Starting phenix.real_space_refine
on Mon Feb 10 21:26:19 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ypg_33999/02_2025/7ypg_33999.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ypg_33999/02_2025/7ypg_33999.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ypg_33999/02_2025/7ypg_33999.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ypg_33999/02_2025/7ypg_33999.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ypg_33999/02_2025/7ypg_33999.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ypg_33999/02_2025/7ypg_33999.cif"
  }
  resolution = 2.5
  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=   0.001 sd=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S       6      5.16       5
     C    1668      2.51       5
     N     486      2.21       5
     O     516      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 2676
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 446
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 59, 446
          Classifications: {'peptide': 59}
          Link IDs: {'PTRANS': 2, 'TRANS': 56}
  Restraints were copied for chains:
    C, B, E, D, F
  Time building chain proxies: 1.91, per 1000 atoms: 0.71
  Number of scatterers: 2676
  At special positions: 0
  Unit cell: (99.6, 110.39, 34.86, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S       6     16.00
     O     516      8.00
     N     486      7.00
     C    1668      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: 0.65
  Conformation dependent library (CDL) restraints added in 351.9 milliseconds
  

  684 Ramachandran restraints generated.
    342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  624

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 10 sheets defined
      0.0% alpha, 18.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.38
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'B' and resid 308 through 310
      removed outlier: 6.673A  pdb=" N   VAL B 309 " --> pdb=" O   TYR D 310 " (cutoff:3.500A)
      removed outlier: 6.673A  pdb=" N   VAL D 309 " --> pdb=" O   TYR E 310 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'B' and resid 316 through 320
    Processing sheet with id=AA3, first strand: chain 'B' and resid 328 through 330
      removed outlier: 6.409A  pdb=" N   HIS B 329 " --> pdb=" O   HIS D 330 " (cutoff:3.500A)
      removed outlier: 6.402A  pdb=" N   HIS D 329 " --> pdb=" O   HIS E 330 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'B' and resid 338 through 340
      removed outlier: 6.652A  pdb=" N   GLU B 338 " --> pdb=" O   VAL D 339 " (cutoff:3.500A)
      removed outlier: 6.649A  pdb=" N   GLU D 338 " --> pdb=" O   VAL E 339 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'B' and resid 349 through 350
    Processing sheet with id=AA6, first strand: chain 'F' and resid 308 through 310
      removed outlier: 6.673A  pdb=" N   VAL F 309 " --> pdb=" O   TYR A 310 " (cutoff:3.500A)
      removed outlier: 6.673A  pdb=" N   VAL A 309 " --> pdb=" O   TYR C 310 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'F' and resid 316 through 320
    Processing sheet with id=AA8, first strand: chain 'F' and resid 328 through 330
      removed outlier: 6.410A  pdb=" N   HIS F 329 " --> pdb=" O   HIS A 330 " (cutoff:3.500A)
      removed outlier: 6.403A  pdb=" N   HIS A 329 " --> pdb=" O   HIS C 330 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'F' and resid 338 through 340
      removed outlier: 6.651A  pdb=" N   GLU F 338 " --> pdb=" O   VAL A 339 " (cutoff:3.500A)
      removed outlier: 6.649A  pdb=" N   GLU A 338 " --> pdb=" O   VAL C 339 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'F' and resid 349 through 350

    20 hydrogen bonds defined for protein.
    60 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.58

  Time building geometry restraints manager: 0.77 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 881
        1.33 -     1.45: 217
        1.45 -     1.56: 1608
        1.56 -     1.67: 0
        1.67 -     1.79: 6
  Bond restraints: 2712
  Sorted by residual:
  bond pdb=" CB  VAL D 306 "
       pdb=" CG2 VAL D 306 "
    ideal  model  delta    sigma   weight residual
    1.521  1.478  0.043 3.30e-02 9.18e+02 1.68e+00
  bond pdb=" CB  VAL A 306 "
       pdb=" CG2 VAL A 306 "
    ideal  model  delta    sigma   weight residual
    1.521  1.478  0.043 3.30e-02 9.18e+02 1.66e+00
  bond pdb=" CB  VAL E 306 "
       pdb=" CG2 VAL E 306 "
    ideal  model  delta    sigma   weight residual
    1.521  1.479  0.042 3.30e-02 9.18e+02 1.65e+00
  bond pdb=" CB  VAL C 306 "
       pdb=" CG2 VAL C 306 "
    ideal  model  delta    sigma   weight residual
    1.521  1.479  0.042 3.30e-02 9.18e+02 1.65e+00
  bond pdb=" CB  VAL F 306 "
       pdb=" CG2 VAL F 306 "
    ideal  model  delta    sigma   weight residual
    1.521  1.479  0.042 3.30e-02 9.18e+02 1.64e+00
  ... (remaining 2707 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.89: 2971
        0.89 -     1.78: 534
        1.78 -     2.67: 65
        2.67 -     3.55: 34
        3.55 -     4.44: 26
  Bond angle restraints: 3630
  Sorted by residual:
  angle pdb=" N   THR A 361 "
        pdb=" CA  THR A 361 "
        pdb=" C   THR A 361 "
      ideal   model   delta    sigma   weight residual
     111.17  114.75   -3.58 1.41e+00 5.03e-01 6.44e+00
  angle pdb=" N   THR F 361 "
        pdb=" CA  THR F 361 "
        pdb=" C   THR F 361 "
      ideal   model   delta    sigma   weight residual
     111.17  114.72   -3.55 1.41e+00 5.03e-01 6.35e+00
  angle pdb=" N   THR D 361 "
        pdb=" CA  THR D 361 "
        pdb=" C   THR D 361 "
      ideal   model   delta    sigma   weight residual
     111.17  114.71   -3.54 1.41e+00 5.03e-01 6.31e+00
  angle pdb=" N   THR C 361 "
        pdb=" CA  THR C 361 "
        pdb=" C   THR C 361 "
      ideal   model   delta    sigma   weight residual
     111.17  114.71   -3.54 1.41e+00 5.03e-01 6.31e+00
  angle pdb=" N   THR E 361 "
        pdb=" CA  THR E 361 "
        pdb=" C   THR E 361 "
      ideal   model   delta    sigma   weight residual
     111.17  114.70   -3.53 1.41e+00 5.03e-01 6.26e+00
  ... (remaining 3625 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.74: 1506
       17.74 -    35.47: 114
       35.47 -    53.21: 30
       53.21 -    70.95: 0
       70.95 -    88.68: 6
  Dihedral angle restraints: 1656
    sinusoidal: 678
      harmonic: 978
  Sorted by residual:
  dihedral pdb=" CB  GLU B 338 "
           pdb=" CG  GLU B 338 "
           pdb=" CD  GLU B 338 "
           pdb=" OE1 GLU B 338 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   88.68  -88.68     1      3.00e+01 1.11e-03 1.04e+01
  dihedral pdb=" CB  GLU D 338 "
           pdb=" CG  GLU D 338 "
           pdb=" CD  GLU D 338 "
           pdb=" OE1 GLU D 338 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   88.66  -88.66     1      3.00e+01 1.11e-03 1.04e+01
  dihedral pdb=" CB  GLU F 338 "
           pdb=" CG  GLU F 338 "
           pdb=" CD  GLU F 338 "
           pdb=" OE1 GLU F 338 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   88.65  -88.65     1      3.00e+01 1.11e-03 1.04e+01
  ... (remaining 1653 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.048: 296
       0.048 -    0.095: 64
       0.095 -    0.143: 36
       0.143 -    0.190: 6
       0.190 -    0.238: 12
  Chirality restraints: 414
  Sorted by residual:
  chirality pdb=" CB  THR D 361 "
            pdb=" CA  THR D 361 "
            pdb=" OG1 THR D 361 "
            pdb=" CG2 THR D 361 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.31    0.24 2.00e-01 2.50e+01 1.42e+00
  chirality pdb=" CB  THR E 361 "
            pdb=" CA  THR E 361 "
            pdb=" OG1 THR E 361 "
            pdb=" CG2 THR E 361 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.32    0.24 2.00e-01 2.50e+01 1.40e+00
  chirality pdb=" CB  THR A 361 "
            pdb=" CA  THR A 361 "
            pdb=" OG1 THR A 361 "
            pdb=" CG2 THR A 361 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.32    0.24 2.00e-01 2.50e+01 1.39e+00
  ... (remaining 411 not shown)

