Starting phenix.real_space_refine
on Fri Aug 22 12:58:02 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ypg_33999/08_2025/7ypg_33999.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ypg_33999/08_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_33999/08_2025/7ypg_33999.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ypg_33999/08_2025/7ypg_33999.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ypg_33999/08_2025/7ypg_33999.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ypg_33999/08_2025/7ypg_33999.cif"
  }
  resolution = 2.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 2676
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "B"
      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:
    D, E, F, A, C
  Time building chain proxies: 0.70, per 1000 atoms: 0.26
  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: 0.22
  Conformation dependent library (CDL) restraints added in 117.3 milliseconds
  
  Enol-peptide restraints added in 1.2 microseconds
  

  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: 0.06
  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: 0.23

  Time building geometry restraints manager: 0.30 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'B'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'A'
  selection = chain 'C'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.530
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.070
  Check model and map are aligned:         0.000
  Set scattering table:                    0.000
  Process input model:                     4.410
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.000
  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:11.490
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.540
-------------------------------------------------------------------------------
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= 0.338
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.001   0.000   ARG B 349 
 TYR   0.009   0.003   TYR E 310 
 PHE   0.005   0.003   PHE F 346 
 HIS   0.002   0.001   HIS E 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00828 ( 2712)
  covalent geometry    : angle       0.79556 ( 3630)
  hydrogen bonds       : bond        0.17302 (   20)
  hydrogen bonds       : angle       6.43548 (   60)

*********************** 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  : 0.120 
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: 0.5838
  time to fit residues: 48.1283
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  : 0.070 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 27 optimal weight:    1.9990
   chunk 12 optimal weight:    4.9990
   chunk 24 optimal weight:   10.0000
   chunk 28 optimal weight:    3.9990
   chunk 13 optimal weight:    7.9990
   chunk 1 optimal weight:    7.9990
   chunk 8 optimal weight:    7.9990
   chunk 16 optimal weight:    7.9990
   chunk 15 optimal weight:    2.9990
   chunk 29 optimal weight:    4.9990
   chunk 25 optimal weight:    3.9990
   overall best weight:    3.5990

-------------------------------------------------------------------------------
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
C 330 HIS

Total number of N/Q/H flips: 17

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4173 r_free = 0.4173 target = 0.132737 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.105034 restraints weight = 3655.595|
|-----------------------------------------------------------------------------|
r_work (start): 0.3845 rms_B_bonded: 2.22
r_work: 0.3753 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3656 rms_B_bonded: 3.74 restraints_weight: 0.2500
r_work (final): 0.3656
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8025
moved from start:          0.1809

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= 0.217
  Angle     :  0.704   6.465   3630  Z= 0.348
  Chirality :  0.054   0.151    414
  Planarity :  0.003   0.012    462
  Dihedral  :  4.874  12.604    360
  Min Nonbonded Distance : 2.641

Molprobity Statistics.
  All-atom Clashscore : 9.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.94 %
    Favored  : 90.06 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 15.71 %
    Favored  : 81.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -5.85 (0.30), residues: 342
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.45 (0.23), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG E 349 
 TYR   0.008   0.002   TYR D 310 
 PHE   0.006   0.003   PHE F 346 
 HIS   0.004   0.001   HIS F 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00505 ( 2712)
  covalent geometry    : angle       0.70410 ( 3630)
  hydrogen bonds       : bond        0.02254 (   20)
  hydrogen bonds       : angle       4.47517 (   60)

*********************** 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
  73 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 63
  time to evaluate  : 0.067 
Fit side-chains
REVERT: B  317 LYS cc_start: 0.7957 (ttmt) cc_final: 0.7734 (mtpm)
REVERT: B  340 LYS cc_start: 0.8034 (ttpt) cc_final: 0.7712 (mtmt)
REVERT: B  348 ASP cc_start: 0.8284 (m-30) cc_final: 0.7808 (m-30)
REVERT: B  349 ARG cc_start: 0.7536 (mtt-85) cc_final: 0.7087 (mtm-85)
REVERT: D  317 LYS cc_start: 0.7900 (ttmt) cc_final: 0.7561 (ttpp)
REVERT: D  340 LYS cc_start: 0.7981 (ttpt) cc_final: 0.7735 (ttpt)
REVERT: D  349 ARG cc_start: 0.7140 (mtt-85) cc_final: 0.6442 (mtp85)
REVERT: D  353 LYS cc_start: 0.7956 (mtpt) cc_final: 0.7698 (mtpp)
REVERT: D  358 ASP cc_start: 0.6364 (m-30) cc_final: 0.5521 (p0)
REVERT: E  317 LYS cc_start: 0.8063 (ttmt) cc_final: 0.7800 (mtpt)
REVERT: E  340 LYS cc_start: 0.8139 (ttpt) cc_final: 0.7874 (ttpt)
REVERT: E  343 LYS cc_start: 0.7951 (tttm) cc_final: 0.7668 (ttmm)
REVERT: E  348 ASP cc_start: 0.7898 (OUTLIER) cc_final: 0.7599 (m-30)
REVERT: E  349 ARG cc_start: 0.7049 (mtt-85) cc_final: 0.6398 (mtp85)
REVERT: E  353 LYS cc_start: 0.8175 (mtpt) cc_final: 0.7117 (mptp)
REVERT: F  317 LYS cc_start: 0.7981 (ttmt) cc_final: 0.7709 (mtpm)
REVERT: F  340 LYS cc_start: 0.8003 (ttpt) cc_final: 0.7774 (tppp)
REVERT: F  348 ASP cc_start: 0.8251 (m-30) cc_final: 0.8006 (m-30)
REVERT: F  349 ARG cc_start: 0.7538 (mtt-85) cc_final: 0.7241 (mtm-85)
REVERT: F  352 SER cc_start: 0.8410 (t) cc_final: 0.7843 (p)
REVERT: F  353 LYS cc_start: 0.8007 (mtpt) cc_final: 0.7346 (mttp)
REVERT: A  317 LYS cc_start: 0.7828 (ttmt) cc_final: 0.7456 (mtpt)
REVERT: A  340 LYS cc_start: 0.7977 (ttpt) cc_final: 0.7657 (mtmt)
REVERT: A  349 ARG cc_start: 0.7114 (mtt-85) cc_final: 0.6489 (mtp-110)
REVERT: A  358 ASP cc_start: 0.6805 (m-30) cc_final: 0.6521 (m-30)
REVERT: C  317 LYS cc_start: 0.8202 (ttmt) cc_final: 0.7750 (ttmm)
REVERT: C  343 LYS cc_start: 0.7890 (tttm) cc_final: 0.7650 (tttm)
REVERT: C  349 ARG cc_start: 0.6979 (mtt-85) cc_final: 0.6381 (mtp-110)
  outliers start: 10
  outliers final: 6
  residues processed: 70
  average time/residue: 0.7015
  time to fit residues: 49.9070
Evaluate side-chains
  68 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 61
  time to evaluate  : 0.159 
-------------------------------------------------------------------------------
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
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 4 optimal weight:    9.9990
   chunk 8 optimal weight:    9.9990
   chunk 17 optimal weight:    0.8980
   chunk 21 optimal weight:    0.9990
   chunk 24 optimal weight:   10.0000
   chunk 0 optimal weight:    6.9990
   chunk 2 optimal weight:    6.9990
   chunk 26 optimal weight:    3.9990
   chunk 10 optimal weight:    6.9990
   chunk 9 optimal weight:    5.9990
   chunk 27 optimal weight:    2.9990
   overall best weight:    2.9788

