Starting phenix.real_space_refine
on Fri Aug 22 14:22:04 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8bgs_16035/08_2025/8bgs_16035.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8bgs_16035/08_2025/8bgs_16035.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.16
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8bgs_16035/08_2025/8bgs_16035.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8bgs_16035/08_2025/8bgs_16035.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8bgs_16035/08_2025/8bgs_16035.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8bgs_16035/08_2025/8bgs_16035.cif"
  }
  resolution = 3.16
  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=   0.000 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       7      5.16       5
     C    2520      2.51       5
     N     742      2.21       5
     O     749      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.00s

  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: 4018
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "r"
      Number of atoms: 574
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 574
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 3, 'TRANS': 71}
  Restraints were copied for chains:
    A, B, C, D, E, F
  Time building chain proxies: 0.61, per 1000 atoms: 0.15
  Number of scatterers: 4018
  At special positions: 0
  Unit cell: (150.15, 72.45, 39.9, 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       7     16.00
     O     749      8.00
     N     742      7.00
     C    2520      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: 0.21
  Conformation dependent library (CDL) restraints added in 187.1 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1022 Ramachandran restraints generated.
    511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  924

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 16 sheets defined
      0.0% alpha, 24.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.20
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'B' and resid 306 through 310
      removed outlier: 6.632A  pdb=" N   GLN r 307 " --> pdb=" O   ILE E 308 " (cutoff:3.500A)
      removed outlier: 8.123A  pdb=" N   TYR E 310 " --> pdb=" O   GLN r 307 " (cutoff:3.500A)
      removed outlier: 6.623A  pdb=" N   VAL r 309 " --> pdb=" O   TYR E 310 " (cutoff:3.500A)
      removed outlier: 6.633A  pdb=" N   GLN E 307 " --> pdb=" O   ILE F 308 " (cutoff:3.500A)
      removed outlier: 8.123A  pdb=" N   TYR F 310 " --> pdb=" O   GLN E 307 " (cutoff:3.500A)
      removed outlier: 6.622A  pdb=" N   VAL E 309 " --> pdb=" O   TYR F 310 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 313 through 314
      removed outlier: 6.705A  pdb=" N   VAL r 313 " --> pdb=" O   ASP E 314 " (cutoff:3.500A)
      removed outlier: 6.706A  pdb=" N   VAL E 313 " --> pdb=" O   ASP F 314 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 317 through 318
      removed outlier: 6.275A  pdb=" N   LYS r 317 " --> pdb=" O   VAL E 318 " (cutoff:3.500A)
      removed outlier: 6.275A  pdb=" N   LYS E 317 " --> pdb=" O   VAL F 318 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 328 through 330
      removed outlier: 6.372A  pdb=" N   ILE r 328 " --> pdb=" O   HIS B 329 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 336 through 340
      removed outlier: 6.443A  pdb=" N   GLN r 336 " --> pdb=" O   VAL E 337 " (cutoff:3.500A)
      removed outlier: 8.246A  pdb=" N   VAL E 339 " --> pdb=" O   GLN r 336 " (cutoff:3.500A)
      removed outlier: 6.526A  pdb=" N   GLU r 338 " --> pdb=" O   VAL E 339 " (cutoff:3.500A)
      removed outlier: 6.442A  pdb=" N   GLN E 336 " --> pdb=" O   VAL F 337 " (cutoff:3.500A)
      removed outlier: 8.246A  pdb=" N   VAL F 339 " --> pdb=" O   GLN E 336 " (cutoff:3.500A)
      removed outlier: 6.526A  pdb=" N   GLU E 338 " --> pdb=" O   VAL F 339 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 351 through 353
      removed outlier: 6.490A  pdb=" N   GLN r 351 " --> pdb=" O   SER E 352 " (cutoff:3.500A)
      removed outlier: 6.489A  pdb=" N   GLN E 351 " --> pdb=" O   SER F 352 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 359 through 362
      removed outlier: 6.537A  pdb=" N   ASN r 359 " --> pdb=" O   ILE B 360 " (cutoff:3.500A)
      removed outlier: 7.839A  pdb=" N   HIS B 362 " --> pdb=" O   ASN r 359 " (cutoff:3.500A)
      removed outlier: 6.313A  pdb=" N   THR r 361 " --> pdb=" O   HIS B 362 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 376 through 377
      removed outlier: 6.501A  pdb=" N   LEU r 376 " --> pdb=" O   THR B 377 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 306 through 310
      removed outlier: 6.633A  pdb=" N   GLN A 307 " --> pdb=" O   ILE C 308 " (cutoff:3.500A)
      removed outlier: 8.122A  pdb=" N   TYR C 310 " --> pdb=" O   GLN A 307 " (cutoff:3.500A)
      removed outlier: 6.622A  pdb=" N   VAL A 309 " --> pdb=" O   TYR C 310 " (cutoff:3.500A)
      removed outlier: 6.632A  pdb=" N   GLN C 307 " --> pdb=" O   ILE D 308 " (cutoff:3.500A)
      removed outlier: 8.122A  pdb=" N   TYR D 310 " --> pdb=" O   GLN C 307 " (cutoff:3.500A)
      removed outlier: 6.622A  pdb=" N   VAL C 309 " --> pdb=" O   TYR D 310 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'A' and resid 313 through 314
      removed outlier: 6.705A  pdb=" N   VAL A 313 " --> pdb=" O   ASP C 314 " (cutoff:3.500A)
      removed outlier: 6.704A  pdb=" N   VAL C 313 " --> pdb=" O   ASP D 314 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1
    Processing sheet with id=AB2, first strand: chain 'A' and resid 317 through 318
      removed outlier: 6.275A  pdb=" N   LYS A 317 " --> pdb=" O   VAL C 318 " (cutoff:3.500A)
      removed outlier: 6.276A  pdb=" N   LYS C 317 " --> pdb=" O   VAL D 318 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB2
    Processing sheet with id=AB3, first strand: chain 'A' and resid 328 through 330
    Processing sheet with id=AB4, first strand: chain 'A' and resid 336 through 340
      removed outlier: 6.442A  pdb=" N   GLN A 336 " --> pdb=" O   VAL C 337 " (cutoff:3.500A)
      removed outlier: 8.246A  pdb=" N   VAL C 339 " --> pdb=" O   GLN A 336 " (cutoff:3.500A)
      removed outlier: 6.526A  pdb=" N   GLU A 338 " --> pdb=" O   VAL C 339 " (cutoff:3.500A)
      removed outlier: 6.443A  pdb=" N   GLN C 336 " --> pdb=" O   VAL D 337 " (cutoff:3.500A)
      removed outlier: 8.246A  pdb=" N   VAL D 339 " --> pdb=" O   GLN C 336 " (cutoff:3.500A)
      removed outlier: 6.527A  pdb=" N   GLU C 338 " --> pdb=" O   VAL D 339 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB4
    Processing sheet with id=AB5, first strand: chain 'A' and resid 351 through 353
      removed outlier: 6.490A  pdb=" N   GLN A 351 " --> pdb=" O   SER C 352 " (cutoff:3.500A)
      removed outlier: 6.490A  pdb=" N   GLN C 351 " --> pdb=" O   SER D 352 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB5
    Processing sheet with id=AB6, first strand: chain 'A' and resid 359 through 362
    Processing sheet with id=AB7, first strand: chain 'A' and resid 376 through 377