  Planarity restraints: 462
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER E 341 "   -0.004 2.00e-02 2.50e+03   7.23e-03 5.22e-01
        pdb=" C   SER E 341 "    0.013 2.00e-02 2.50e+03
        pdb=" O   SER E 341 "   -0.005 2.00e-02 2.50e+03
        pdb=" N   GLU E 342 "   -0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER B 341 "   -0.004 2.00e-02 2.50e+03   7.11e-03 5.06e-01
        pdb=" C   SER B 341 "    0.012 2.00e-02 2.50e+03
        pdb=" O   SER B 341 "   -0.005 2.00e-02 2.50e+03
        pdb=" N   GLU B 342 "   -0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER D 341 "   -0.003 2.00e-02 2.50e+03   6.96e-03 4.84e-01
        pdb=" C   SER D 341 "    0.012 2.00e-02 2.50e+03
        pdb=" O   SER D 341 "   -0.005 2.00e-02 2.50e+03
        pdb=" N   GLU D 342 "   -0.004 2.00e-02 2.50e+03
  ... (remaining 459 not shown)

  Histogram of nonbonded interaction distances:
        2.33 -     2.84: 799
        2.84 -     3.36: 2167
        3.36 -     3.87: 4389
        3.87 -     4.39: 4578
        4.39 -     4.90: 9317
  Nonbonded interactions: 21250
  Sorted by model distance:
  nonbonded pdb=" NE2 GLN D 336 "
            pdb=" O   GLN A 336 "
     model   vdw
     2.331 3.120
  nonbonded pdb=" O   GLN B 336 "
            pdb=" NE2 GLN A 336 "
     model   vdw
     2.343 3.120
  nonbonded pdb=" O   GLN D 336 "
            pdb=" NE2 GLN C 336 "
     model   vdw
     2.346 3.120
  nonbonded pdb=" NE2 GLN B 336 "
            pdb=" O   GLN F 336 "
     model   vdw
     2.355 3.120
  nonbonded pdb=" NE2 GLN E 336 "
            pdb=" O   GLN C 336 "
     model   vdw
     2.356 3.120
  ... (remaining 21245 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 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
  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:             1.000
  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:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     11.070
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.010
  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:13.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.620
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7901
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      :  0.008   0.047   2712  Z= 0.563
  Angle     :  0.796   4.443   3630  Z= 0.430
  Chirality :  0.064   0.238    414
  Planarity :  0.003   0.007    462
  Dihedral  : 14.504  88.683   1032
  Min Nonbonded Distance : 2.331

Molprobity Statistics.
  All-atom Clashscore : 9.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.28 %
    Favored  : 87.72 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.77 %
    Favored  : 94.23 %
  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: -5.97 (0.30), residues: 342
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.55 (0.23), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS E 362 
 PHE   0.005   0.003   PHE F 346 
 TYR   0.009   0.003   TYR E 310 
 ARG   0.001   0.000   ARG B 349 

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

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

  684 Ramachandran restraints generated.
    342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  684 Ramachandran restraints generated.
    342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.347 
Fit side-chains
REVERT: B  317 LYS cc_start: 0.7820 (ttmt) cc_final: 0.7519 (mtpm)
REVERT: B  343 LYS cc_start: 0.7919 (tttm) cc_final: 0.7707 (ttpt)
REVERT: B  349 ARG cc_start: 0.7178 (mtt-85) cc_final: 0.6597 (mtm-85)
REVERT: D  317 LYS cc_start: 0.7743 (ttmt) cc_final: 0.7464 (mtpp)
REVERT: D  340 LYS cc_start: 0.7845 (ttpt) cc_final: 0.7541 (ttpt)
REVERT: D  348 ASP cc_start: 0.7762 (m-30) cc_final: 0.7318 (m-30)
REVERT: D  349 ARG cc_start: 0.6921 (mtt-85) cc_final: 0.6352 (mtp85)
REVERT: D  353 LYS cc_start: 0.7983 (mtpt) cc_final: 0.7781 (mtpp)
REVERT: E  317 LYS cc_start: 0.7939 (ttmt) cc_final: 0.7712 (mtpt)
REVERT: E  340 LYS cc_start: 0.7980 (ttpt) cc_final: 0.7644 (ttpt)
REVERT: E  343 LYS cc_start: 0.7817 (tttm) cc_final: 0.7516 (ttmm)
REVERT: E  349 ARG cc_start: 0.6799 (mtt-85) cc_final: 0.6325 (mtp85)
REVERT: E  353 LYS cc_start: 0.8137 (mtpt) cc_final: 0.7282 (mttm)
REVERT: F  317 LYS cc_start: 0.7880 (ttmt) cc_final: 0.7551 (mtpm)
REVERT: F  348 ASP cc_start: 0.7820 (m-30) cc_final: 0.7565 (m-30)
REVERT: F  349 ARG cc_start: 0.7140 (mtt-85) cc_final: 0.6885 (mtt90)
REVERT: F  353 LYS cc_start: 0.8156 (mtpt) cc_final: 0.7451 (mttp)
REVERT: A  317 LYS cc_start: 0.7575 (ttmt) cc_final: 0.7144 (mtpt)
REVERT: A  349 ARG cc_start: 0.6752 (mtt-85) cc_final: 0.6532 (mtt90)
REVERT: A  353 LYS cc_start: 0.7834 (mtpt) cc_final: 0.7206 (tptt)
REVERT: C  317 LYS cc_start: 0.7976 (ttmt) cc_final: 0.7664 (tttt)
REVERT: C  343 LYS cc_start: 0.7674 (tttm) cc_final: 0.7455 (tttm)
REVERT: C  349 ARG cc_start: 0.6699 (mtt-85) cc_final: 0.6313 (mtt-85)
REVERT: C  353 LYS cc_start: 0.8039 (mtpt) cc_final: 0.7325 (mttp)
  outliers start: 0
  outliers final: 0
  residues processed: 81
  average time/residue: 1.4434
  time to fit residues: 119.1709
Evaluate side-chains
  56 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 56
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 25 optimal weight:    0.8980
   chunk 22 optimal weight:    0.8980
   chunk 12 optimal weight:    4.9990
   chunk 7 optimal weight:    0.9990
   chunk 15 optimal weight:    2.9990
   chunk 23 optimal weight:    5.9990
   chunk 9 optimal weight:    3.9990
   chunk 14 optimal weight:   10.0000
   chunk 17 optimal weight:    0.8980
   chunk 27 optimal weight:    4.9990
   chunk 8 optimal weight:    6.9990
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
B 307 GLN
B 329 HIS
B 330 HIS
D 307 GLN
D 329 HIS
D 330 HIS
E 307 GLN
E 329 HIS
F 307 GLN
F 329 HIS
F 330 HIS
A 307 GLN
A 329 HIS
A 330 HIS
C 307 GLN
C 329 HIS

Total number of N/Q/H flips: 16

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4203 r_free = 0.4203 target = 0.136450 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.108456 restraints weight = 3504.463|
|-----------------------------------------------------------------------------|
r_work (start): 0.3870 rms_B_bonded: 2.26
r_work: 0.3776 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3677 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.3677
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8016
moved from start:          0.1911

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.017   2712  Z= 0.182
  Angle     :  0.579   4.521   3630  Z= 0.287
  Chirality :  0.053   0.144    414
  Planarity :  0.002   0.014    462
  Dihedral  :  4.155  10.510    360
  Min Nonbonded Distance : 2.633