-------------------------------------------------------------------------------
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 = 0.4194 r_free = 0.4194 target = 0.135327 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.107234 restraints weight = 3568.786|
|-----------------------------------------------------------------------------|
r_work (start): 0.3868 rms_B_bonded: 2.25
r_work: 0.3775 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.3676 rms_B_bonded: 3.86 restraints_weight: 0.2500
r_work (final): 0.3676
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8010
moved from start:          0.2158

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= 0.188
  Angle     :  0.647   5.520   3630  Z= 0.319
  Chirality :  0.053   0.149    414
  Planarity :  0.003   0.015    462
  Dihedral  :  4.635  12.088    360
  Min Nonbonded Distance : 2.641

Molprobity Statistics.
  All-atom Clashscore : 9.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.36 %
    Favored  : 90.64 %
  Rotamer:
    Outliers :  5.13 %
    Allowed  : 15.38 %
    Favored  : 79.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -5.77 (0.31), residues: 342
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.39 (0.24), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG E 349 
 TYR   0.007   0.002   TYR C 310 
 PHE   0.005   0.002   PHE E 346 
 HIS   0.003   0.001   HIS E 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00435 ( 2712)
  covalent geometry    : angle       0.64732 ( 3630)
  hydrogen bonds       : bond        0.02147 (   20)
  hydrogen bonds       : angle       4.24002 (   60)

*********************** 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
  77 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 61
  time to evaluate  : 0.100 
Fit side-chains
REVERT: B  348 ASP cc_start: 0.8248 (m-30) cc_final: 0.7788 (m-30)
REVERT: B  349 ARG cc_start: 0.7569 (mtt-85) cc_final: 0.7127 (mtm-85)
REVERT: B  353 LYS cc_start: 0.8058 (OUTLIER) cc_final: 0.7596 (mtpt)
REVERT: D  311 LYS cc_start: 0.8193 (OUTLIER) cc_final: 0.7967 (mmtp)
REVERT: D  317 LYS cc_start: 0.7878 (ttmt) cc_final: 0.7579 (ttpp)
REVERT: D  340 LYS cc_start: 0.7907 (ttpt) cc_final: 0.7677 (ttpt)
REVERT: D  349 ARG cc_start: 0.7160 (mtt-85) cc_final: 0.6512 (mtp85)
REVERT: D  353 LYS cc_start: 0.8001 (mtpt) cc_final: 0.7205 (mptt)
REVERT: E  317 LYS cc_start: 0.8114 (ttmt) cc_final: 0.7831 (ttpp)
REVERT: E  340 LYS cc_start: 0.8104 (ttpt) cc_final: 0.7841 (ttpt)
REVERT: E  343 LYS cc_start: 0.7994 (tttm) cc_final: 0.7688 (ttmm)
REVERT: E  348 ASP cc_start: 0.7883 (OUTLIER) cc_final: 0.7588 (m-30)
REVERT: E  349 ARG cc_start: 0.7099 (mtt-85) cc_final: 0.6469 (mtp85)
REVERT: E  353 LYS cc_start: 0.8128 (mtpt) cc_final: 0.7516 (tttm)
REVERT: F  317 LYS cc_start: 0.7972 (ttmt) cc_final: 0.7649 (mtpm)
REVERT: F  340 LYS cc_start: 0.7967 (ttpt) cc_final: 0.7734 (tppp)
REVERT: F  348 ASP cc_start: 0.8300 (m-30) cc_final: 0.8058 (m-30)
REVERT: F  349 ARG cc_start: 0.7541 (mtt-85) cc_final: 0.7188 (mtm-85)
REVERT: A  317 LYS cc_start: 0.7863 (ttmt) cc_final: 0.7502 (mtpt)
REVERT: A  340 LYS cc_start: 0.7955 (ttpt) cc_final: 0.7665 (mtmt)
REVERT: A  349 ARG cc_start: 0.7163 (mtt-85) cc_final: 0.6526 (mtp-110)
REVERT: A  357 LEU cc_start: 0.7786 (tt) cc_final: 0.7292 (tp)
REVERT: C  317 LYS cc_start: 0.8187 (ttmt) cc_final: 0.7745 (ttmm)
REVERT: C  343 LYS cc_start: 0.7922 (tttm) cc_final: 0.7701 (ttmm)
REVERT: C  349 ARG cc_start: 0.7019 (mtt-85) cc_final: 0.6412 (mtp-110)
  outliers start: 16
  outliers final: 9
  residues processed: 73
  average time/residue: 0.7478
  time to fit residues: 55.5116
Evaluate side-chains
  72 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 60
  time to evaluate  : 0.111 
-------------------------------------------------------------------------------
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  316 SER
Chi-restraints excluded: chain D residue  348 ASP
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  306 VAL
Chi-restraints excluded: chain A residue  316 SER
Chi-restraints excluded: chain A residue  348 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 16 optimal weight:    4.9990
   chunk 4 optimal weight:   10.0000
   chunk 2 optimal weight:    0.2980
   chunk 29 optimal weight:    8.9990
   chunk 24 optimal weight:    0.9990
   chunk 14 optimal weight:    7.9990
   chunk 12 optimal weight:    4.9990
   chunk 15 optimal weight:    7.9990
   chunk 10 optimal weight:    0.0870
   chunk 26 optimal weight:   20.0000
   chunk 19 optimal weight:    5.9990
   overall best weight:    2.2764