    36 hydrogen bonds defined for protein.
    108 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: 0.66

  Time building geometry restraints manager: 0.32 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 945
        1.33 -     1.45: 912
        1.45 -     1.57: 2217
        1.57 -     1.70: 0
        1.70 -     1.82: 7
  Bond restraints: 4081
  Sorted by residual:
  bond pdb=" CB  HIS C 362 "
       pdb=" CG  HIS C 362 "
    ideal  model  delta    sigma   weight residual
    1.497  1.458  0.039 1.40e-02 5.10e+03 7.93e+00
  bond pdb=" CB  HIS E 362 "
       pdb=" CG  HIS E 362 "
    ideal  model  delta    sigma   weight residual
    1.497  1.458  0.039 1.40e-02 5.10e+03 7.93e+00
  bond pdb=" CB  HIS F 362 "
       pdb=" CG  HIS F 362 "
    ideal  model  delta    sigma   weight residual
    1.497  1.458  0.039 1.40e-02 5.10e+03 7.90e+00
  bond pdb=" CB  HIS D 362 "
       pdb=" CG  HIS D 362 "
    ideal  model  delta    sigma   weight residual
    1.497  1.458  0.039 1.40e-02 5.10e+03 7.84e+00
  bond pdb=" CB  HIS A 362 "
       pdb=" CG  HIS A 362 "
    ideal  model  delta    sigma   weight residual
    1.497  1.458  0.039 1.40e-02 5.10e+03 7.80e+00
  ... (remaining 4076 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.95: 4256
        1.95 -     3.89: 1099
        3.89 -     5.84: 91
        5.84 -     7.79: 7
        7.79 -     9.74: 7
  Bond angle restraints: 5460
  Sorted by residual:
  angle pdb=" N   PRO A 332 "
        pdb=" CA  PRO A 332 "
        pdb=" C   PRO A 332 "
      ideal   model   delta    sigma   weight residual
     110.21  119.95   -9.74 1.64e+00 3.72e-01 3.52e+01
  angle pdb=" N   PRO B 332 "
        pdb=" CA  PRO B 332 "
        pdb=" C   PRO B 332 "
      ideal   model   delta    sigma   weight residual
     110.21  119.94   -9.73 1.64e+00 3.72e-01 3.52e+01
  angle pdb=" N   PRO C 332 "
        pdb=" CA  PRO C 332 "
        pdb=" C   PRO C 332 "
      ideal   model   delta    sigma   weight residual
     110.21  119.93   -9.72 1.64e+00 3.72e-01 3.51e+01
  angle pdb=" N   PRO E 332 "
        pdb=" CA  PRO E 332 "
        pdb=" C   PRO E 332 "
      ideal   model   delta    sigma   weight residual
     110.21  119.93   -9.72 1.64e+00 3.72e-01 3.51e+01
  angle pdb=" N   PRO D 332 "
        pdb=" CA  PRO D 332 "
        pdb=" C   PRO D 332 "
      ideal   model   delta    sigma   weight residual
     110.21  119.93   -9.72 1.64e+00 3.72e-01 3.51e+01
  ... (remaining 5455 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.14: 2170
       13.14 -    26.28: 231
       26.28 -    39.41: 56
       39.41 -    52.55: 28
       52.55 -    65.69: 7
  Dihedral angle restraints: 2492
    sinusoidal: 1043
      harmonic: 1449
  Sorted by residual:
  dihedral pdb=" CA  LYS B 321 "
           pdb=" C   LYS B 321 "
           pdb=" N   CYS B 322 "
           pdb=" CA  CYS B 322 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -148.63  -31.37     0      5.00e+00 4.00e-02 3.94e+01
  dihedral pdb=" CA  LYS D 321 "
           pdb=" C   LYS D 321 "
           pdb=" N   CYS D 322 "
           pdb=" CA  CYS D 322 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -148.64  -31.36     0      5.00e+00 4.00e-02 3.93e+01
  dihedral pdb=" CA  LYS C 321 "
           pdb=" C   LYS C 321 "
           pdb=" N   CYS C 322 "
           pdb=" CA  CYS C 322 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -148.65  -31.35     0      5.00e+00 4.00e-02 3.93e+01
  ... (remaining 2489 not shown)

  Histogram of chiral volume deviations from ideal:
       0.002 -    0.059: 259
       0.059 -    0.116: 224
       0.116 -    0.172: 84
       0.172 -    0.229: 42
       0.229 -    0.286: 7
  Chirality restraints: 616
  Sorted by residual:
  chirality pdb=" CA  LYS E 347 "
            pdb=" N   LYS E 347 "
            pdb=" C   LYS E 347 "
            pdb=" CB  LYS E 347 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.22    0.29 2.00e-01 2.50e+01 2.04e+00
  chirality pdb=" CA  LYS C 347 "
            pdb=" N   LYS C 347 "
            pdb=" C   LYS C 347 "
            pdb=" CB  LYS C 347 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.23    0.29 2.00e-01 2.50e+01 2.03e+00
  chirality pdb=" CA  LYS r 347 "
            pdb=" N   LYS r 347 "
            pdb=" C   LYS r 347 "
            pdb=" CB  LYS r 347 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.23    0.28 2.00e-01 2.50e+01 2.03e+00
  ... (remaining 613 not shown)