Molprobity Statistics.
  All-atom Clashscore : 7.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.73 %
    Favored  : 93.27 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 13.46 %
    Favored  : 83.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.54 (0.32), residues: 342
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.21 (0.24), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS D 362 
 PHE   0.003   0.001   PHE E 346 
 TYR   0.004   0.001   TYR C 310 
 ARG   0.001   0.000   ARG E 349 

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

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

  684 Ramachandran restraints generated.
    342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  684 Ramachandran restraints generated.
    342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 69
  time to evaluate  : 0.355 
Fit side-chains
REVERT: B  340 LYS cc_start: 0.8025 (ttpt) cc_final: 0.7705 (ttmm)
REVERT: B  349 ARG cc_start: 0.7522 (mtt-85) cc_final: 0.7075 (mtm-85)
REVERT: D  317 LYS cc_start: 0.7948 (ttmt) cc_final: 0.7673 (ttpp)
REVERT: D  340 LYS cc_start: 0.8062 (ttpt) cc_final: 0.7843 (ttpt)
REVERT: D  348 ASP cc_start: 0.8043 (m-30) cc_final: 0.7738 (m-30)
REVERT: D  349 ARG cc_start: 0.7269 (mtt-85) cc_final: 0.6674 (mtp85)
REVERT: D  353 LYS cc_start: 0.8001 (mtpt) cc_final: 0.7150 (mppt)
REVERT: E  317 LYS cc_start: 0.8209 (ttmt) cc_final: 0.7824 (tttt)
REVERT: E  343 LYS cc_start: 0.7968 (tttm) cc_final: 0.7718 (ttmm)
REVERT: E  348 ASP cc_start: 0.7816 (OUTLIER) cc_final: 0.7555 (m-30)
REVERT: E  349 ARG cc_start: 0.7056 (mtt-85) cc_final: 0.6513 (mtp85)
REVERT: F  317 LYS cc_start: 0.8013 (ttmt) cc_final: 0.7769 (mtpm)
REVERT: F  348 ASP cc_start: 0.8239 (m-30) cc_final: 0.7933 (m-30)
REVERT: F  349 ARG cc_start: 0.7534 (mtt-85) cc_final: 0.7213 (mtm-85)
REVERT: F  353 LYS cc_start: 0.7981 (mtpt) cc_final: 0.7342 (mttp)
REVERT: A  340 LYS cc_start: 0.8085 (ttpt) cc_final: 0.7881 (ttpt)
REVERT: A  349 ARG cc_start: 0.7161 (mtt-85) cc_final: 0.6828 (mtt90)
REVERT: A  357 LEU cc_start: 0.7895 (tt) cc_final: 0.7579 (tp)
REVERT: C  317 LYS cc_start: 0.8272 (ttmt) cc_final: 0.7878 (tttt)
REVERT: C  348 ASP cc_start: 0.8032 (m-30) cc_final: 0.7718 (m-30)
REVERT: C  349 ARG cc_start: 0.6994 (mtt-85) cc_final: 0.6372 (mtp-110)
REVERT: C  353 LYS cc_start: 0.8128 (mtpt) cc_final: 0.7404 (mttp)
  outliers start: 8
  outliers final: 4
  residues processed: 72
  average time/residue: 1.6116
  time to fit residues: 118.1774
Evaluate side-chains
  60 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 55
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain E residue  320 SER
Chi-restraints excluded: chain E residue  348 ASP
Chi-restraints excluded: chain F residue  315 LEU
Chi-restraints excluded: chain A residue  348 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 17 optimal weight:    0.9990
   chunk 2 optimal weight:    1.9990
   chunk 29 optimal weight:    7.9990
   chunk 19 optimal weight:    5.9990
   chunk 21 optimal weight:    9.9990
   chunk 20 optimal weight:    6.9990
   chunk 28 optimal weight:   10.0000
   chunk 12 optimal weight:    0.8980
   chunk 8 optimal weight:    8.9990
   chunk 0 optimal weight:    7.9990
   chunk 14 optimal weight:    1.9990
   overall best weight:    2.3788

-------------------------------------------------------------------------------
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 = 0.4187 r_free = 0.4187 target = 0.134444 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.107336 restraints weight = 3571.099|
|-----------------------------------------------------------------------------|
r_work (start): 0.3868 rms_B_bonded: 2.17
r_work: 0.3779 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3684 rms_B_bonded: 3.73 restraints_weight: 0.2500
r_work (final): 0.3684
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8006
moved from start:          0.2143

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   2712  Z= 0.253
  Angle     :  0.607   5.241   3630  Z= 0.298
  Chirality :  0.052   0.147    414
  Planarity :  0.002   0.013    462
  Dihedral  :  4.318  11.334    360
  Min Nonbonded Distance : 2.640

Molprobity Statistics.
  All-atom Clashscore : 8.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.19 %
    Favored  : 91.81 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 16.67 %
    Favored  : 79.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.60 (0.32), residues: 342
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.26 (0.24), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS E 362 
 PHE   0.004   0.002   PHE E 346 
 TYR   0.006   0.002   TYR A 310 
 ARG   0.001   0.000   ARG E 349 

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

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

  684 Ramachandran restraints generated.
    342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  684 Ramachandran restraints generated.
    342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 60
  time to evaluate  : 0.312 
Fit side-chains
REVERT: B  340 LYS cc_start: 0.7924 (ttpt) cc_final: 0.7719 (ttpp)
REVERT: B  349 ARG cc_start: 0.7547 (mtt-85) cc_final: 0.7141 (mtm-85)
REVERT: D  317 LYS cc_start: 0.7935 (ttmt) cc_final: 0.7636 (ttpp)
REVERT: D  340 LYS cc_start: 0.7898 (ttpt) cc_final: 0.7663 (ttpt)
REVERT: D  348 ASP cc_start: 0.8009 (m-30) cc_final: 0.7719 (m-30)
REVERT: D  349 ARG cc_start: 0.7184 (mtt-85) cc_final: 0.6517 (mtp85)
REVERT: D  353 LYS cc_start: 0.7956 (mtpt) cc_final: 0.7098 (mppt)
REVERT: D  358 ASP cc_start: 0.6346 (m-30) cc_final: 0.5542 (p0)
REVERT: E  317 LYS cc_start: 0.8098 (ttmt) cc_final: 0.7825 (ttpp)
REVERT: E  343 LYS cc_start: 0.8081 (tttm) cc_final: 0.7780 (ttmm)
REVERT: E  348 ASP cc_start: 0.7849 (OUTLIER) cc_final: 0.7586 (m-30)
REVERT: E  349 ARG cc_start: 0.6978 (mtt-85) cc_final: 0.6436 (mtp85)
REVERT: F  317 LYS cc_start: 0.7971 (ttmt) cc_final: 0.7675 (mtpm)
REVERT: F  348 ASP cc_start: 0.8262 (m-30) cc_final: 0.8026 (m-30)
REVERT: F  349 ARG cc_start: 0.7538 (mtt-85) cc_final: 0.7293 (mtm-85)
REVERT: A  317 LYS cc_start: 0.7862 (ttmt) cc_final: 0.7492 (mtpt)
REVERT: A  349 ARG cc_start: 0.7136 (mtt-85) cc_final: 0.6531 (mtp-110)
REVERT: A  357 LEU cc_start: 0.7774 (tt) cc_final: 0.7345 (tp)
REVERT: A  358 ASP cc_start: 0.6852 (m-30) cc_final: 0.6532 (m-30)
REVERT: C  317 LYS cc_start: 0.8171 (ttmt) cc_final: 0.7712 (ttmm)
REVERT: C  349 ARG cc_start: 0.6939 (mtt-85) cc_final: 0.6328 (mtp-110)
REVERT: C  353 LYS cc_start: 0.8175 (mtpt) cc_final: 0.7443 (mttp)
  outliers start: 11
  outliers final: 7
  residues processed: 68
  average time/residue: 1.5715
  time to fit residues: 108.8696
Evaluate side-chains
  65 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 57
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain D residue  316 SER
Chi-restraints excluded: chain E residue  320 SER
Chi-restraints excluded: chain E residue  348 ASP
Chi-restraints excluded: chain F residue  315 LEU
Chi-restraints excluded: chain A residue  316 SER
Chi-restraints excluded: chain A residue  348 ASP
Chi-restraints excluded: chain C residue  311 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 2 optimal weight:    7.9990
   chunk 14 optimal weight:    9.9990
   chunk 8 optimal weight:    5.9990
   chunk 1 optimal weight:    3.9990
   chunk 10 optimal weight:    7.9990
   chunk 26 optimal weight:    9.9990
   chunk 16 optimal weight:    5.9990
   chunk 7 optimal weight:    5.9990
   chunk 9 optimal weight:    5.9990
   chunk 15 optimal weight:    8.9990
   chunk 29 optimal weight:    6.9990
   overall best weight:    5.5990

