Starting phenix.real_space_refine
on Tue Feb  3 19:11:11 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9jxd_61859/02_2026/9jxd_61859.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9jxd_61859/02_2026/9jxd_61859.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.29
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9jxd_61859/02_2026/9jxd_61859.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9jxd_61859/02_2026/9jxd_61859.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9jxd_61859/02_2026/9jxd_61859.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9jxd_61859/02_2026/9jxd_61859.map"
  }
  resolution = 3.29
  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=   0.004 sd=   0.085
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      32      5.16       5
     C    4252      2.51       5
     N    1008      2.21       5
     O    1012      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6304
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3152
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 377, 3152
          Classifications: {'peptide': 377}
          Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 364}
          Chain breaks: 2
  Restraints were copied for chains:
    B
  Time building chain proxies: 1.37, per 1000 atoms: 0.22
  Number of scatterers: 6304
  At special positions: 0
  Unit cell: (66.465, 124.49, 72.795, 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      32     16.00
     O    1012      8.00
     N    1008      7.00
     C    4252      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 415 " - pdb=" SG  CYS A 440 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 415 " - pdb=" SG  CYS B 440 " distance=2.03

  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: 0.34
  Conformation dependent library (CDL) restraints added in 322.1 milliseconds
  

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1432

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 0 sheets defined
      77.7% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.16
  Creating SS restraints...
    Processing helix  chain 'A' and resid 231 through 257
    Processing helix  chain 'A' and resid 265 through 270
    Processing helix  chain 'A' and resid 271 through 296
      removed outlier: 4.596A  pdb=" N   GLY A 275 " --> pdb=" O   ILE A 271 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 298 through 303
      removed outlier: 4.000A  pdb=" N   ILE A 302 " --> pdb=" O   ASN A 298 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   PHE A 303 " --> pdb=" O   HIS A 299 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 298 through 303'
    Processing helix  chain 'A' and resid 312 through 336
      removed outlier: 3.712A  pdb=" N   LEU A 316 " --> pdb=" O   SER A 312 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 345 through 358
      removed outlier: 3.991A  pdb=" N   LEU A 349 " --> pdb=" O   TYR A 345 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 367 through 383
      removed outlier: 3.588A  pdb=" N   LYS A 376 " --> pdb=" O   PHE A 372 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 384 through 387
    Processing helix  chain 'A' and resid 391 through 403
    Processing helix  chain 'A' and resid 403 through 417
      removed outlier: 4.063A  pdb=" N   LEU A 407 " --> pdb=" O   LEU A 403 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 446 through 471
      removed outlier: 3.842A  pdb=" N   GLN A 452 " --> pdb=" O   ARG A 448 " (cutoff:3.500A)
      Proline residue:  A 455  - end of helix
    Processing helix  chain 'A' and resid 472 through 477
      removed outlier: 4.083A  pdb=" N   HIS A 476 " --> pdb=" O   ARG A 472 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 480 through 503
      removed outlier: 4.096A  pdb=" N   THR A 485 " --> pdb=" O   GLY A 481 " (cutoff:3.500A)
      removed outlier: 4.809A  pdb=" N   THR A 486 " --> pdb=" O   LYS A 482 " (cutoff:3.500A)
      removed outlier: 4.056A  pdb=" N   PHE A 487 " --> pdb=" O   TYR A 483 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 506 through 532
    Processing helix  chain 'A' and resid 555 through 582
      removed outlier: 4.118A  pdb=" N   TYR A 559 " --> pdb=" O   GLN A 555 " (cutoff:3.500A)
      removed outlier: 4.014A  pdb=" N   ILE A 564 " --> pdb=" O   TYR A 560 " (cutoff:3.500A)
      removed outlier: 4.078A  pdb=" N   PHE A 571 " --> pdb=" O   VAL A 567 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   ALA A 572 " --> pdb=" O   ILE A 568 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 591 through 619
      Proline residue:  A 598  - end of helix
      removed outlier: 3.553A  pdb=" N   ASN A 614 " --> pdb=" O   PHE A 610 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 231 through 257
    Processing helix  chain 'B' and resid 265 through 270
    Processing helix  chain 'B' and resid 271 through 296
      removed outlier: 4.596A  pdb=" N   GLY B 275 " --> pdb=" O   ILE B 271 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 298 through 303
      removed outlier: 4.000A  pdb=" N   ILE B 302 " --> pdb=" O   ASN B 298 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   PHE B 303 " --> pdb=" O   HIS B 299 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 298 through 303'
    Processing helix  chain 'B' and resid 312 through 336
      removed outlier: 3.713A  pdb=" N   LEU B 316 " --> pdb=" O   SER B 312 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 345 through 358
      removed outlier: 3.991A  pdb=" N   LEU B 349 " --> pdb=" O   TYR B 345 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 367 through 383
      removed outlier: 3.589A  pdb=" N   LYS B 376 " --> pdb=" O   PHE B 372 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 384 through 387
    Processing helix  chain 'B' and resid 391 through 403
    Processing helix  chain 'B' and resid 403 through 417
      removed outlier: 4.063A  pdb=" N   LEU B 407 " --> pdb=" O   LEU B 403 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 446 through 471
      removed outlier: 3.842A  pdb=" N   GLN B 452 " --> pdb=" O   ARG B 448 " (cutoff:3.500A)
      Proline residue:  B 455  - end of helix
    Processing helix  chain 'B' and resid 472 through 477
      removed outlier: 4.083A  pdb=" N   HIS B 476 " --> pdb=" O   ARG B 472 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 480 through 503
      removed outlier: 4.096A  pdb=" N   THR B 485 " --> pdb=" O   GLY B 481 " (cutoff:3.500A)
      removed outlier: 4.809A  pdb=" N   THR B 486 " --> pdb=" O   LYS B 482 " (cutoff:3.500A)
      removed outlier: 4.055A  pdb=" N   PHE B 487 " --> pdb=" O   TYR B 483 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 506 through 532
    Processing helix  chain 'B' and resid 555 through 582
      removed outlier: 4.118A  pdb=" N   TYR B 559 " --> pdb=" O   GLN B 555 " (cutoff:3.500A)
      removed outlier: 4.014A  pdb=" N   ILE B 564 " --> pdb=" O   TYR B 560 " (cutoff:3.500A)
      removed outlier: 4.078A  pdb=" N   PHE B 571 " --> pdb=" O   VAL B 567 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   ALA B 572 " --> pdb=" O   ILE B 568 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 591 through 619
      Proline residue:  B 598  - end of helix
      removed outlier: 3.553A  pdb=" N   ASN B 614 " --> pdb=" O   PHE B 610 " (cutoff:3.500A)