  Planarity restraints: 693
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY B 334 "   -0.009 2.00e-02 2.50e+03   1.91e-02 3.64e+00
        pdb=" C   GLY B 334 "    0.033 2.00e-02 2.50e+03
        pdb=" O   GLY B 334 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   GLY B 335 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY E 334 "   -0.009 2.00e-02 2.50e+03   1.89e-02 3.59e+00
        pdb=" C   GLY E 334 "    0.033 2.00e-02 2.50e+03
        pdb=" O   GLY E 334 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   GLY E 335 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY F 334 "   -0.009 2.00e-02 2.50e+03   1.89e-02 3.58e+00
        pdb=" C   GLY F 334 "    0.033 2.00e-02 2.50e+03
        pdb=" O   GLY F 334 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   GLY F 335 "   -0.011 2.00e-02 2.50e+03
  ... (remaining 690 not shown)

  Histogram of nonbonded interaction distances:
        2.37 -     2.87: 1370
        2.87 -     3.38: 3423
        3.38 -     3.89: 6494
        3.89 -     4.39: 7137
        4.39 -     4.90: 14326
  Nonbonded interactions: 32750
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP B 314 "
            pdb=" OG  SER B 316 "
     model   vdw
     2.368 3.040
  nonbonded pdb=" OD1 ASP D 314 "
            pdb=" OG  SER D 316 "
     model   vdw
     2.368 3.040
  nonbonded pdb=" OD1 ASP A 314 "
            pdb=" OG  SER A 316 "
     model   vdw
     2.369 3.040
  nonbonded pdb=" OD1 ASP r 314 "
            pdb=" OG  SER r 316 "
     model   vdw
     2.369 3.040
  nonbonded pdb=" OD1 ASP F 314 "
            pdb=" OG  SER F 316 "
     model   vdw
     2.369 3.040
  ... (remaining 32745 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'r'
  selection = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.410
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.050
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.200
  Find NCS groups from input model:        0.050
  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:1.880
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.630
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8377
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      :  0.009   0.043   4081  Z= 0.669
  Angle     :  1.642   9.736   5460  Z= 1.123
  Chirality :  0.095   0.286    616
  Planarity :  0.009   0.043    693
  Dihedral  : 13.075  65.689   1568
  Min Nonbonded Distance : 2.368

Molprobity Statistics.
  All-atom Clashscore : 1.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.85 %
    Favored  : 93.15 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.06 %
    Favored  : 93.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 1.41 %

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: -3.72 (0.26), residues: 511
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.83 (0.20), residues: 511

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.002   ARG D 349 
 TYR   0.025   0.009   TYR C 310 
 PHE   0.010   0.004   PHE D 378 
 HIS   0.011   0.004   HIS B 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00919 ( 4081)
  covalent geometry    : angle       1.64220 ( 5460)
  hydrogen bonds       : bond        0.06368 (   36)
  hydrogen bonds       : angle       5.65165 (  108)

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

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

  1022 Ramachandran restraints generated.
    511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1022 Ramachandran restraints generated.
    511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 0.168 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: r  345 ASP cc_start: 0.8517 (t0) cc_final: 0.8316 (t0)
REVERT: A  316 SER cc_start: 0.9053 (p) cc_final: 0.8612 (p)
REVERT: C  353 LYS cc_start: 0.8959 (mtpt) cc_final: 0.8571 (mtpt)
REVERT: F  316 SER cc_start: 0.8981 (p) cc_final: 0.8624 (p)
REVERT: F  331 LYS cc_start: 0.9181 (mtpt) cc_final: 0.8058 (tmtt)
  outliers start: 0
  outliers final: 0
  residues processed: 105
  average time/residue: 0.1123
  time to fit residues: 13.4793
Evaluate side-chains
  82 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 0.100 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 24 optimal weight:    7.9990
   chunk 48 optimal weight:    5.9990
   chunk 26 optimal weight:    2.9990
   chunk 2 optimal weight:    0.5980
   chunk 16 optimal weight:    0.9980
   chunk 32 optimal weight:    5.9990
   chunk 31 optimal weight:    4.9990
   chunk 25 optimal weight:    8.9990
   chunk 19 optimal weight:    0.9980
   chunk 30 optimal weight:    6.9990
   chunk 22 optimal weight:   20.0000
   overall best weight:    2.1184

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

Flipped N/Q/H residues before XYZ refinement:
r 330 HIS
r 362 HIS
A 330 HIS
** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 362 HIS
B 330 HIS
B 362 HIS
C 330 HIS
C 362 HIS
D 330 HIS
D 336 GLN
D 362 HIS
E 330 HIS
E 362 HIS
F 330 HIS
F 362 HIS

Total number of N/Q/H flips: 15

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4269 r_free = 0.4269 target = 0.148481 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.122654 restraints weight = 4335.210|
|-----------------------------------------------------------------------------|
r_work (start): 0.3966 rms_B_bonded: 2.54
r_work: 0.3825 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.3692 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.3692
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7849
moved from start:          0.2857

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   4081  Z= 0.146
  Angle     :  0.764  12.496   5460  Z= 0.377
  Chirality :  0.052   0.135    616
  Planarity :  0.003   0.029    693
  Dihedral  :  7.610  22.742    539
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 2.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  0.87 %
    Allowed  : 11.90 %
    Favored  : 87.23 %
  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: -2.87 (0.28), residues: 511
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.18 (0.22), residues: 511

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG r 379 
 TYR   0.008   0.002   TYR r 310 
 PHE   0.005   0.001   PHE A 346 
 HIS   0.003   0.001   HIS A 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 4081)
  covalent geometry    : angle       0.76404 ( 5460)
  hydrogen bonds       : bond        0.01799 (   36)
  hydrogen bonds       : angle       4.25549 (  108)