-------------------------------------------------------------------------------
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 = 0.4172 r_free = 0.4172 target = 0.132783 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.105750 restraints weight = 3611.487|
|-----------------------------------------------------------------------------|
r_work (start): 0.3849 rms_B_bonded: 2.16
r_work: 0.3759 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.3661 rms_B_bonded: 3.69 restraints_weight: 0.2500
r_work (final): 0.3661
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8013
moved from start:          0.2280

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.047   2712  Z= 0.478
  Angle     :  0.779   7.089   3630  Z= 0.386
  Chirality :  0.056   0.151    414
  Planarity :  0.004   0.015    462
  Dihedral  :  5.197  14.316    360
  Min Nonbonded Distance : 2.647

Molprobity Statistics.
  All-atom Clashscore : 10.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.91 %
    Favored  : 85.09 %
  Rotamer:
    Outliers :  8.33 %
    Allowed  : 14.42 %
    Favored  : 77.24 %
  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: -5.77 (0.31), residues: 342
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.39 (0.23), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS F 362 
 PHE   0.007   0.003   PHE F 346 
 TYR   0.012   0.003   TYR C 310 
 ARG   0.003   0.001   ARG E 349 

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

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

  684 Ramachandran restraints generated.
    342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  684 Ramachandran restraints generated.
    342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 61
  time to evaluate  : 0.316 
Fit side-chains
REVERT: B  340 LYS cc_start: 0.7882 (ttpt) cc_final: 0.7620 (ttpp)
REVERT: B  348 ASP cc_start: 0.8233 (m-30) cc_final: 0.7720 (m-30)
REVERT: B  349 ARG cc_start: 0.7593 (mtt-85) cc_final: 0.7173 (mtm-85)
REVERT: B  353 LYS cc_start: 0.8094 (OUTLIER) cc_final: 0.7643 (mtpt)
REVERT: D  317 LYS cc_start: 0.7943 (ttmt) cc_final: 0.7625 (ttpp)
REVERT: D  349 ARG cc_start: 0.7124 (mtt-85) cc_final: 0.6437 (mtp85)
REVERT: D  353 LYS cc_start: 0.8027 (mtpt) cc_final: 0.7758 (mtpp)
REVERT: D  358 ASP cc_start: 0.6236 (m-30) cc_final: 0.5947 (t0)
REVERT: E  317 LYS cc_start: 0.8131 (ttmt) cc_final: 0.7844 (ttpp)
REVERT: E  325 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8264 (pp)
REVERT: E  343 LYS cc_start: 0.7969 (tttm) cc_final: 0.7684 (ttmm)
REVERT: E  349 ARG cc_start: 0.7123 (mtt-85) cc_final: 0.6426 (mtp85)
REVERT: F  317 LYS cc_start: 0.8023 (ttmt) cc_final: 0.7777 (mtpm)
REVERT: F  348 ASP cc_start: 0.8263 (m-30) cc_final: 0.8031 (m-30)
REVERT: F  349 ARG cc_start: 0.7492 (mtt-85) cc_final: 0.7081 (mtm-85)
REVERT: F  353 LYS cc_start: 0.8011 (mtpt) cc_final: 0.7386 (mttp)
REVERT: A  317 LYS cc_start: 0.7804 (ttmt) cc_final: 0.7322 (mttt)
REVERT: A  340 LYS cc_start: 0.7923 (OUTLIER) cc_final: 0.7655 (ttpp)
REVERT: A  349 ARG cc_start: 0.7052 (mtt-85) cc_final: 0.6368 (mtp-110)
REVERT: A  357 LEU cc_start: 0.8046 (tt) cc_final: 0.7638 (tp)
REVERT: C  317 LYS cc_start: 0.8177 (ttmt) cc_final: 0.7733 (ttmm)
REVERT: C  349 ARG cc_start: 0.7034 (mtt-85) cc_final: 0.6438 (mtp-110)
  outliers start: 26
  outliers final: 15
  residues processed: 82
  average time/residue: 1.3258
  time to fit residues: 110.9653
Evaluate side-chains
  75 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 57
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain B residue  353 LYS
Chi-restraints excluded: chain D residue  306 VAL
Chi-restraints excluded: chain D residue  315 LEU
Chi-restraints excluded: chain D residue  316 SER
Chi-restraints excluded: chain E residue  306 VAL
Chi-restraints excluded: chain E residue  316 SER
Chi-restraints excluded: chain E residue  320 SER
Chi-restraints excluded: chain E residue  325 LEU
Chi-restraints excluded: chain E residue  348 ASP
Chi-restraints excluded: chain A residue  306 VAL
Chi-restraints excluded: chain A residue  316 SER
Chi-restraints excluded: chain A residue  322 CYS
Chi-restraints excluded: chain A residue  340 LYS
Chi-restraints excluded: chain A residue  348 ASP
Chi-restraints excluded: chain C residue  311 LYS
Chi-restraints excluded: chain C residue  316 SER
Chi-restraints excluded: chain C residue  348 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 28 optimal weight:    5.9990
   chunk 0 optimal weight:    4.9990
   chunk 29 optimal weight:    9.9990
   chunk 11 optimal weight:    5.9990
   chunk 8 optimal weight:   10.0000
   chunk 20 optimal weight:    0.9980
   chunk 6 optimal weight:    6.9990
   chunk 21 optimal weight:    9.9990
   chunk 17 optimal weight:    2.9990
   chunk 19 optimal weight:   10.0000
   chunk 26 optimal weight:    6.9990
   overall best weight:    4.1988

-------------------------------------------------------------------------------
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 = 0.4178 r_free = 0.4178 target = 0.134013 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.106587 restraints weight = 3547.102|
|-----------------------------------------------------------------------------|
r_work (start): 0.3861 rms_B_bonded: 2.18
r_work: 0.3769 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3671 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.3671
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8007
moved from start:          0.2498

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.038   2712  Z= 0.376
  Angle     :  0.702   6.056   3630  Z= 0.348
  Chirality :  0.054   0.147    414
  Planarity :  0.003   0.016    462
  Dihedral  :  4.996  13.515    360
  Min Nonbonded Distance : 2.649

Molprobity Statistics.
  All-atom Clashscore : 10.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.11 %
    Favored  : 88.89 %
  Rotamer:
    Outliers :  7.37 %
    Allowed  : 16.99 %
    Favored  : 75.64 %
  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: -5.67 (0.31), residues: 342
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.31 (0.24), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS F 362 
 PHE   0.006   0.003   PHE F 346 
 TYR   0.009   0.002   TYR C 310 
 ARG   0.002   0.001   ARG E 349 