-------------------------------------------------------------------------------
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 = 0.4223 r_free = 0.4223 target = 0.137312 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.109056 restraints weight = 3475.105|
|-----------------------------------------------------------------------------|
r_work (start): 0.3901 rms_B_bonded: 2.24
r_work: 0.3809 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.3710 rms_B_bonded: 3.83 restraints_weight: 0.2500
r_work (final): 0.3710
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7994
moved from start:          0.2400

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= 0.158
  Angle     :  0.597   5.096   3630  Z= 0.295
  Chirality :  0.052   0.144    414
  Planarity :  0.002   0.015    462
  Dihedral  :  4.436  11.838    360
  Min Nonbonded Distance : 2.641

Molprobity Statistics.
  All-atom Clashscore : 8.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.36 %
    Favored  : 90.64 %
  Rotamer:
    Outliers :  6.41 %
    Allowed  : 16.67 %
    Favored  : 76.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -5.63 (0.32), residues: 342
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.28 (0.24), residues: 342

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 2712)
  covalent geometry    : angle       0.59651 ( 3630)
  hydrogen bonds       : bond        0.01842 (   20)
  hydrogen bonds       : angle       4.10723 (   60)

*********************** 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
  84 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 64
  time to evaluate  : 0.117 
Fit side-chains
REVERT: B  348 ASP cc_start: 0.8244 (m-30) cc_final: 0.7781 (m-30)
REVERT: B  349 ARG cc_start: 0.7576 (mtt-85) cc_final: 0.7172 (mtm-85)
REVERT: B  353 LYS cc_start: 0.8024 (OUTLIER) cc_final: 0.7549 (mtpt)
REVERT: D  311 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7973 (mmtp)
REVERT: D  317 LYS cc_start: 0.7940 (ttmt) cc_final: 0.7625 (ttpp)
REVERT: D  340 LYS cc_start: 0.7868 (ttpt) cc_final: 0.7617 (mtmt)
REVERT: D  349 ARG cc_start: 0.7172 (mtt-85) cc_final: 0.6496 (mtp85)
REVERT: D  353 LYS cc_start: 0.8004 (mtpt) cc_final: 0.7186 (mptt)
REVERT: E  317 LYS cc_start: 0.8085 (ttmt) cc_final: 0.7811 (ttpp)
REVERT: E  325 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8338 (pp)
REVERT: E  340 LYS cc_start: 0.8131 (ttpt) cc_final: 0.7863 (ttpt)
REVERT: E  343 LYS cc_start: 0.8045 (tttm) cc_final: 0.7737 (ttmm)
REVERT: E  348 ASP cc_start: 0.7828 (OUTLIER) cc_final: 0.7528 (m-30)
REVERT: E  349 ARG cc_start: 0.7041 (mtt-85) cc_final: 0.6426 (mtp85)
REVERT: E  353 LYS cc_start: 0.8101 (mtpt) cc_final: 0.7474 (tttm)
REVERT: F  317 LYS cc_start: 0.7971 (ttmt) cc_final: 0.7696 (mtpm)
REVERT: F  340 LYS cc_start: 0.7889 (ttpt) cc_final: 0.7673 (tppp)
REVERT: F  348 ASP cc_start: 0.8297 (m-30) cc_final: 0.8045 (m-30)
REVERT: F  349 ARG cc_start: 0.7489 (mtt-85) cc_final: 0.7099 (mtm-85)
REVERT: A  317 LYS cc_start: 0.7869 (ttmt) cc_final: 0.7517 (mtpt)
REVERT: A  340 LYS cc_start: 0.7868 (ttpt) cc_final: 0.7668 (ttpp)
REVERT: A  349 ARG cc_start: 0.7088 (mtt-85) cc_final: 0.6472 (mtp-110)
REVERT: A  357 LEU cc_start: 0.7749 (tt) cc_final: 0.7298 (tp)
REVERT: C  317 LYS cc_start: 0.8183 (ttmt) cc_final: 0.7727 (ttmm)
REVERT: C  343 LYS cc_start: 0.7947 (tttm) cc_final: 0.7710 (ttmm)
REVERT: C  349 ARG cc_start: 0.7005 (mtt-85) cc_final: 0.6391 (mtp-110)
  outliers start: 20
  outliers final: 10
  residues processed: 80
  average time/residue: 0.6752
  time to fit residues: 55.0040
Evaluate side-chains
  76 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 62
  time to evaluate  : 0.105 
-------------------------------------------------------------------------------
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  316 SER
Chi-restraints excluded: chain D residue  348 ASP
Chi-restraints excluded: chain E residue  306 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  348 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 15 optimal weight:    8.9990
   chunk 3 optimal weight:   10.0000
   chunk 22 optimal weight:    0.6980
   chunk 2 optimal weight:    4.9990
   chunk 13 optimal weight:    6.9990
   chunk 6 optimal weight:    9.9990
   chunk 20 optimal weight:    1.9990
   chunk 5 optimal weight:    5.9990
   chunk 21 optimal weight:    2.9990
   chunk 26 optimal weight:    5.9990
   chunk 8 optimal weight:    4.9990
   overall best weight:    3.1388

-------------------------------------------------------------------------------
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 = 0.4210 r_free = 0.4210 target = 0.135806 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.107946 restraints weight = 3545.730|
|-----------------------------------------------------------------------------|
r_work (start): 0.3895 rms_B_bonded: 2.21
r_work: 0.3804 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3706 rms_B_bonded: 3.75 restraints_weight: 0.2500
r_work (final): 0.3706
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7992
moved from start:          0.2459

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   2712  Z= 0.192
  Angle     :  0.641   6.016   3630  Z= 0.316
  Chirality :  0.053   0.146    414
  Planarity :  0.003   0.015    462
  Dihedral  :  4.644  12.763    360
  Min Nonbonded Distance : 2.644

Molprobity Statistics.
  All-atom Clashscore : 9.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.82 %
    Favored  : 89.18 %
  Rotamer:
    Outliers :  7.05 %
    Allowed  : 17.31 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -5.66 (0.32), 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
 ARG   0.002   0.001   ARG C 349 
 TYR   0.007   0.002   TYR C 310 
 PHE   0.005   0.002   PHE E 346 
 HIS   0.002   0.001   HIS F 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00447 ( 2712)
  covalent geometry    : angle       0.64081 ( 3630)
  hydrogen bonds       : bond        0.01788 (   20)
  hydrogen bonds       : angle       4.07343 (   60)