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

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

  1022 Ramachandran restraints generated.
    511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1022 Ramachandran restraints generated.
    511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 100
  time to evaluate  : 0.206 
Fit side-chains
REVERT: r  340 LYS cc_start: 0.8401 (mttt) cc_final: 0.7969 (mptt)
REVERT: r  369 LYS cc_start: 0.8233 (mttt) cc_final: 0.7595 (mtpp)
REVERT: A  311 LYS cc_start: 0.8278 (tttm) cc_final: 0.7752 (ttmt)
REVERT: A  315 LEU cc_start: 0.8778 (tt) cc_final: 0.8526 (mp)
REVERT: A  331 LYS cc_start: 0.8841 (mtpt) cc_final: 0.7387 (tptp)
REVERT: A  340 LYS cc_start: 0.8536 (mttt) cc_final: 0.8102 (mptt)
REVERT: A  369 LYS cc_start: 0.8223 (mttt) cc_final: 0.7889 (mttt)
REVERT: B  311 LYS cc_start: 0.8370 (tttm) cc_final: 0.7817 (ttmt)
REVERT: B  336 GLN cc_start: 0.8925 (tt0) cc_final: 0.8603 (tt0)
REVERT: B  340 LYS cc_start: 0.8730 (mttt) cc_final: 0.8449 (mttm)
REVERT: D  311 LYS cc_start: 0.8527 (tttm) cc_final: 0.8019 (ttmt)
REVERT: D  315 LEU cc_start: 0.8799 (tt) cc_final: 0.8585 (mp)
REVERT: D  372 GLU cc_start: 0.8627 (mm-30) cc_final: 0.8419 (tp30)
REVERT: E  331 LYS cc_start: 0.9044 (mtpt) cc_final: 0.8706 (mtpp)
REVERT: E  372 GLU cc_start: 0.8386 (tp30) cc_final: 0.8176 (tp30)
REVERT: F  315 LEU cc_start: 0.8559 (tt) cc_final: 0.8300 (mp)
REVERT: F  372 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.8009 (mm-30)
  outliers start: 4
  outliers final: 1
  residues processed: 102
  average time/residue: 0.1278
  time to fit residues: 14.8277
Evaluate side-chains
  79 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 77
  time to evaluate  : 0.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  379 ARG
Chi-restraints excluded: chain F residue  372 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 2 optimal weight:   10.0000
   chunk 31 optimal weight:    6.9990
   chunk 26 optimal weight:    5.9990
   chunk 29 optimal weight:    6.9990
   chunk 28 optimal weight:    9.9990
   chunk 23 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 12 optimal weight:    2.9990
   chunk 36 optimal weight:    6.9990
   chunk 13 optimal weight:    9.9990
   chunk 4 optimal weight:    0.3980
   overall best weight:    3.8788

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

Flipped N/Q/H residues before XYZ refinement:
** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 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 = 0.4216 r_free = 0.4216 target = 0.142416 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.118784 restraints weight = 4567.115|
|-----------------------------------------------------------------------------|
r_work (start): 0.3933 rms_B_bonded: 2.43
r_work: 0.3793 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3661 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.3661
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7858
moved from start:          0.3350

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.030   4081  Z= 0.225
  Angle     :  0.728  14.225   5460  Z= 0.371
  Chirality :  0.053   0.138    616
  Planarity :  0.004   0.033    693
  Dihedral  :  7.116  19.521    539
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 3.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  0.87 %
    Allowed  : 17.53 %
    Favored  : 81.60 %
  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: -2.61 (0.30), residues: 511
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.98 (0.23), residues: 511

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG r 379 
 TYR   0.017   0.004   TYR r 310 
 PHE   0.004   0.001   PHE E 346 
 HIS   0.003   0.001   HIS r 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00484 ( 4081)
  covalent geometry    : angle       0.72831 ( 5460)
  hydrogen bonds       : bond        0.01922 (   36)
  hydrogen bonds       : angle       3.83599 (  108)

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

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

  1022 Ramachandran restraints generated.
    511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1022 Ramachandran restraints generated.
    511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 86
  time to evaluate  : 0.166 
Fit side-chains
   revert: symmetry clash
REVERT: A  340 LYS cc_start: 0.8438 (mttt) cc_final: 0.8025 (mptt)
REVERT: D  311 LYS cc_start: 0.8620 (tttm) cc_final: 0.8188 (ttmt)
REVERT: D  372 GLU cc_start: 0.8425 (mm-30) cc_final: 0.8203 (tp30)
REVERT: E  331 LYS cc_start: 0.9047 (mtpt) cc_final: 0.8662 (mtpp)
REVERT: F  316 SER cc_start: 0.8823 (p) cc_final: 0.8527 (p)
REVERT: F  342 GLU cc_start: 0.4676 (pm20) cc_final: 0.3408 (mm-30)
REVERT: F  372 GLU cc_start: 0.8332 (tp30) cc_final: 0.8036 (mm-30)
  outliers start: 4
  outliers final: 4
  residues processed: 86
  average time/residue: 0.1026
  time to fit residues: 10.4023
Evaluate side-chains
  86 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 82
  time to evaluate  : 0.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  379 ARG
Chi-restraints excluded: chain D residue  320 SER
Chi-restraints excluded: chain E residue  379 ARG
Chi-restraints excluded: chain F residue  371 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 12 optimal weight:    9.9990
   chunk 41 optimal weight:    2.9990
   chunk 11 optimal weight:    3.9990
   chunk 43 optimal weight:    1.9990
   chunk 13 optimal weight:    9.9990
   chunk 17 optimal weight:   10.0000
   chunk 23 optimal weight:    8.9990
   chunk 33 optimal weight:    6.9990
   chunk 28 optimal weight:   20.0000
   chunk 44 optimal weight:    4.9990
   chunk 39 optimal weight:    9.9990
   overall best weight:    4.1990

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

Flipped N/Q/H residues before XYZ refinement:
** D 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 = 0.4195 r_free = 0.4195 target = 0.140300 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.117357 restraints weight = 4700.413|
|-----------------------------------------------------------------------------|
r_work (start): 0.3919 rms_B_bonded: 2.39
r_work: 0.3785 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3661 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.3661
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7842
moved from start:          0.3610