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

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

  684 Ramachandran restraints generated.
    342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  684 Ramachandran restraints generated.
    342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 56
  time to evaluate  : 0.345 
Fit side-chains
REVERT: B  348 ASP cc_start: 0.8184 (m-30) cc_final: 0.7693 (m-30)
REVERT: B  349 ARG cc_start: 0.7593 (mtt-85) cc_final: 0.7175 (mtm-85)
REVERT: B  353 LYS cc_start: 0.8064 (OUTLIER) cc_final: 0.7601 (mtpt)
REVERT: D  311 LYS cc_start: 0.8219 (OUTLIER) cc_final: 0.7998 (mmtp)
REVERT: D  317 LYS cc_start: 0.7964 (ttmt) cc_final: 0.7662 (ttpp)
REVERT: D  349 ARG cc_start: 0.7147 (mtt-85) cc_final: 0.6510 (mtp85)
REVERT: D  353 LYS cc_start: 0.8052 (mtpt) cc_final: 0.7780 (mtpp)
REVERT: E  317 LYS cc_start: 0.8109 (ttmt) cc_final: 0.7846 (ttpp)
REVERT: E  325 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8316 (pp)
REVERT: E  342 GLU cc_start: 0.8060 (pt0) cc_final: 0.7585 (pt0)
REVERT: E  343 LYS cc_start: 0.8018 (tttm) cc_final: 0.7715 (ttmm)
REVERT: E  348 ASP cc_start: 0.7924 (OUTLIER) cc_final: 0.7633 (m-30)
REVERT: E  349 ARG cc_start: 0.7142 (mtt-85) cc_final: 0.6489 (mtp85)
REVERT: F  317 LYS cc_start: 0.7981 (ttmt) cc_final: 0.7707 (mtpm)
REVERT: F  348 ASP cc_start: 0.8279 (m-30) cc_final: 0.8042 (m-30)
REVERT: F  349 ARG cc_start: 0.7474 (mtt-85) cc_final: 0.7074 (mtm-85)
REVERT: F  353 LYS cc_start: 0.7949 (mtpt) cc_final: 0.7315 (mttp)
REVERT: A  317 LYS cc_start: 0.7813 (ttmt) cc_final: 0.7461 (mtpt)
REVERT: A  340 LYS cc_start: 0.7879 (OUTLIER) cc_final: 0.7630 (ttpp)
REVERT: A  349 ARG cc_start: 0.7114 (mtt-85) cc_final: 0.6451 (mtp-110)
REVERT: A  357 LEU cc_start: 0.8012 (tt) cc_final: 0.7582 (tp)
REVERT: C  317 LYS cc_start: 0.8183 (ttmt) cc_final: 0.7738 (ttmm)
REVERT: C  349 ARG cc_start: 0.7043 (mtt-85) cc_final: 0.6468 (mtp-110)
  outliers start: 23
  outliers final: 15
  residues processed: 73
  average time/residue: 1.4139
  time to fit residues: 105.3354
Evaluate side-chains
  73 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 53
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain B residue  353 LYS
Chi-restraints excluded: chain D residue  306 VAL
Chi-restraints excluded: chain D residue  311 LYS
Chi-restraints excluded: chain D residue  315 LEU
Chi-restraints excluded: chain D residue  316 SER
Chi-restraints excluded: chain D residue  348 ASP
Chi-restraints excluded: chain E residue  320 SER
Chi-restraints excluded: chain E residue  325 LEU
Chi-restraints excluded: chain E residue  348 ASP
Chi-restraints excluded: chain F residue  315 LEU
Chi-restraints excluded: chain F residue  325 LEU
Chi-restraints excluded: chain A residue  306 VAL
Chi-restraints excluded: chain A residue  316 SER
Chi-restraints excluded: chain A residue  322 CYS
Chi-restraints excluded: chain A residue  340 LYS
Chi-restraints excluded: chain A residue  348 ASP
Chi-restraints excluded: chain C residue  306 VAL
Chi-restraints excluded: chain C residue  311 LYS
Chi-restraints excluded: chain C residue  348 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 12 optimal weight:    0.9990
   chunk 6 optimal weight:   10.0000
   chunk 28 optimal weight:    9.9990
   chunk 8 optimal weight:    6.9990
   chunk 1 optimal weight:    3.9990
   chunk 3 optimal weight:    1.9990
   chunk 10 optimal weight:    3.9990
   chunk 4 optimal weight:    2.9990
   chunk 15 optimal weight:    6.9990
   chunk 29 optimal weight:    9.9990
   chunk 9 optimal weight:    1.9990
   overall best weight:    2.3990

-------------------------------------------------------------------------------
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 = 0.136030 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.108620 restraints weight = 3612.228|
|-----------------------------------------------------------------------------|
r_work (start): 0.3890 rms_B_bonded: 2.19
r_work: 0.3801 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3703 rms_B_bonded: 3.77 restraints_weight: 0.2500
r_work (final): 0.3703
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7985
moved from start:          0.2677

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   2712  Z= 0.250
  Angle     :  0.612   5.424   3630  Z= 0.301
  Chirality :  0.052   0.142    414
  Planarity :  0.002   0.017    462
  Dihedral  :  4.579  12.713    360
  Min Nonbonded Distance : 2.643

Molprobity Statistics.
  All-atom Clashscore : 8.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.06 %
    Favored  : 90.94 %
  Rotamer:
    Outliers :  6.09 %
    Allowed  : 19.87 %
    Favored  : 74.04 %
  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: -5.49 (0.32), residues: 342
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.18 (0.25), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS E 362 
 PHE   0.004   0.002   PHE C 346 
 TYR   0.005   0.002   TYR C 310 
 ARG   0.002   0.001   ARG A 349 

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

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

  684 Ramachandran restraints generated.
    342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  684 Ramachandran restraints generated.
    342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 54
  time to evaluate  : 0.326 
Fit side-chains
REVERT: B  348 ASP cc_start: 0.8204 (m-30) cc_final: 0.7726 (m-30)
REVERT: B  349 ARG cc_start: 0.7565 (mtt-85) cc_final: 0.7189 (mtm-85)
REVERT: D  317 LYS cc_start: 0.7992 (ttmt) cc_final: 0.7703 (ttpp)
REVERT: D  349 ARG cc_start: 0.7179 (mtt-85) cc_final: 0.6551 (mtp85)
REVERT: D  353 LYS cc_start: 0.8028 (mtpt) cc_final: 0.7158 (mppt)
REVERT: E  317 LYS cc_start: 0.8106 (ttmt) cc_final: 0.7811 (ttpp)
REVERT: E  342 GLU cc_start: 0.8012 (pt0) cc_final: 0.7585 (pt0)
REVERT: E  343 LYS cc_start: 0.8071 (tttm) cc_final: 0.7773 (ttmm)
REVERT: E  348 ASP cc_start: 0.7871 (OUTLIER) cc_final: 0.7595 (m-30)
REVERT: E  349 ARG cc_start: 0.7067 (mtt-85) cc_final: 0.6482 (mtp85)
REVERT: F  317 LYS cc_start: 0.7937 (ttmt) cc_final: 0.7669 (mtpm)
REVERT: F  348 ASP cc_start: 0.8285 (m-30) cc_final: 0.8032 (m-30)
REVERT: F  349 ARG cc_start: 0.7464 (mtt-85) cc_final: 0.6787 (mtm-85)
REVERT: A  317 LYS cc_start: 0.7862 (ttmt) cc_final: 0.7514 (mtpt)
REVERT: A  349 ARG cc_start: 0.7107 (mtt-85) cc_final: 0.6543 (mtp85)
REVERT: A  357 LEU cc_start: 0.7888 (tt) cc_final: 0.7447 (tp)
REVERT: C  317 LYS cc_start: 0.8189 (ttmt) cc_final: 0.7728 (ttmm)
REVERT: C  349 ARG cc_start: 0.7018 (mtt-85) cc_final: 0.6474 (mtp-110)
  outliers start: 19
  outliers final: 13
  residues processed: 68
  average time/residue: 1.3631
  time to fit residues: 94.6047
Evaluate side-chains
  68 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 54
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain D residue  306 VAL
Chi-restraints excluded: chain D residue  316 SER
Chi-restraints excluded: chain D residue  348 ASP
Chi-restraints excluded: chain E residue  306 VAL
Chi-restraints excluded: chain E residue  318 VAL
Chi-restraints excluded: chain E residue  320 SER
Chi-restraints excluded: chain E residue  348 ASP
Chi-restraints excluded: chain F residue  315 LEU
Chi-restraints excluded: chain F residue  325 LEU
Chi-restraints excluded: chain A residue  306 VAL
Chi-restraints excluded: chain A residue  316 SER
Chi-restraints excluded: chain A residue  348 ASP
Chi-restraints excluded: chain C residue  311 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 19 optimal weight:   10.0000
   chunk 29 optimal weight:    7.9990
   chunk 20 optimal weight:    6.9990
   chunk 27 optimal weight:    8.9990
   chunk 21 optimal weight:   20.0000
   chunk 25 optimal weight:    0.1980
   chunk 13 optimal weight:    9.9990
   chunk 6 optimal weight:   20.0000
   chunk 14 optimal weight:    8.9990
   chunk 24 optimal weight:    5.9990
   chunk 1 optimal weight:    1.9990
   overall best weight:    4.6388