*********************** 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
  83 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 61
  time to evaluate  : 0.114 
Fit side-chains
REVERT: B  348 ASP cc_start: 0.8248 (m-30) cc_final: 0.7763 (m-30)
REVERT: B  349 ARG cc_start: 0.7604 (mtt-85) cc_final: 0.7191 (mtm-85)
REVERT: B  353 LYS cc_start: 0.8047 (OUTLIER) cc_final: 0.7565 (mtpt)
REVERT: D  311 LYS cc_start: 0.8190 (OUTLIER) cc_final: 0.7967 (mmtp)
REVERT: D  317 LYS cc_start: 0.7896 (ttmt) cc_final: 0.7604 (ttpp)
REVERT: D  340 LYS cc_start: 0.7793 (ttpt) cc_final: 0.7577 (mtmt)
REVERT: D  349 ARG cc_start: 0.7179 (mtt-85) cc_final: 0.6529 (mtp85)
REVERT: D  353 LYS cc_start: 0.8020 (mtpt) cc_final: 0.7057 (mppt)
REVERT: E  317 LYS cc_start: 0.8105 (ttmt) cc_final: 0.7822 (ttpp)
REVERT: E  325 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8300 (pp)
REVERT: E  340 LYS cc_start: 0.8127 (ttpt) cc_final: 0.7877 (ttpt)
REVERT: E  343 LYS cc_start: 0.8000 (tttm) cc_final: 0.7669 (ttmm)
REVERT: E  348 ASP cc_start: 0.7851 (OUTLIER) cc_final: 0.7559 (m-30)
REVERT: E  349 ARG cc_start: 0.7051 (mtt-85) cc_final: 0.6427 (mtp85)
REVERT: E  353 LYS cc_start: 0.8094 (mtpt) cc_final: 0.6994 (mptp)
REVERT: F  317 LYS cc_start: 0.7973 (ttmt) cc_final: 0.7703 (mtpm)
REVERT: F  340 LYS cc_start: 0.7869 (ttpt) cc_final: 0.7643 (tppp)
REVERT: F  348 ASP cc_start: 0.8313 (m-30) cc_final: 0.8054 (m-30)
REVERT: F  349 ARG cc_start: 0.7466 (mtt-85) cc_final: 0.7090 (mtm-85)
REVERT: A  317 LYS cc_start: 0.7824 (ttmt) cc_final: 0.7473 (mtpt)
REVERT: A  349 ARG cc_start: 0.7068 (mtt-85) cc_final: 0.6451 (mtp-110)
REVERT: A  357 LEU cc_start: 0.7823 (tt) cc_final: 0.7332 (tp)
REVERT: C  317 LYS cc_start: 0.8194 (ttmt) cc_final: 0.7731 (ttmm)
REVERT: C  343 LYS cc_start: 0.7912 (tttm) cc_final: 0.7692 (ttmm)
REVERT: C  349 ARG cc_start: 0.6985 (mtt-85) cc_final: 0.6381 (mtp-110)
  outliers start: 22
  outliers final: 15
  residues processed: 78
  average time/residue: 0.6796
  time to fit residues: 53.9890
Evaluate side-chains
  79 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 60
  time to evaluate  : 0.111 
-------------------------------------------------------------------------------
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  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  316 SER
Chi-restraints excluded: chain A residue  348 ASP
Chi-restraints excluded: chain C residue  306 VAL
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 6 optimal weight:   10.0000
   chunk 15 optimal weight:    7.9990
   chunk 17 optimal weight:    0.7980
   chunk 2 optimal weight:    4.9990
   chunk 18 optimal weight:    6.9990
   chunk 25 optimal weight:    2.9990
   chunk 23 optimal weight:    5.9990
   chunk 24 optimal weight:    9.9990
   chunk 9 optimal weight:    9.9990
   chunk 0 optimal weight:    7.9990
   chunk 7 optimal weight:    0.7980
   overall best weight:    3.1186

-------------------------------------------------------------------------------
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 = 0.4214 r_free = 0.4214 target = 0.135986 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.108363 restraints weight = 3554.685|
|-----------------------------------------------------------------------------|
r_work (start): 0.3900 rms_B_bonded: 2.20
r_work: 0.3810 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3711 rms_B_bonded: 3.75 restraints_weight: 0.2500
r_work (final): 0.3711
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7992
moved from start:          0.2521

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   2712  Z= 0.190
  Angle     :  0.638   5.860   3630  Z= 0.315
  Chirality :  0.053   0.145    414
  Planarity :  0.003   0.015    462
  Dihedral  :  4.686  12.939    360
  Min Nonbonded Distance : 2.644

Molprobity Statistics.
  All-atom Clashscore : 9.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.23 %
    Favored  : 89.77 %
  Rotamer:
    Outliers :  8.33 %
    Allowed  : 16.99 %
    Favored  : 74.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -5.62 (0.32), residues: 342
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.27 (0.24), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG C 349 
 TYR   0.007   0.002   TYR C 310 
 PHE   0.005   0.002   PHE E 346 
 HIS   0.002   0.001   HIS F 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00442 ( 2712)
  covalent geometry    : angle       0.63778 ( 3630)
  hydrogen bonds       : bond        0.01776 (   20)
  hydrogen bonds       : angle       4.03905 (   60)