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.028   4081  Z= 0.235
  Angle     :  0.676   5.918   5460  Z= 0.356
  Chirality :  0.052   0.139    616
  Planarity :  0.004   0.035    693
  Dihedral  :  6.888  22.529    539
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 3.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 16.88 %
    Favored  : 81.17 %
  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: -2.69 (0.31), residues: 511
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.05 (0.23), residues: 511

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG r 379 
 TYR   0.016   0.004   TYR r 310 
 PHE   0.004   0.001   PHE D 378 
 HIS   0.003   0.001   HIS F 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00510 ( 4081)
  covalent geometry    : angle       0.67632 ( 5460)
  hydrogen bonds       : bond        0.01904 (   36)
  hydrogen bonds       : angle       3.80557 (  108)

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

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

  1022 Ramachandran restraints generated.
    511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1022 Ramachandran restraints generated.
    511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 82
  time to evaluate  : 0.168 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  331 LYS cc_start: 0.8748 (mtpt) cc_final: 0.7336 (tptt)
REVERT: A  340 LYS cc_start: 0.8471 (mttt) cc_final: 0.7983 (mmtm)
REVERT: A  343 LYS cc_start: 0.7917 (ptmm) cc_final: 0.5877 (tppt)
REVERT: A  369 LYS cc_start: 0.8257 (mttt) cc_final: 0.7920 (mttt)
REVERT: B  311 LYS cc_start: 0.8426 (tttm) cc_final: 0.7997 (ttmt)
REVERT: C  342 GLU cc_start: 0.7591 (mm-30) cc_final: 0.7290 (mm-30)
REVERT: D  311 LYS cc_start: 0.8573 (tttm) cc_final: 0.8144 (ttmt)
REVERT: D  372 GLU cc_start: 0.8511 (mm-30) cc_final: 0.8282 (tp30)
REVERT: E  331 LYS cc_start: 0.9061 (mtpt) cc_final: 0.8672 (mtpp)
REVERT: F  372 GLU cc_start: 0.8260 (tp30) cc_final: 0.7867 (mm-30)
  outliers start: 9
  outliers final: 5
  residues processed: 87
  average time/residue: 0.1047
  time to fit residues: 10.5767
Evaluate side-chains
  84 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 79
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  379 ARG
Chi-restraints excluded: chain D residue  315 LEU
Chi-restraints excluded: chain D residue  320 SER
Chi-restraints excluded: chain E residue  379 ARG
Chi-restraints excluded: chain F residue  371 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 14 optimal weight:    9.9990
   chunk 24 optimal weight:    9.9990
   chunk 36 optimal weight:   10.0000
   chunk 44 optimal weight:   20.0000
   chunk 4 optimal weight:    0.9990
   chunk 37 optimal weight:    5.9990
   chunk 6 optimal weight:    5.9990
   chunk 41 optimal weight:    6.9990
   chunk 17 optimal weight:    2.9990
   chunk 1 optimal weight:    9.9990
   chunk 25 optimal weight:   10.0000
   overall best weight:    4.5990

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

Flipped N/Q/H residues before XYZ refinement:
** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 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 = 0.4187 r_free = 0.4187 target = 0.138677 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.115785 restraints weight = 4702.602|
|-----------------------------------------------------------------------------|
r_work (start): 0.3902 rms_B_bonded: 2.36
r_work: 0.3771 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3645 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.3645
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7857
moved from start:          0.3764

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.049   4081  Z= 0.256
  Angle     :  0.682   7.422   5460  Z= 0.361
  Chirality :  0.052   0.143    616
  Planarity :  0.004   0.036    693
  Dihedral  :  6.774  20.756    539
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 3.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 17.97 %
    Favored  : 79.87 %
  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: -2.80 (0.31), residues: 511
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.13 (0.23), residues: 511

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG r 379 
 TYR   0.017   0.004   TYR C 310 
 PHE   0.004   0.001   PHE D 378 
 HIS   0.004   0.001   HIS F 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00557 ( 4081)
  covalent geometry    : angle       0.68193 ( 5460)
  hydrogen bonds       : bond        0.01966 (   36)
  hydrogen bonds       : angle       3.80549 (  108)

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

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

  1022 Ramachandran restraints generated.
    511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1022 Ramachandran restraints generated.
    511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 90
  time to evaluate  : 0.133 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  331 LYS cc_start: 0.8757 (mtpt) cc_final: 0.7598 (tmtt)
REVERT: A  343 LYS cc_start: 0.7958 (ptmm) cc_final: 0.5859 (tppt)
REVERT: A  359 ASN cc_start: 0.9083 (m-40) cc_final: 0.8787 (m110)
REVERT: A  369 LYS cc_start: 0.8289 (mttt) cc_final: 0.7963 (mttt)
REVERT: B  311 LYS cc_start: 0.8445 (tttm) cc_final: 0.8031 (ttmt)
REVERT: B  336 GLN cc_start: 0.8982 (tt0) cc_final: 0.8768 (tt0)
REVERT: D  372 GLU cc_start: 0.8497 (mm-30) cc_final: 0.8265 (tp30)
REVERT: E  331 LYS cc_start: 0.9050 (mtpt) cc_final: 0.8652 (mtpp)
REVERT: F  372 GLU cc_start: 0.8241 (tp30) cc_final: 0.7900 (mm-30)
  outliers start: 10
  outliers final: 7
  residues processed: 92
  average time/residue: 0.1018
  time to fit residues: 10.9200
Evaluate side-chains
  95 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 88
  time to evaluate  : 0.111 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain r residue  371 ILE
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain B residue  379 ARG
Chi-restraints excluded: chain D residue  315 LEU
Chi-restraints excluded: chain D residue  320 SER
Chi-restraints excluded: chain E residue  379 ARG
Chi-restraints excluded: chain F residue  371 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 46 optimal weight:    7.9990
   chunk 32 optimal weight:    8.9990
   chunk 22 optimal weight:    0.0670
   chunk 24 optimal weight:    7.9990
   chunk 39 optimal weight:   10.0000
   chunk 20 optimal weight:    0.8980
   chunk 30 optimal weight:    2.9990
   chunk 4 optimal weight:    6.9990
   chunk 40 optimal weight:    0.9990
   chunk 15 optimal weight:    4.9990
   chunk 36 optimal weight:   10.0000
   overall best weight:    1.9924