-------------------------------------------------------------------------------
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 = 0.4179 r_free = 0.4179 target = 0.133911 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.106563 restraints weight = 3713.105|
|-----------------------------------------------------------------------------|
r_work (start): 0.3860 rms_B_bonded: 2.21
r_work: 0.3769 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3670 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.3670
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8004
moved from start:          0.2667

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.041   2712  Z= 0.406
  Angle     :  0.723   6.316   3630  Z= 0.357
  Chirality :  0.055   0.147    414
  Planarity :  0.003   0.014    462
  Dihedral  :  5.091  14.128    360
  Min Nonbonded Distance : 2.648

Molprobity Statistics.
  All-atom Clashscore : 10.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.91 %
    Favored  : 85.09 %
  Rotamer:
    Outliers :  9.29 %
    Allowed  : 17.31 %
    Favored  : 73.40 %
  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: -5.60 (0.31), residues: 342
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.26 (0.24), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS F 362 
 PHE   0.006   0.003   PHE E 346 
 TYR   0.010   0.003   TYR C 310 
 ARG   0.002   0.001   ARG F 349 

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

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

  684 Ramachandran restraints generated.
    342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  684 Ramachandran restraints generated.
    342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 56
  time to evaluate  : 0.323 
Fit side-chains
REVERT: B  348 ASP cc_start: 0.8231 (m-30) cc_final: 0.7741 (m-30)
REVERT: B  349 ARG cc_start: 0.7657 (mtt-85) cc_final: 0.7279 (mtm-85)
REVERT: B  353 LYS cc_start: 0.8071 (OUTLIER) cc_final: 0.7601 (mtpt)
REVERT: D  317 LYS cc_start: 0.7989 (ttmt) cc_final: 0.7691 (ttpp)
REVERT: D  349 ARG cc_start: 0.7174 (mtt-85) cc_final: 0.6540 (mtp85)
REVERT: D  353 LYS cc_start: 0.8048 (mtpt) cc_final: 0.7181 (mppt)
REVERT: E  317 LYS cc_start: 0.8125 (ttmt) cc_final: 0.7828 (ttpp)
REVERT: E  325 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8206 (pp)
REVERT: E  343 LYS cc_start: 0.8054 (tttm) cc_final: 0.7771 (ttmm)
REVERT: E  349 ARG cc_start: 0.7116 (mtt-85) cc_final: 0.6435 (mtp85)
REVERT: F  317 LYS cc_start: 0.8040 (ttmt) cc_final: 0.7775 (mtpm)
REVERT: F  348 ASP cc_start: 0.8303 (m-30) cc_final: 0.8044 (m-30)
REVERT: F  349 ARG cc_start: 0.7452 (mtt-85) cc_final: 0.7132 (mtm-85)
REVERT: F  353 LYS cc_start: 0.7937 (mtpt) cc_final: 0.7302 (mttp)
REVERT: A  317 LYS cc_start: 0.7827 (ttmt) cc_final: 0.7471 (mtpt)
REVERT: A  340 LYS cc_start: 0.7813 (OUTLIER) cc_final: 0.7562 (ttpp)
REVERT: A  349 ARG cc_start: 0.7073 (mtt-85) cc_final: 0.6479 (mtp-110)
REVERT: A  353 LYS cc_start: 0.7719 (mtpt) cc_final: 0.7178 (tptt)
REVERT: A  357 LEU cc_start: 0.7993 (tt) cc_final: 0.7582 (tp)
REVERT: C  317 LYS cc_start: 0.8194 (ttmt) cc_final: 0.7751 (ttmm)
REVERT: C  349 ARG cc_start: 0.7023 (mtt-85) cc_final: 0.6414 (mtp-110)
  outliers start: 29
  outliers final: 20
  residues processed: 77
  average time/residue: 1.3367
  time to fit residues: 105.1749
Evaluate side-chains
  78 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 55
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain B residue  353 LYS
Chi-restraints excluded: chain D residue  306 VAL
Chi-restraints excluded: chain D residue  316 SER
Chi-restraints excluded: chain D residue  348 ASP
Chi-restraints excluded: chain E residue  306 VAL
Chi-restraints excluded: chain E residue  316 SER
Chi-restraints excluded: chain E residue  318 VAL
Chi-restraints excluded: chain E residue  320 SER
Chi-restraints excluded: chain E residue  325 LEU
Chi-restraints excluded: chain E residue  348 ASP
Chi-restraints excluded: chain F residue  315 LEU
Chi-restraints excluded: chain F residue  325 LEU
Chi-restraints excluded: chain A residue  306 VAL
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain A residue  316 SER
Chi-restraints excluded: chain A residue  322 CYS
Chi-restraints excluded: chain A residue  340 LYS
Chi-restraints excluded: chain A residue  348 ASP
Chi-restraints excluded: chain C residue  306 VAL
Chi-restraints excluded: chain C residue  311 LYS
Chi-restraints excluded: chain C residue  316 SER
Chi-restraints excluded: chain C residue  348 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 0 optimal weight:    6.9990
   chunk 14 optimal weight:    6.9990
   chunk 18 optimal weight:    8.9990
   chunk 6 optimal weight:    6.9990
   chunk 13 optimal weight:    0.7980
   chunk 29 optimal weight:    9.9990
   chunk 8 optimal weight:    1.9990
   chunk 20 optimal weight:    4.9990
   chunk 26 optimal weight:    7.9990
   chunk 4 optimal weight:    6.9990
   chunk 10 optimal weight:    0.9990
   overall best weight:    3.1588

-------------------------------------------------------------------------------
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 = 0.4195 r_free = 0.4195 target = 0.135911 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.108337 restraints weight = 3466.755|
|-----------------------------------------------------------------------------|
r_work (start): 0.3880 rms_B_bonded: 2.17
r_work: 0.3789 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3690 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.3690
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7991
moved from start:          0.2744

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   2712  Z= 0.303
  Angle     :  0.654   5.997   3630  Z= 0.322
  Chirality :  0.053   0.144    414
  Planarity :  0.003   0.017    462
  Dihedral  :  4.844  13.439    360
  Min Nonbonded Distance : 2.647

Molprobity Statistics.
  All-atom Clashscore : 10.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.94 %
    Favored  : 90.06 %
  Rotamer:
    Outliers :  8.01 %
    Allowed  : 19.23 %
    Favored  : 72.76 %
  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: -5.50 (0.32), residues: 342
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.19 (0.24), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS F 362 
 PHE   0.004   0.002   PHE C 346 
 TYR   0.007   0.002   TYR C 310 
 ARG   0.002   0.001   ARG E 349 