*********************** 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
  87 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 61
  time to evaluate  : 0.138 
Fit side-chains
REVERT: B  348 ASP cc_start: 0.8257 (m-30) cc_final: 0.7766 (m-30)
REVERT: B  349 ARG cc_start: 0.7606 (mtt-85) cc_final: 0.7308 (mtp85)
REVERT: B  353 LYS cc_start: 0.8057 (OUTLIER) cc_final: 0.7581 (mtpt)
REVERT: D  311 LYS cc_start: 0.8183 (OUTLIER) cc_final: 0.7929 (mmtp)
REVERT: D  317 LYS cc_start: 0.7943 (ttmt) cc_final: 0.7662 (ttpp)
REVERT: D  340 LYS cc_start: 0.7777 (ttpt) cc_final: 0.7554 (ttpp)
REVERT: D  349 ARG cc_start: 0.7173 (mtt-85) cc_final: 0.6726 (mtp85)
REVERT: D  353 LYS cc_start: 0.8041 (mtpt) cc_final: 0.7208 (mppt)
REVERT: E  317 LYS cc_start: 0.8108 (ttmt) cc_final: 0.7908 (tttt)
REVERT: E  325 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8311 (pp)
REVERT: E  338 GLU cc_start: 0.7981 (tt0) cc_final: 0.7703 (mt-10)
REVERT: E  340 LYS cc_start: 0.8124 (ttpt) cc_final: 0.7877 (ttpt)
REVERT: E  343 LYS cc_start: 0.8027 (tttm) cc_final: 0.7723 (ttmm)
REVERT: E  348 ASP cc_start: 0.7854 (OUTLIER) cc_final: 0.7551 (m-30)
REVERT: E  349 ARG cc_start: 0.7065 (mtt-85) cc_final: 0.6699 (mtt90)
REVERT: E  353 LYS cc_start: 0.8083 (mtpt) cc_final: 0.7516 (ttpp)
REVERT: F  317 LYS cc_start: 0.7964 (ttmt) cc_final: 0.7698 (mtpm)
REVERT: F  348 ASP cc_start: 0.8287 (m-30) cc_final: 0.8032 (m-30)
REVERT: F  349 ARG cc_start: 0.7463 (mtt-85) cc_final: 0.6866 (mtm-85)
REVERT: A  317 LYS cc_start: 0.7821 (ttmt) cc_final: 0.7475 (mtpt)
REVERT: A  349 ARG cc_start: 0.7074 (mtt-85) cc_final: 0.6516 (mtp85)
REVERT: A  357 LEU cc_start: 0.7844 (tt) cc_final: 0.7340 (tp)
REVERT: C  317 LYS cc_start: 0.8200 (ttmt) cc_final: 0.7722 (ttmm)
REVERT: C  343 LYS cc_start: 0.7937 (tttm) cc_final: 0.7705 (ttmm)
REVERT: C  349 ARG cc_start: 0.7009 (mtt-85) cc_final: 0.6410 (mtp-110)
  outliers start: 26
  outliers final: 18
  residues processed: 80
  average time/residue: 0.6405
  time to fit residues: 52.2259
Evaluate side-chains
  80 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 58
  time to evaluate  : 0.126 
-------------------------------------------------------------------------------
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  316 SER
Chi-restraints excluded: chain D residue  322 CYS
Chi-restraints excluded: chain D residue  325 LEU
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  316 SER
Chi-restraints excluded: chain A residue  348 ASP
Chi-restraints excluded: chain C residue  306 VAL
Chi-restraints excluded: chain C residue  316 SER
Chi-restraints excluded: chain C residue  348 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 27 optimal weight:    5.9990
   chunk 26 optimal weight:    8.9990
   chunk 14 optimal weight:    6.9990
   chunk 19 optimal weight:   10.0000
   chunk 2 optimal weight:    6.9990
   chunk 22 optimal weight:    3.9990
   chunk 16 optimal weight:    6.9990
   chunk 10 optimal weight:    2.9990
   chunk 29 optimal weight:    7.9990
   chunk 21 optimal weight:    5.9990
   chunk 11 optimal weight:    0.9990
   overall best weight:    3.9990

-------------------------------------------------------------------------------
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 = 0.4205 r_free = 0.4205 target = 0.134942 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.107346 restraints weight = 3565.319|
|-----------------------------------------------------------------------------|
r_work (start): 0.3891 rms_B_bonded: 2.19
r_work: 0.3799 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3698 rms_B_bonded: 3.75 restraints_weight: 0.2500
r_work (final): 0.3698
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7999
moved from start:          0.2544

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   2712  Z= 0.228
  Angle     :  0.691   6.441   3630  Z= 0.341
  Chirality :  0.054   0.146    414
  Planarity :  0.003   0.014    462
  Dihedral  :  4.921  13.715    360
  Min Nonbonded Distance : 2.645

Molprobity Statistics.
  All-atom Clashscore : 11.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.04 %
    Favored  : 85.96 %
  Rotamer:
    Outliers :  8.97 %
    Allowed  : 16.35 %
    Favored  : 74.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -5.66 (0.32), 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
 ARG   0.002   0.001   ARG F 349 
 TYR   0.009   0.002   TYR C 310 
 PHE   0.005   0.002   PHE E 346 
 HIS   0.003   0.001   HIS F 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00538 ( 2712)
  covalent geometry    : angle       0.69137 ( 3630)
  hydrogen bonds       : bond        0.01824 (   20)
  hydrogen bonds       : angle       4.06213 (   60)