-------------------------------------------------------------------------------
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 = 0.4282 r_free = 0.4282 target = 0.146688 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.123508 restraints weight = 4628.927|
|-----------------------------------------------------------------------------|
r_work (start): 0.4012 rms_B_bonded: 2.42
r_work: 0.3875 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3748 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.3748
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7825
moved from start:          0.4114

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4081  Z= 0.131
  Angle     :  0.584   7.347   5460  Z= 0.304
  Chirality :  0.050   0.126    616
  Planarity :  0.004   0.032    693
  Dihedral  :  6.127  20.020    539
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 3.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.98 %
    Favored  : 99.02 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 18.83 %
    Favored  : 79.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -2.69 (0.31), residues: 511
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.04 (0.24), residues: 511

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG r 379 
 TYR   0.008   0.002   TYR r 310 
 PHE   0.003   0.001   PHE r 346 
 HIS   0.002   0.001   HIS D 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 4081)
  covalent geometry    : angle       0.58426 ( 5460)
  hydrogen bonds       : bond        0.01619 (   36)
  hydrogen bonds       : angle       3.90967 (  108)

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

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

  1022 Ramachandran restraints generated.
    511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1022 Ramachandran restraints generated.
    511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 96
  time to evaluate  : 0.110 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  331 LYS cc_start: 0.8778 (mtpt) cc_final: 0.7483 (tptt)
REVERT: A  343 LYS cc_start: 0.7897 (ptmm) cc_final: 0.5643 (tppt)
REVERT: A  345 ASP cc_start: 0.7850 (t0) cc_final: 0.7608 (t0)
REVERT: A  359 ASN cc_start: 0.8937 (m-40) cc_final: 0.8652 (m110)
REVERT: A  369 LYS cc_start: 0.8218 (mttt) cc_final: 0.7918 (mttt)
REVERT: B  311 LYS cc_start: 0.8353 (tttm) cc_final: 0.7955 (ttmt)
REVERT: B  336 GLN cc_start: 0.8944 (tt0) cc_final: 0.8737 (tt0)
REVERT: B  340 LYS cc_start: 0.8680 (mttt) cc_final: 0.8399 (mttm)
REVERT: B  359 ASN cc_start: 0.8857 (m-40) cc_final: 0.8400 (m-40)
REVERT: E  331 LYS cc_start: 0.9048 (mtpt) cc_final: 0.8667 (mtpp)
REVERT: F  372 GLU cc_start: 0.8167 (tp30) cc_final: 0.7922 (mm-30)
  outliers start: 8
  outliers final: 6
  residues processed: 98
  average time/residue: 0.0935
  time to fit residues: 10.7259
Evaluate side-chains
  98 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 92
  time to evaluate  : 0.168 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain B residue  344 LEU
Chi-restraints excluded: chain B residue  379 ARG
Chi-restraints excluded: chain D residue  315 LEU
Chi-restraints excluded: chain E residue  318 VAL
Chi-restraints excluded: chain E residue  379 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 4 optimal weight:    6.9990
   chunk 44 optimal weight:    2.9990
   chunk 15 optimal weight:    9.9990
   chunk 9 optimal weight:    0.5980
   chunk 11 optimal weight:    0.0770
   chunk 18 optimal weight:    7.9990
   chunk 34 optimal weight:    4.9990
   chunk 22 optimal weight:   20.0000
   chunk 40 optimal weight:    8.9990
   chunk 38 optimal weight:    8.9990
   chunk 37 optimal weight:    4.9990
   overall best weight:    2.7344

-------------------------------------------------------------------------------
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 = 0.4253 r_free = 0.4253 target = 0.144340 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.120730 restraints weight = 4603.671|
|-----------------------------------------------------------------------------|
r_work (start): 0.3970 rms_B_bonded: 2.43
r_work: 0.3837 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3711 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.3711
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7841
moved from start:          0.4130

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   4081  Z= 0.167
  Angle     :  0.608   7.732   5460  Z= 0.316
  Chirality :  0.050   0.129    616
  Planarity :  0.004   0.032    693
  Dihedral  :  6.115  19.161    539
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 3.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 19.70 %
    Favored  : 78.35 %
  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: -2.74 (0.31), residues: 511
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.08 (0.24), residues: 511

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG r 379 
 TYR   0.012   0.003   TYR A 310 
 PHE   0.004   0.001   PHE E 346 
 HIS   0.002   0.001   HIS A 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 ( 4081)
  covalent geometry    : angle       0.60827 ( 5460)
  hydrogen bonds       : bond        0.01761 (   36)
  hydrogen bonds       : angle       3.88883 (  108)

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

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

  1022 Ramachandran restraints generated.
    511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1022 Ramachandran restraints generated.
    511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 89
  time to evaluate  : 0.167 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  331 LYS cc_start: 0.8788 (mtpt) cc_final: 0.7570 (tmtt)
REVERT: A  343 LYS cc_start: 0.7911 (ptmm) cc_final: 0.5656 (tppt)
REVERT: A  345 ASP cc_start: 0.7859 (t0) cc_final: 0.7619 (t0)
REVERT: A  359 ASN cc_start: 0.8970 (m-40) cc_final: 0.8684 (m110)
REVERT: A  369 LYS cc_start: 0.8236 (mttt) cc_final: 0.7967 (mttt)
REVERT: B  311 LYS cc_start: 0.8342 (tttm) cc_final: 0.7977 (ttmt)
REVERT: B  340 LYS cc_start: 0.8660 (mttt) cc_final: 0.8383 (mttm)
REVERT: B  359 ASN cc_start: 0.8975 (m-40) cc_final: 0.8522 (m-40)
REVERT: D  372 GLU cc_start: 0.8532 (tp30) cc_final: 0.8316 (mt-10)
REVERT: E  331 LYS cc_start: 0.9048 (mtpt) cc_final: 0.8673 (mtpp)
REVERT: F  372 GLU cc_start: 0.8207 (tp30) cc_final: 0.7909 (mm-30)
  outliers start: 9
  outliers final: 6
  residues processed: 92
  average time/residue: 0.0966
  time to fit residues: 10.3402
Evaluate side-chains
  94 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 88
  time to evaluate  : 0.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain B residue  379 ARG
Chi-restraints excluded: chain C residue  318 VAL
Chi-restraints excluded: chain D residue  315 LEU
Chi-restraints excluded: chain E residue  318 VAL
Chi-restraints excluded: chain E residue  379 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 1 optimal weight:    4.9990
   chunk 31 optimal weight:    9.9990
   chunk 22 optimal weight:   10.0000
   chunk 38 optimal weight:    7.9990
   chunk 25 optimal weight:    8.9990
   chunk 12 optimal weight:    0.0970
   chunk 28 optimal weight:    0.9980
   chunk 18 optimal weight:    6.9990
   chunk 43 optimal weight:    6.9990
   chunk 47 optimal weight:    0.4980
   chunk 36 optimal weight:    1.9990
   overall best weight:    1.7182