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

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

  684 Ramachandran restraints generated.
    342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  684 Ramachandran restraints generated.
    342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 54
  time to evaluate  : 0.257 
Fit side-chains
REVERT: B  348 ASP cc_start: 0.8238 (m-30) cc_final: 0.7740 (m-30)
REVERT: B  349 ARG cc_start: 0.7636 (mtt-85) cc_final: 0.7274 (mtm-85)
REVERT: B  353 LYS cc_start: 0.8049 (OUTLIER) cc_final: 0.7569 (mtpt)
REVERT: D  317 LYS cc_start: 0.7991 (ttmt) cc_final: 0.7713 (ttpp)
REVERT: D  349 ARG cc_start: 0.7197 (mtt-85) cc_final: 0.6584 (mtp85)
REVERT: D  353 LYS cc_start: 0.8033 (mtpt) cc_final: 0.7154 (mppt)
REVERT: E  317 LYS cc_start: 0.8119 (ttmt) cc_final: 0.7831 (ttpp)
REVERT: E  325 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8257 (pp)
REVERT: E  342 GLU cc_start: 0.8006 (pt0) cc_final: 0.7559 (pt0)
REVERT: E  343 LYS cc_start: 0.8087 (tttm) cc_final: 0.7771 (ttmm)
REVERT: E  348 ASP cc_start: 0.7880 (OUTLIER) cc_final: 0.7608 (m-30)
REVERT: E  349 ARG cc_start: 0.7103 (mtt-85) cc_final: 0.6491 (mtp85)
REVERT: F  317 LYS cc_start: 0.7947 (ttmt) cc_final: 0.7687 (mtpm)
REVERT: F  348 ASP cc_start: 0.8289 (m-30) cc_final: 0.8036 (m-30)
REVERT: F  349 ARG cc_start: 0.7458 (mtt-85) cc_final: 0.7133 (mtm-85)
REVERT: A  317 LYS cc_start: 0.7822 (ttmt) cc_final: 0.7493 (mtpt)
REVERT: A  349 ARG cc_start: 0.7113 (mtt-85) cc_final: 0.6477 (mtp-110)
REVERT: A  357 LEU cc_start: 0.7956 (tt) cc_final: 0.7521 (tp)
REVERT: C  317 LYS cc_start: 0.8188 (ttmt) cc_final: 0.7735 (ttmm)
REVERT: C  349 ARG cc_start: 0.7057 (mtt-85) cc_final: 0.6466 (mtp-110)
  outliers start: 25
  outliers final: 17
  residues processed: 73
  average time/residue: 1.3394
  time to fit residues: 99.8652
Evaluate side-chains
  74 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 54
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain B residue  353 LYS
Chi-restraints excluded: chain D residue  306 VAL
Chi-restraints excluded: chain D residue  316 SER
Chi-restraints excluded: chain D residue  348 ASP
Chi-restraints excluded: chain D residue  358 ASP
Chi-restraints excluded: chain E residue  306 VAL
Chi-restraints excluded: chain E residue  316 SER
Chi-restraints excluded: chain E residue  318 VAL
Chi-restraints excluded: chain E residue  320 SER
Chi-restraints excluded: chain E residue  325 LEU
Chi-restraints excluded: chain E residue  348 ASP
Chi-restraints excluded: chain F residue  315 LEU
Chi-restraints excluded: chain F residue  325 LEU
Chi-restraints excluded: chain A residue  306 VAL
Chi-restraints excluded: chain A residue  316 SER
Chi-restraints excluded: chain A residue  322 CYS
Chi-restraints excluded: chain A residue  348 ASP
Chi-restraints excluded: chain C residue  306 VAL
Chi-restraints excluded: chain C residue  311 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 14 optimal weight:    8.9990
   chunk 21 optimal weight:   20.0000
   chunk 11 optimal weight:    5.9990
   chunk 0 optimal weight:    8.9990
   chunk 23 optimal weight:    9.9990
   chunk 20 optimal weight:    5.9990
   chunk 8 optimal weight:    6.9990
   chunk 29 optimal weight:    5.9990
   chunk 26 optimal weight:    1.9990
   chunk 27 optimal weight:    2.9990
   chunk 15 optimal weight:    0.8980
   overall best weight:    3.5788

-------------------------------------------------------------------------------
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 = 0.4190 r_free = 0.4190 target = 0.135612 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.108158 restraints weight = 3505.442|
|-----------------------------------------------------------------------------|
r_work (start): 0.3877 rms_B_bonded: 2.18
r_work: 0.3786 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3687 rms_B_bonded: 3.77 restraints_weight: 0.2500
r_work (final): 0.3687
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7994
moved from start:          0.2748

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033   2712  Z= 0.332
  Angle     :  0.680   6.229   3630  Z= 0.333
  Chirality :  0.054   0.145    414
  Planarity :  0.003   0.016    462
  Dihedral  :  4.918  13.839    360
  Min Nonbonded Distance : 2.645

Molprobity Statistics.
  All-atom Clashscore : 10.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.87 %
    Favored  : 87.13 %
  Rotamer:
    Outliers :  8.01 %
    Allowed  : 19.23 %
    Favored  : 72.76 %
  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: -5.52 (0.32), residues: 342
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.20 (0.24), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS F 362 
 PHE   0.004   0.002   PHE E 346 
 TYR   0.008   0.002   TYR C 310 
 ARG   0.002   0.001   ARG A 349 

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

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

  684 Ramachandran restraints generated.
    342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  684 Ramachandran restraints generated.
    342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 57
  time to evaluate  : 0.372 
Fit side-chains
REVERT: B  348 ASP cc_start: 0.8255 (m-30) cc_final: 0.7742 (m-30)
REVERT: B  349 ARG cc_start: 0.7649 (mtt-85) cc_final: 0.7398 (mtp85)
REVERT: B  353 LYS cc_start: 0.8040 (OUTLIER) cc_final: 0.7565 (mtpt)
REVERT: D  317 LYS cc_start: 0.7989 (ttmt) cc_final: 0.7706 (ttpp)
REVERT: D  349 ARG cc_start: 0.7163 (mtt-85) cc_final: 0.6779 (mtp85)
REVERT: D  353 LYS cc_start: 0.8036 (mtpt) cc_final: 0.7121 (mppt)
REVERT: E  317 LYS cc_start: 0.8113 (ttmt) cc_final: 0.7827 (ttpp)
REVERT: E  325 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8207 (pp)
REVERT: E  343 LYS cc_start: 0.8086 (tttm) cc_final: 0.7787 (ttmm)
REVERT: E  348 ASP cc_start: 0.7915 (OUTLIER) cc_final: 0.7610 (m-30)
REVERT: E  349 ARG cc_start: 0.7114 (mtt-85) cc_final: 0.6721 (mtt90)
REVERT: F  317 LYS cc_start: 0.7983 (ttmt) cc_final: 0.7724 (mtpm)
REVERT: F  348 ASP cc_start: 0.8305 (m-30) cc_final: 0.8050 (m-30)
REVERT: F  349 ARG cc_start: 0.7435 (mtt-85) cc_final: 0.7123 (mtm-85)
REVERT: A  317 LYS cc_start: 0.7815 (ttmt) cc_final: 0.7488 (mtpt)
REVERT: A  349 ARG cc_start: 0.7137 (mtt-85) cc_final: 0.6499 (mtp-110)
REVERT: A  353 LYS cc_start: 0.7710 (mtpt) cc_final: 0.7164 (tptt)
REVERT: A  357 LEU cc_start: 0.7957 (tt) cc_final: 0.7511 (tp)
REVERT: C  317 LYS cc_start: 0.8186 (ttmt) cc_final: 0.7728 (ttmm)
REVERT: C  349 ARG cc_start: 0.7068 (mtt-85) cc_final: 0.6468 (mtp-110)
  outliers start: 25
  outliers final: 20
  residues processed: 75
  average time/residue: 1.2885
  time to fit residues: 98.7533
Evaluate side-chains
  79 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 56
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain B residue  353 LYS
Chi-restraints excluded: chain D residue  306 VAL
Chi-restraints excluded: chain D residue  316 SER
Chi-restraints excluded: chain D residue  325 LEU
Chi-restraints excluded: chain D residue  348 ASP
Chi-restraints excluded: chain D residue  358 ASP
Chi-restraints excluded: chain E residue  306 VAL
Chi-restraints excluded: chain E residue  316 SER
Chi-restraints excluded: chain E residue  318 VAL
Chi-restraints excluded: chain E residue  320 SER
Chi-restraints excluded: chain E residue  325 LEU
Chi-restraints excluded: chain E residue  348 ASP
Chi-restraints excluded: chain F residue  315 LEU
Chi-restraints excluded: chain F residue  325 LEU
Chi-restraints excluded: chain A residue  306 VAL
Chi-restraints excluded: chain A residue  316 SER
Chi-restraints excluded: chain A residue  322 CYS
Chi-restraints excluded: chain A residue  348 ASP
Chi-restraints excluded: chain C residue  306 VAL
Chi-restraints excluded: chain C residue  311 LYS
Chi-restraints excluded: chain C residue  316 SER
Chi-restraints excluded: chain C residue  348 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 17 optimal weight:    0.7980
   chunk 11 optimal weight:    6.9990
   chunk 9 optimal weight:    1.9990
   chunk 4 optimal weight:    3.9990
   chunk 14 optimal weight:    5.9990
   chunk 10 optimal weight:    0.9980
   chunk 21 optimal weight:   10.0000
   chunk 15 optimal weight:    7.9990
   chunk 8 optimal weight:    5.9990
   chunk 25 optimal weight:    3.9990
   chunk 24 optimal weight:   10.0000
   overall best weight:    2.3586