*********************** 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
  86 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 58
  time to evaluate  : 0.123 
Fit side-chains
REVERT: B  348 ASP cc_start: 0.8250 (m-30) cc_final: 0.7760 (m-30)
REVERT: B  349 ARG cc_start: 0.7638 (mtt-85) cc_final: 0.7330 (mtp85)
REVERT: B  353 LYS cc_start: 0.8059 (OUTLIER) cc_final: 0.7596 (mtpt)
REVERT: B  358 ASP cc_start: 0.6246 (m-30) cc_final: 0.5953 (p0)
REVERT: D  311 LYS cc_start: 0.8182 (OUTLIER) cc_final: 0.7914 (mmtp)
REVERT: D  317 LYS cc_start: 0.7987 (ttmt) cc_final: 0.7710 (ttpp)
REVERT: D  349 ARG cc_start: 0.7194 (mtt-85) cc_final: 0.6798 (mtp85)
REVERT: D  353 LYS cc_start: 0.8065 (mtpt) cc_final: 0.7105 (mppt)
REVERT: E  317 LYS cc_start: 0.8097 (ttmt) cc_final: 0.7893 (tttt)
REVERT: E  325 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8276 (pp)
REVERT: E  338 GLU cc_start: 0.7931 (tt0) cc_final: 0.7698 (mt-10)
REVERT: E  340 LYS cc_start: 0.8116 (ttpt) cc_final: 0.7863 (ttpt)
REVERT: E  343 LYS cc_start: 0.8015 (tttm) cc_final: 0.7724 (ttmm)
REVERT: E  348 ASP cc_start: 0.7905 (OUTLIER) cc_final: 0.7605 (m-30)
REVERT: E  349 ARG cc_start: 0.7118 (mtt-85) cc_final: 0.6724 (mtt90)
REVERT: E  353 LYS cc_start: 0.8090 (mtpt) cc_final: 0.7024 (mptp)
REVERT: F  317 LYS cc_start: 0.7982 (ttmt) cc_final: 0.7735 (mtpm)
REVERT: F  348 ASP cc_start: 0.8298 (m-30) cc_final: 0.8050 (m-30)
REVERT: F  349 ARG cc_start: 0.7445 (mtt-85) cc_final: 0.7137 (mtm-85)
REVERT: A  317 LYS cc_start: 0.7869 (ttmt) cc_final: 0.7551 (mtpt)
REVERT: A  349 ARG cc_start: 0.7107 (mtt-85) cc_final: 0.6452 (mtp-110)
REVERT: A  357 LEU cc_start: 0.7904 (tt) cc_final: 0.7344 (tp)
REVERT: C  317 LYS cc_start: 0.8190 (ttmt) cc_final: 0.7720 (ttmm)
REVERT: C  343 LYS cc_start: 0.7986 (tttm) cc_final: 0.7755 (ttmm)
REVERT: C  349 ARG cc_start: 0.7035 (mtt-85) cc_final: 0.6470 (mtp-110)
  outliers start: 28
  outliers final: 19
  residues processed: 80
  average time/residue: 0.6649
  time to fit residues: 54.2198
Evaluate side-chains
  80 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 57
  time to evaluate  : 0.119 
-------------------------------------------------------------------------------
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  322 CYS
Chi-restraints excluded: chain D residue  325 LEU
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  316 SER
Chi-restraints excluded: chain A residue  348 ASP
Chi-restraints excluded: chain C residue  306 VAL
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 25 optimal weight:    2.9990
   chunk 14 optimal weight:    5.9990
   chunk 22 optimal weight:    0.8980
   chunk 28 optimal weight:    8.9990
   chunk 1 optimal weight:    4.9990
   chunk 11 optimal weight:    6.9990
   chunk 26 optimal weight:    4.9990
   chunk 24 optimal weight:   10.0000
   chunk 9 optimal weight:    9.9990
   chunk 7 optimal weight:    6.9990
   chunk 23 optimal weight:    3.9990
   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 = 0.4207 r_free = 0.4207 target = 0.135239 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.107689 restraints weight = 3608.778|
|-----------------------------------------------------------------------------|
r_work (start): 0.3892 rms_B_bonded: 2.21
r_work: 0.3800 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3701 rms_B_bonded: 3.77 restraints_weight: 0.2500
r_work (final): 0.3701
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7997
moved from start:          0.2594

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   2712  Z= 0.210
  Angle     :  0.675   6.380   3630  Z= 0.332
  Chirality :  0.053   0.145    414
  Planarity :  0.003   0.015    462
  Dihedral  :  4.886  13.440    360
  Min Nonbonded Distance : 2.644

Molprobity Statistics.
  All-atom Clashscore : 9.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.11 %
    Favored  : 88.89 %
  Rotamer:
    Outliers :  7.69 %
    Allowed  : 17.95 %
    Favored  : 74.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -5.62 (0.32), residues: 342
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.28 (0.24), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG A 349 
 TYR   0.008   0.002   TYR C 310 
 PHE   0.004   0.002   PHE E 346 
 HIS   0.003   0.001   HIS F 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00492 ( 2712)
  covalent geometry    : angle       0.67483 ( 3630)
  hydrogen bonds       : bond        0.01774 (   20)
  hydrogen bonds       : angle       4.04910 (   60)

*********************** 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
  80 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 56
  time to evaluate  : 0.127 
Fit side-chains
REVERT: B  348 ASP cc_start: 0.8259 (m-30) cc_final: 0.7753 (m-30)
REVERT: B  349 ARG cc_start: 0.7649 (mtt-85) cc_final: 0.7341 (mtp85)
REVERT: B  353 LYS cc_start: 0.8042 (OUTLIER) cc_final: 0.7575 (mtpt)
REVERT: D  311 LYS cc_start: 0.8201 (OUTLIER) cc_final: 0.7940 (mmtp)
REVERT: D  317 LYS cc_start: 0.7974 (ttmt) cc_final: 0.7693 (ttpp)
REVERT: D  349 ARG cc_start: 0.7162 (mtt-85) cc_final: 0.6773 (mtp85)
REVERT: D  353 LYS cc_start: 0.8049 (mtpt) cc_final: 0.7095 (mppt)
REVERT: E  317 LYS cc_start: 0.8102 (ttmt) cc_final: 0.7900 (tttt)
REVERT: E  325 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8268 (pp)
REVERT: E  338 GLU cc_start: 0.7932 (tt0) cc_final: 0.7685 (mt-10)
REVERT: E  340 LYS cc_start: 0.8125 (ttpt) cc_final: 0.7856 (ttpt)
REVERT: E  343 LYS cc_start: 0.8033 (tttm) cc_final: 0.7733 (ttmm)
REVERT: E  348 ASP cc_start: 0.7890 (OUTLIER) cc_final: 0.7591 (m-30)
REVERT: E  349 ARG cc_start: 0.7101 (mtt-85) cc_final: 0.6711 (mtt90)
REVERT: E  353 LYS cc_start: 0.8057 (mtpt) cc_final: 0.7025 (mptp)
REVERT: F  317 LYS cc_start: 0.7991 (ttmt) cc_final: 0.7732 (mtpm)
REVERT: F  348 ASP cc_start: 0.8307 (m-30) cc_final: 0.8026 (m-30)
REVERT: F  349 ARG cc_start: 0.7457 (mtt-85) cc_final: 0.7131 (mtm-85)
REVERT: A  317 LYS cc_start: 0.7869 (ttmt) cc_final: 0.7548 (mtpt)
REVERT: A  349 ARG cc_start: 0.7130 (mtt-85) cc_final: 0.6477 (mtp-110)
REVERT: A  357 LEU cc_start: 0.7878 (tt) cc_final: 0.7333 (tp)
REVERT: C  317 LYS cc_start: 0.8211 (ttmt) cc_final: 0.7789 (ttmm)
REVERT: C  342 GLU cc_start: 0.8044 (pt0) cc_final: 0.7792 (pt0)
REVERT: C  343 LYS cc_start: 0.7938 (tttm) cc_final: 0.7697 (ttmm)
REVERT: C  349 ARG cc_start: 0.7014 (mtt-85) cc_final: 0.6436 (mtp-110)
  outliers start: 24
  outliers final: 18
  residues processed: 75
  average time/residue: 0.6379
  time to fit residues: 48.7161
Evaluate side-chains
  78 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 56
  time to evaluate  : 0.072 
-------------------------------------------------------------------------------
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  316 SER
Chi-restraints excluded: chain D residue  322 CYS
Chi-restraints excluded: chain D residue  325 LEU
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  316 SER
Chi-restraints excluded: chain A residue  348 ASP
Chi-restraints excluded: chain C residue  306 VAL
Chi-restraints excluded: chain C residue  316 SER
Chi-restraints excluded: chain C residue  348 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 14 optimal weight:    5.9990
   chunk 17 optimal weight:    0.9980
   chunk 11 optimal weight:    5.9990
   chunk 18 optimal weight:    7.9990
   chunk 29 optimal weight:    5.9990
   chunk 25 optimal weight:    3.9990
   chunk 28 optimal weight:    4.9990
   chunk 21 optimal weight:    9.9990
   chunk 15 optimal weight:    7.9990
   chunk 2 optimal weight:    0.4980
   chunk 13 optimal weight:    0.9990
   overall best weight:    2.2986

