)
REVERT: F  311 LYS cc_start: 0.8372 (tttp) cc_final: 0.7377 (tppt)
REVERT: F  343 LYS cc_start: 0.8059 (mptt) cc_final: 0.7635 (mppt)
REVERT: F  370 LYS cc_start: 0.8415 (tttt) cc_final: 0.6720 (mttt)
REVERT: F  375 LYS cc_start: 0.6410 (mttt) cc_final: 0.5632 (mmtm)
  outliers start: 5
  outliers final: 2
  residues processed: 74
  average time/residue: 2.7390
  time to fit residues: 208.1991
Evaluate side-chains
  79 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 74
  time to evaluate  : 0.623 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  331 LYS
Chi-restraints excluded: chain A residue  356 SER
Chi-restraints excluded: chain A residue  369 LYS
Chi-restraints excluded: chain B residue  325 LEU
Chi-restraints excluded: chain C residue  342 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 20 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9980
   chunk 23 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   chunk 9 optimal weight:    0.2980
   chunk 25 optimal weight:    1.9990
   chunk 40 optimal weight:    0.7980
   chunk 17 optimal weight:    1.9990
   chunk 31 optimal weight:    0.5980
   chunk 34 optimal weight:    0.9980
   chunk 36 optimal weight:    1.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
E 351 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4294 r_free = 0.4294 target = 0.154376 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.128997 restraints weight = 10995.917|
|-----------------------------------------------------------------------------|
r_work (start): 0.4012 rms_B_bonded: 1.88
r_work: 0.3925 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.3827 rms_B_bonded: 3.44 restraints_weight: 0.2500
r_work (final): 0.3827
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7672
moved from start:          0.6575

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   3474  Z= 0.204
  Angle     :  0.539   4.463   4644  Z= 0.274
  Chirality :  0.050   0.134    516
  Planarity :  0.003   0.029    594
  Dihedral  :  6.423  18.931    456
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 3.74
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  8.33 %
    Favored  : 91.44 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 21.28 %
    Favored  : 77.44 %
  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: -2.80 (0.33), residues: 432
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.13 (0.25), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS C 374 
 PHE   0.005   0.001   PHE F 346 
 TYR   0.007   0.002   TYR A 310 
 ARG   0.002   0.000   ARG E 379 

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

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

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 75
  time to evaluate  : 0.676 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  311 LYS cc_start: 0.8044 (tttt) cc_final: 0.7720 (ttmm)
REVERT: A  331 LYS cc_start: 0.8878 (OUTLIER) cc_final: 0.8478 (mttm)
REVERT: A  342 GLU cc_start: 0.7553 (mt-10) cc_final: 0.7089 (mp0)
REVERT: A  369 LYS cc_start: 0.8506 (OUTLIER) cc_final: 0.8039 (mttm)
REVERT: B  311 LYS cc_start: 0.7852 (tttt) cc_final: 0.7137 (tmmt)
REVERT: B  331 LYS cc_start: 0.8905 (mttt) cc_final: 0.8684 (mtpt)
REVERT: B  342 GLU cc_start: 0.7599 (mt-10) cc_final: 0.7078 (mp0)
REVERT: B  343 LYS cc_start: 0.8186 (mptt) cc_final: 0.7772 (mppt)
REVERT: B  351 GLN cc_start: 0.8357 (mt0) cc_final: 0.8077 (mt0)
REVERT: B  379 ARG cc_start: 0.6617 (ttt180) cc_final: 0.5435 (mpp80)
REVERT: C  342 GLU cc_start: 0.7683 (mt-10) cc_final: 0.7310 (mt-10)
REVERT: D  317 LYS cc_start: 0.7340 (mttp) cc_final: 0.6806 (ttmt)
REVERT: D  340 LYS cc_start: 0.8193 (mttt) cc_final: 0.7656 (mtpt)
REVERT: D  342 GLU cc_start: 0.7706 (mm-30) cc_final: 0.7278 (mt-10)
REVERT: D  343 LYS cc_start: 0.8122 (mptp) cc_final: 0.7796 (mmtt)
REVERT: E  314 ASP cc_start: 0.8302 (t0) cc_final: 0.8028 (t0)
REVERT: F  311 LYS cc_start: 0.8361 (tttp) cc_final: 0.7404 (tppt)
REVERT: F  343 LYS cc_start: 0.8089 (mptt) cc_final: 0.7685 (mppt)
REVERT: F  370 LYS cc_start: 0.8438 (tttt) cc_final: 0.6764 (mttt)
REVERT: F  375 LYS cc_start: 0.6395 (mttt) cc_final: 0.6037 (mmmm)
  outliers start: 5
  outliers final: 2
  residues processed: 76
  average time/residue: 2.7879
  time to fit residues: 217.5477
Evaluate side-chains
  79 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 75
  time to evaluate  : 0.557 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  331 LYS
Chi-restraints excluded: chain A residue  356 SER
Chi-restraints excluded: chain A residue  369 LYS
Chi-restraints excluded: chain B residue  325 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 3 optimal weight:    1.9990
   chunk 16 optimal weight:    0.6980
   chunk 28 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9990
   chunk 5 optimal weight:    0.3980
   chunk 38 optimal weight:    0.7980
   chunk 18 optimal weight:    0.5980
   chunk 12 optimal weight:    0.9980
   chunk 21 optimal weight:    0.8980
   chunk 7 optimal weight:    0.5980
   chunk 10 optimal weight:    0.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
E 351 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4304 r_free = 0.4304 target = 0.155346 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.130191 restraints weight = 10855.404|
|-----------------------------------------------------------------------------|
r_work (start): 0.3955 rms_B_bonded: 1.86
r_work: 0.3867 rms_B_bonded: 2.01 restraints_weight: 0.5000
r_work: 0.3769 rms_B_bonded: 3.41 restraints_weight: 0.2500
r_work (final): 0.3769
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7597
moved from start:          0.6632

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3474  Z= 0.183
  Angle     :  0.530   4.401   4644  Z= 0.269
  Chirality :  0.050   0.135    516
  Planarity :  0.003   0.027    594
  Dihedral  :  6.328  18.875    456
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 3.74
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  7.64 %
    Favored  : 92.13 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 21.28 %
    Favored  : 77.44 %
  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: -2.80 (0.33), residues: 432
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.12 (0.25), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.000   HIS C 374 
 PHE   0.005   0.001   PHE E 346 
 TYR   0.007   0.002   TYR C 310 
 ARG   0.002   0.000   ARG E 379 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6902.66 seconds
wall clock time: 121 minutes 33.15 seconds (7293.15 seconds total)