-------------------------------------------------------------------------------
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 = 0.4217 r_free = 0.4217 target = 0.136717 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.109386 restraints weight = 3581.038|
|-----------------------------------------------------------------------------|
r_work (start): 0.3905 rms_B_bonded: 2.17
r_work: 0.3816 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3718 rms_B_bonded: 3.77 restraints_weight: 0.2500
r_work (final): 0.3718
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7978
moved from start:          0.2837

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024   2712  Z= 0.245
  Angle     :  0.627   6.454   3630  Z= 0.304
  Chirality :  0.052   0.142    414
  Planarity :  0.002   0.017    462
  Dihedral  :  4.584  12.826    360
  Min Nonbonded Distance : 2.642

Molprobity Statistics.
  All-atom Clashscore : 9.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.89 %
    Favored  : 92.11 %
  Rotamer:
    Outliers :  6.09 %
    Allowed  : 21.15 %
    Favored  : 72.76 %
  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: -5.39 (0.33), residues: 342
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.10 (0.25), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS E 362 
 PHE   0.004   0.001   PHE C 346 
 TYR   0.005   0.002   TYR C 310 
 ARG   0.001   0.001   ARG A 349 

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

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

  684 Ramachandran restraints generated.
    342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  684 Ramachandran restraints generated.
    342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 56
  time to evaluate  : 0.339 
Fit side-chains
REVERT: B  348 ASP cc_start: 0.8249 (m-30) cc_final: 0.7754 (m-30)
REVERT: B  349 ARG cc_start: 0.7640 (mtt-85) cc_final: 0.7378 (mtp85)
REVERT: B  353 LYS cc_start: 0.7934 (OUTLIER) cc_final: 0.7468 (mtpt)
REVERT: D  317 LYS cc_start: 0.7973 (ttmt) cc_final: 0.7697 (ttpp)
REVERT: D  349 ARG cc_start: 0.7202 (mtt-85) cc_final: 0.6770 (mtp85)
REVERT: D  353 LYS cc_start: 0.8012 (mtpt) cc_final: 0.7142 (mppt)
REVERT: E  317 LYS cc_start: 0.8109 (ttmt) cc_final: 0.7825 (ttpp)
REVERT: E  325 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8266 (pp)
REVERT: E  342 GLU cc_start: 0.7915 (pt0) cc_final: 0.7483 (pt0)
REVERT: E  343 LYS cc_start: 0.8102 (tttm) cc_final: 0.7770 (ttmm)
REVERT: E  348 ASP cc_start: 0.7879 (OUTLIER) cc_final: 0.7589 (m-30)
REVERT: E  349 ARG cc_start: 0.7068 (mtt-85) cc_final: 0.6737 (mtt90)
REVERT: F  317 LYS cc_start: 0.7941 (ttmt) cc_final: 0.7679 (mtpm)
REVERT: F  348 ASP cc_start: 0.8339 (m-30) cc_final: 0.8044 (m-30)
REVERT: F  349 ARG cc_start: 0.7446 (mtt-85) cc_final: 0.5965 (mpp-170)
REVERT: A  317 LYS cc_start: 0.7867 (ttmt) cc_final: 0.7546 (mtpt)
REVERT: A  349 ARG cc_start: 0.7229 (mtt-85) cc_final: 0.6579 (mtp-110)
REVERT: A  357 LEU cc_start: 0.7934 (tt) cc_final: 0.7494 (tp)
REVERT: C  317 LYS cc_start: 0.8187 (ttmt) cc_final: 0.7784 (ttmm)
REVERT: C  349 ARG cc_start: 0.7064 (mtt-85) cc_final: 0.6484 (mtp-110)
  outliers start: 19
  outliers final: 16
  residues processed: 70
  average time/residue: 1.3177
  time to fit residues: 94.2818
Evaluate side-chains
  75 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 56
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain B residue  353 LYS
Chi-restraints excluded: chain D residue  306 VAL
Chi-restraints excluded: chain D residue  316 SER
Chi-restraints excluded: chain D residue  325 LEU
Chi-restraints excluded: chain D residue  348 ASP
Chi-restraints excluded: chain D residue  358 ASP
Chi-restraints excluded: chain E residue  306 VAL
Chi-restraints excluded: chain E residue  318 VAL
Chi-restraints excluded: chain E residue  320 SER
Chi-restraints excluded: chain E residue  325 LEU
Chi-restraints excluded: chain E residue  348 ASP
Chi-restraints excluded: chain F residue  315 LEU
Chi-restraints excluded: chain A residue  306 VAL
Chi-restraints excluded: chain A residue  316 SER
Chi-restraints excluded: chain A residue  322 CYS
Chi-restraints excluded: chain A residue  348 ASP
Chi-restraints excluded: chain C residue  306 VAL
Chi-restraints excluded: chain C residue  311 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 5 optimal weight:    5.9990
   chunk 19 optimal weight:   10.0000
   chunk 27 optimal weight:    9.9990
   chunk 28 optimal weight:    3.9990
   chunk 12 optimal weight:    0.5980
   chunk 10 optimal weight:    0.9990
   chunk 9 optimal weight:    0.9990
   chunk 2 optimal weight:    5.9990
   chunk 29 optimal weight:    7.9990
   chunk 15 optimal weight:    8.9990
   chunk 1 optimal weight:    3.9990
   overall best weight:    2.1188

-------------------------------------------------------------------------------
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 = 0.4220 r_free = 0.4220 target = 0.139191 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.111942 restraints weight = 3442.305|
|-----------------------------------------------------------------------------|
r_work (start): 0.3913 rms_B_bonded: 2.11
r_work: 0.3823 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.3730 rms_B_bonded: 3.69 restraints_weight: 0.2500
r_work (final): 0.3730
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7971
moved from start:          0.2896

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   2712  Z= 0.230
  Angle     :  0.627   7.210   3630  Z= 0.299
  Chirality :  0.052   0.141    414
  Planarity :  0.002   0.016    462
  Dihedral  :  4.453  12.711    360
  Min Nonbonded Distance : 2.640

Molprobity Statistics.
  All-atom Clashscore : 9.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.48 %
    Favored  : 91.52 %
  Rotamer:
    Outliers :  6.09 %
    Allowed  : 21.15 %
    Favored  : 72.76 %
  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: -5.34 (0.33), residues: 342
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.06 (0.25), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS E 362 
 PHE   0.004   0.001   PHE C 346 
 TYR   0.005   0.001   TYR C 310 
 ARG   0.001   0.000   ARG A 349 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2934.83 seconds
wall clock time: 52 minutes 21.07 seconds (3141.07 seconds total)