-------------------------------------------------------------------------------
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 = 0.4224 r_free = 0.4224 target = 0.139060 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.111725 restraints weight = 3463.537|
|-----------------------------------------------------------------------------|
r_work (start): 0.3918 rms_B_bonded: 2.12
r_work: 0.3826 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.3729 rms_B_bonded: 3.71 restraints_weight: 0.2500
r_work (final): 0.3729
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7982
moved from start:          0.2696

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= 0.157
  Angle     :  0.617   6.217   3630  Z= 0.299
  Chirality :  0.052   0.141    414
  Planarity :  0.002   0.016    462
  Dihedral  :  4.541  12.704    360
  Min Nonbonded Distance : 2.641

Molprobity Statistics.
  All-atom Clashscore : 8.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.48 %
    Favored  : 91.52 %
  Rotamer:
    Outliers :  7.69 %
    Allowed  : 17.95 %
    Favored  : 74.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -5.49 (0.33), residues: 342
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.17 (0.25), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.001   ARG A 349 
 TYR   0.005   0.002   TYR C 310 
 PHE   0.003   0.001   PHE E 346 
 HIS   0.002   0.001   HIS E 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 ( 2712)
  covalent geometry    : angle       0.61702 ( 3630)
  hydrogen bonds       : bond        0.01734 (   20)
  hydrogen bonds       : angle       4.02563 (   60)

*********************** 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
  83 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 59
  time to evaluate  : 0.125 
Fit side-chains
REVERT: B  348 ASP cc_start: 0.8212 (m-30) cc_final: 0.7778 (m-30)
REVERT: B  349 ARG cc_start: 0.7618 (mtt-85) cc_final: 0.7316 (mtp85)
REVERT: B  353 LYS cc_start: 0.8015 (OUTLIER) cc_final: 0.7552 (mtpt)
REVERT: D  311 LYS cc_start: 0.8171 (OUTLIER) cc_final: 0.7949 (mmtp)
REVERT: D  317 LYS cc_start: 0.8025 (ttmt) cc_final: 0.7779 (ttpp)
REVERT: D  349 ARG cc_start: 0.7193 (mtt-85) cc_final: 0.6780 (mtp85)
REVERT: D  353 LYS cc_start: 0.8013 (mtpt) cc_final: 0.7230 (mppt)
REVERT: E  317 LYS cc_start: 0.8085 (ttmt) cc_final: 0.7884 (tttt)
REVERT: E  325 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8288 (pp)
REVERT: E  338 GLU cc_start: 0.7914 (tt0) cc_final: 0.7631 (mt-10)
REVERT: E  340 LYS cc_start: 0.8094 (ttpt) cc_final: 0.7869 (ttpt)
REVERT: E  343 LYS cc_start: 0.8056 (tttm) cc_final: 0.7795 (ttmm)
REVERT: E  348 ASP cc_start: 0.7847 (OUTLIER) cc_final: 0.7576 (m-30)
REVERT: E  349 ARG cc_start: 0.7132 (mtt-85) cc_final: 0.6813 (mtt90)
REVERT: E  353 LYS cc_start: 0.8074 (mtpt) cc_final: 0.7588 (ttpp)
REVERT: F  317 LYS cc_start: 0.7953 (ttmt) cc_final: 0.7738 (mtpm)
REVERT: F  348 ASP cc_start: 0.8272 (m-30) cc_final: 0.7988 (m-30)
REVERT: F  349 ARG cc_start: 0.7460 (mtt-85) cc_final: 0.6014 (mpp-170)
REVERT: A  317 LYS cc_start: 0.7901 (ttmt) cc_final: 0.7611 (mtpt)
REVERT: A  349 ARG cc_start: 0.7161 (mtt-85) cc_final: 0.6588 (mtp-110)
REVERT: A  357 LEU cc_start: 0.7833 (tt) cc_final: 0.7311 (tp)
REVERT: C  317 LYS cc_start: 0.8224 (ttmt) cc_final: 0.7800 (ttmm)
REVERT: C  342 GLU cc_start: 0.7901 (pt0) cc_final: 0.7662 (pt0)
REVERT: C  343 LYS cc_start: 0.7950 (tttm) cc_final: 0.7736 (ttmm)
REVERT: C  349 ARG cc_start: 0.7139 (mtt-85) cc_final: 0.6594 (mtp-110)
  outliers start: 24
  outliers final: 17
  residues processed: 78
  average time/residue: 0.5733
  time to fit residues: 45.6667
Evaluate side-chains
  78 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 57
  time to evaluate  : 0.143 
-------------------------------------------------------------------------------
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  316 SER
Chi-restraints excluded: chain D residue  322 CYS
Chi-restraints excluded: chain D residue  325 LEU
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  316 SER
Chi-restraints excluded: chain A residue  343 LYS
Chi-restraints excluded: chain A residue  348 ASP
Chi-restraints excluded: chain C residue  306 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 22 optimal weight:    0.9990
   chunk 29 optimal weight:    6.9990
   chunk 1 optimal weight:    0.9990
   chunk 2 optimal weight:    2.9990
   chunk 17 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9980
   chunk 24 optimal weight:    5.9990
   chunk 3 optimal weight:    7.9990
   chunk 5 optimal weight:    0.8980
   chunk 25 optimal weight:    1.9990
   overall best weight:    0.9786