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

Flipped N/Q/H residues before XYZ refinement:
B 336 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4311 r_free = 0.4311 target = 0.150650 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.126373 restraints weight = 4353.236|
|-----------------------------------------------------------------------------|
r_work (start): 0.4031 rms_B_bonded: 2.42
r_work: 0.3906 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3780 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.3780
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7826
moved from start:          0.4392

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4081  Z= 0.118
  Angle     :  0.570   7.763   5460  Z= 0.291
  Chirality :  0.049   0.124    616
  Planarity :  0.004   0.030    693
  Dihedral  :  5.754  18.119    539
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 3.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.98 %
    Favored  : 99.02 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 20.35 %
    Favored  : 77.71 %
  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: -2.71 (0.32), residues: 511
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.06 (0.24), residues: 511

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG r 379 
 TYR   0.008   0.002   TYR r 310 
 PHE   0.004   0.001   PHE r 346 
 HIS   0.003   0.001   HIS D 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 ( 4081)
  covalent geometry    : angle       0.56983 ( 5460)
  hydrogen bonds       : bond        0.01517 (   36)
  hydrogen bonds       : angle       3.98598 (  108)

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

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

  1022 Ramachandran restraints generated.
    511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1022 Ramachandran restraints generated.
    511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 96
  time to evaluate  : 0.098 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  331 LYS cc_start: 0.8817 (mtpt) cc_final: 0.7339 (tptt)
REVERT: A  343 LYS cc_start: 0.8045 (ptmm) cc_final: 0.5831 (tppt)
REVERT: A  345 ASP cc_start: 0.7807 (t0) cc_final: 0.7525 (t0)
REVERT: A  369 LYS cc_start: 0.8257 (mttt) cc_final: 0.7989 (mttt)
REVERT: B  311 LYS cc_start: 0.8384 (tttm) cc_final: 0.8007 (ttmt)
REVERT: B  340 LYS cc_start: 0.8705 (mttt) cc_final: 0.8421 (mttm)
REVERT: B  356 SER cc_start: 0.8570 (m) cc_final: 0.8249 (p)
REVERT: E  342 GLU cc_start: 0.8205 (mm-30) cc_final: 0.8004 (mm-30)
REVERT: F  372 GLU cc_start: 0.8206 (tp30) cc_final: 0.7955 (mm-30)
  outliers start: 9
  outliers final: 7
  residues processed: 100
  average time/residue: 0.1019
  time to fit residues: 11.6621
Evaluate side-chains
  100 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 93
  time to evaluate  : 0.101 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain B residue  379 ARG
Chi-restraints excluded: chain C residue  318 VAL
Chi-restraints excluded: chain D residue  315 LEU
Chi-restraints excluded: chain E residue  318 VAL
Chi-restraints excluded: chain E residue  320 SER
Chi-restraints excluded: chain E residue  379 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 24 optimal weight:   10.0000
   chunk 4 optimal weight:    6.9990
   chunk 45 optimal weight:    3.9990
   chunk 9 optimal weight:    9.9990
   chunk 11 optimal weight:    2.9990
   chunk 40 optimal weight:    1.9990
   chunk 36 optimal weight:    5.9990
   chunk 13 optimal weight:    1.9990
   chunk 16 optimal weight:    0.8980
   chunk 33 optimal weight:    1.9990
   chunk 17 optimal weight:    9.9990
   overall best weight:    1.9788

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4299 r_free = 0.4299 target = 0.149459 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.124887 restraints weight = 4502.799|
|-----------------------------------------------------------------------------|
r_work (start): 0.4022 rms_B_bonded: 2.45
r_work: 0.3894 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3767 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.3767
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7856
moved from start:          0.4419

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4081  Z= 0.133
  Angle     :  0.580   7.710   5460  Z= 0.296
  Chirality :  0.050   0.123    616
  Planarity :  0.004   0.032    693
  Dihedral  :  5.718  17.616    539
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 3.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.98 %
    Favored  : 99.02 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 20.13 %
    Favored  : 78.14 %
  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: -2.72 (0.32), residues: 511
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.07 (0.24), residues: 511

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 379 
 TYR   0.009   0.002   TYR A 310 
 PHE   0.004   0.001   PHE r 346 
 HIS   0.003   0.001   HIS D 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 4081)
  covalent geometry    : angle       0.57996 ( 5460)
  hydrogen bonds       : bond        0.01611 (   36)
  hydrogen bonds       : angle       3.94148 (  108)