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

Flipped N/Q/H residues before XYZ refinement:
** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4278 r_free = 0.4278 target = 0.144323 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.116934 restraints weight = 3416.818|
|-----------------------------------------------------------------------------|
r_work (start): 0.3981 rms_B_bonded: 2.12
r_work: 0.3894 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3799 rms_B_bonded: 3.75 restraints_weight: 0.2500
r_work (final): 0.3799
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7937
moved from start:          0.2959

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.016   2712  Z= 0.108
  Angle     :  0.555   6.021   3630  Z= 0.265
  Chirality :  0.051   0.134    414
  Planarity :  0.002   0.018    462
  Dihedral  :  3.990  11.355    360
  Min Nonbonded Distance : 2.635

Molprobity Statistics.
  All-atom Clashscore : 8.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 22.76 %
    Favored  : 74.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -5.29 (0.34), residues: 342
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.02 (0.26), residues: 342

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00230 ( 2712)
  covalent geometry    : angle       0.55496 ( 3630)
  hydrogen bonds       : bond        0.01714 (   20)
  hydrogen bonds       : angle       4.02489 (   60)

********************** 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
  71 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 63
  time to evaluate  : 0.072 
Fit side-chains
REVERT: B  348 ASP cc_start: 0.8182 (m-30) cc_final: 0.7779 (m-30)
REVERT: B  349 ARG cc_start: 0.7593 (mtt-85) cc_final: 0.7304 (mtp85)
REVERT: D  317 LYS cc_start: 0.8028 (ttmt) cc_final: 0.7787 (ttpp)
REVERT: D  349 ARG cc_start: 0.7230 (mtt-85) cc_final: 0.6941 (mtp85)
REVERT: D  352 SER cc_start: 0.8301 (t) cc_final: 0.8100 (p)
REVERT: D  353 LYS cc_start: 0.7979 (mtpt) cc_final: 0.7211 (mppt)
REVERT: E  317 LYS cc_start: 0.8056 (ttmt) cc_final: 0.7830 (tttt)
REVERT: E  325 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8261 (pp)
REVERT: E  342 GLU cc_start: 0.7902 (pt0) cc_final: 0.7541 (pt0)
REVERT: E  343 LYS cc_start: 0.8158 (tttm) cc_final: 0.7859 (ttmm)
REVERT: E  348 ASP cc_start: 0.7810 (OUTLIER) cc_final: 0.7553 (m-30)
REVERT: E  349 ARG cc_start: 0.7125 (mtt-85) cc_final: 0.6010 (mmt180)
REVERT: E  353 LYS cc_start: 0.8113 (mtpt) cc_final: 0.7652 (ttpp)
REVERT: F  317 LYS cc_start: 0.7929 (ttmt) cc_final: 0.7711 (mtpm)
REVERT: F  348 ASP cc_start: 0.8305 (m-30) cc_final: 0.8041 (m-30)
REVERT: F  349 ARG cc_start: 0.7481 (mtt-85) cc_final: 0.5959 (mpp-170)
REVERT: A  317 LYS cc_start: 0.7965 (ttmt) cc_final: 0.7662 (mtpt)
REVERT: A  349 ARG cc_start: 0.7271 (mtt-85) cc_final: 0.6871 (mtp85)
REVERT: A  357 LEU cc_start: 0.7745 (tt) cc_final: 0.7259 (tp)
REVERT: C  317 LYS cc_start: 0.8222 (ttmt) cc_final: 0.7791 (ttmm)
REVERT: C  342 GLU cc_start: 0.7805 (pt0) cc_final: 0.7549 (pt0)
REVERT: C  343 LYS cc_start: 0.8009 (tttm) cc_final: 0.7756 (ttmm)
REVERT: C  348 ASP cc_start: 0.7913 (m-30) cc_final: 0.7634 (m-30)
REVERT: C  349 ARG cc_start: 0.7051 (mtt-85) cc_final: 0.6557 (mtt-85)
  outliers start: 8
  outliers final: 3
  residues processed: 68
  average time/residue: 0.6513
  time to fit residues: 45.0799
Evaluate side-chains
  61 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 56
  time to evaluate  : 0.110 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain E residue  325 LEU
Chi-restraints excluded: chain E residue  348 ASP
Chi-restraints excluded: chain A residue  343 LYS
Chi-restraints excluded: chain A residue  348 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 13 optimal weight:    9.9990
   chunk 1 optimal weight:    4.9990
   chunk 5 optimal weight:    3.9990
   chunk 21 optimal weight:   20.0000
   chunk 29 optimal weight:    6.9990
   chunk 12 optimal weight:    7.9990
   chunk 24 optimal weight:   10.0000
   chunk 25 optimal weight:    6.9990
   chunk 7 optimal weight:    1.9990
   chunk 27 optimal weight:   10.0000
   chunk 16 optimal weight:    3.9990
   overall best weight:    4.3990

-------------------------------------------------------------------------------
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 = 0.4191 r_free = 0.4191 target = 0.134878 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.107314 restraints weight = 3670.506|
|-----------------------------------------------------------------------------|
r_work (start): 0.3880 rms_B_bonded: 2.25
r_work: 0.3789 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.3690 rms_B_bonded: 3.84 restraints_weight: 0.2500
r_work (final): 0.3690
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7996
moved from start:          0.2712

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.040   2712  Z= 0.246
  Angle     :  0.743   7.753   3630  Z= 0.358
  Chirality :  0.055   0.146    414
  Planarity :  0.003   0.014    462
  Dihedral  :  4.947  13.828    360
  Min Nonbonded Distance : 2.642

Molprobity Statistics.
  All-atom Clashscore : 11.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.28 %
    Favored  : 87.72 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 22.12 %
    Favored  : 73.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -5.54 (0.32), residues: 342
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.21 (0.25), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG C 349 
 TYR   0.010   0.003   TYR C 310 
 PHE   0.005   0.003   PHE E 346 
 HIS   0.003   0.001   HIS F 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00585 ( 2712)
  covalent geometry    : angle       0.74288 ( 3630)
  hydrogen bonds       : bond        0.01956 (   20)
  hydrogen bonds       : angle       3.97722 (   60)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1518.14 seconds
wall clock time: 26 minutes 45.00 seconds (1605.00 seconds total)