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

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

  1022 Ramachandran restraints generated.
    511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1022 Ramachandran restraints generated.
    511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 94
  time to evaluate  : 0.128 
Fit side-chains
   revert: symmetry clash
REVERT: A  331 LYS cc_start: 0.8836 (mtpt) cc_final: 0.7384 (tptt)
REVERT: A  340 LYS cc_start: 0.8569 (mttt) cc_final: 0.8147 (mmtm)
REVERT: A  343 LYS cc_start: 0.8089 (ptmm) cc_final: 0.5844 (tppt)
REVERT: A  345 ASP cc_start: 0.7852 (t0) cc_final: 0.7549 (t0)
REVERT: A  369 LYS cc_start: 0.8296 (mttt) cc_final: 0.8033 (mttt)
REVERT: B  311 LYS cc_start: 0.8392 (tttm) cc_final: 0.8009 (ttmt)
REVERT: B  340 LYS cc_start: 0.8744 (mttt) cc_final: 0.8472 (mttm)
REVERT: E  340 LYS cc_start: 0.8519 (mttt) cc_final: 0.8150 (mttm)
REVERT: E  342 GLU cc_start: 0.8110 (mm-30) cc_final: 0.7890 (mm-30)
REVERT: F  372 GLU cc_start: 0.8227 (tp30) cc_final: 0.7974 (mm-30)
  outliers start: 8
  outliers final: 7
  residues processed: 97
  average time/residue: 0.0992
  time to fit residues: 11.0551
Evaluate side-chains
  101 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 94
  time to evaluate  : 0.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain B residue  379 ARG
Chi-restraints excluded: chain C residue  318 VAL
Chi-restraints excluded: chain D residue  315 LEU
Chi-restraints excluded: chain E residue  318 VAL
Chi-restraints excluded: chain E residue  320 SER
Chi-restraints excluded: chain E residue  379 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 8 optimal weight:    9.9990
   chunk 25 optimal weight:    9.9990
   chunk 0 optimal weight:   10.0000
   chunk 24 optimal weight:    4.9990
   chunk 42 optimal weight:   10.0000
   chunk 10 optimal weight:    5.9990
   chunk 7 optimal weight:   10.0000
   chunk 41 optimal weight:   10.0000
   chunk 5 optimal weight:   10.0000
   chunk 14 optimal weight:    7.9990
   chunk 6 optimal weight:    0.7980
   overall best weight:    5.9588

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

Flipped N/Q/H residues before XYZ refinement:
** D 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 = 0.4166 r_free = 0.4166 target = 0.136507 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.113456 restraints weight = 4745.884|
|-----------------------------------------------------------------------------|
r_work (start): 0.3885 rms_B_bonded: 2.36
r_work: 0.3756 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3628 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.3628
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7878
moved from start:          0.4117

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.074   4081  Z= 0.327
  Angle     :  0.753   8.700   5460  Z= 0.397
  Chirality :  0.054   0.150    616
  Planarity :  0.004   0.032    693
  Dihedral  :  6.608  20.085    539
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 4.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.83 %
    Favored  : 92.17 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 19.91 %
    Favored  : 77.71 %
  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: -2.94 (0.31), residues: 511
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.23 (0.23), residues: 511

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG C 379 
 TYR   0.021   0.005   TYR B 310 
 PHE   0.007   0.002   PHE A 378 
 HIS   0.005   0.001   HIS F 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00730 ( 4081)
  covalent geometry    : angle       0.75311 ( 5460)
  hydrogen bonds       : bond        0.02101 (   36)
  hydrogen bonds       : angle       3.85240 (  108)

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

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

  1022 Ramachandran restraints generated.
    511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1022 Ramachandran restraints generated.
    511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 91
  time to evaluate  : 0.100 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  331 LYS cc_start: 0.8780 (mtpt) cc_final: 0.7525 (tmtt)
REVERT: A  343 LYS cc_start: 0.8094 (ptmm) cc_final: 0.6158 (tppt)
REVERT: A  369 LYS cc_start: 0.8267 (mttt) cc_final: 0.7977 (mttt)
REVERT: C  340 LYS cc_start: 0.8497 (mttt) cc_final: 0.8217 (mttp)
REVERT: C  342 GLU cc_start: 0.7885 (mm-30) cc_final: 0.7558 (mm-30)
REVERT: E  340 LYS cc_start: 0.8536 (mttt) cc_final: 0.8125 (mttm)
REVERT: F  340 LYS cc_start: 0.8888 (mttt) cc_final: 0.8558 (mttp)
REVERT: F  372 GLU cc_start: 0.8292 (tp30) cc_final: 0.7925 (mm-30)
  outliers start: 11
  outliers final: 9
  residues processed: 96
  average time/residue: 0.0873
  time to fit residues: 9.7009
Evaluate side-chains
  99 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 90
  time to evaluate  : 0.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain B residue  379 ARG
Chi-restraints excluded: chain C residue  318 VAL
Chi-restraints excluded: chain D residue  315 LEU
Chi-restraints excluded: chain D residue  352 SER
Chi-restraints excluded: chain E residue  318 VAL
Chi-restraints excluded: chain E residue  320 SER
Chi-restraints excluded: chain E residue  352 SER
Chi-restraints excluded: chain E residue  379 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 8 optimal weight:    6.9990
   chunk 46 optimal weight:    0.9990
   chunk 24 optimal weight:    5.9990
   chunk 19 optimal weight:    0.9990
   chunk 36 optimal weight:    8.9990
   chunk 15 optimal weight:    6.9990
   chunk 3 optimal weight:    3.9990
   chunk 32 optimal weight:    1.9990
   chunk 10 optimal weight:    5.9990
   chunk 34 optimal weight:    2.9990
   chunk 26 optimal weight:    0.7980
   overall best weight:    1.5588

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4300 r_free = 0.4300 target = 0.147917 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4009 r_free = 0.4009 target = 0.124565 restraints weight = 4586.301|
|-----------------------------------------------------------------------------|
r_work (start): 0.4028 rms_B_bonded: 2.42
r_work: 0.3900 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3777 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.3777
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7776
moved from start:          0.4495

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   4081  Z= 0.116
  Angle     :  0.604   8.231   5460  Z= 0.306
  Chirality :  0.050   0.125    616
  Planarity :  0.004   0.032    693
  Dihedral  :  5.863  17.949    539
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 3.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 21.43 %
    Favored  : 76.84 %
  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: -2.80 (0.31), residues: 511
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.12 (0.24), residues: 511

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG r 379 
 TYR   0.007   0.002   TYR r 310 
 PHE   0.004   0.001   PHE r 346 
 HIS   0.003   0.001   HIS D 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 ( 4081)
  covalent geometry    : angle       0.60400 ( 5460)
  hydrogen bonds       : bond        0.01585 (   36)
  hydrogen bonds       : angle       3.88930 (  108)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1124.05 seconds
wall clock time: 20 minutes 9.12 seconds (1209.12 seconds total)