    414 hydrogen bonds defined for protein.
    1236 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: 0.53 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 894
        1.31 -     1.43: 2116
        1.43 -     1.56: 3464
        1.56 -     1.68: 0
        1.68 -     1.81: 44
  Bond restraints: 6518
  Sorted by residual:
  bond pdb=" C   PHE B 610 "
       pdb=" O   PHE B 610 "
    ideal  model  delta    sigma   weight residual
    1.236  1.184  0.052 1.32e-02 5.74e+03 1.56e+01
  bond pdb=" C   PHE A 610 "
       pdb=" O   PHE A 610 "
    ideal  model  delta    sigma   weight residual
    1.236  1.186  0.050 1.32e-02 5.74e+03 1.46e+01
  bond pdb=" CB  VAL B 246 "
       pdb=" CG1 VAL B 246 "
    ideal  model  delta    sigma   weight residual
    1.521  1.437  0.084 3.30e-02 9.18e+02 6.52e+00
  bond pdb=" CB  VAL A 246 "
       pdb=" CG1 VAL A 246 "
    ideal  model  delta    sigma   weight residual
    1.521  1.437  0.084 3.30e-02 9.18e+02 6.48e+00
  bond pdb=" C   PHE A 609 "
       pdb=" O   PHE A 609 "
    ideal  model  delta    sigma   weight residual
    1.236  1.204  0.032 1.32e-02 5.74e+03 5.72e+00
  ... (remaining 6513 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.49: 8729
        2.49 -     4.98: 117
        4.98 -     7.48: 14
        7.48 -     9.97: 2
        9.97 -    12.46: 2
  Bond angle restraints: 8864
  Sorted by residual:
  angle pdb=" CA  PHE A 609 "
        pdb=" CB  PHE A 609 "
        pdb=" CG  PHE A 609 "
      ideal   model   delta    sigma   weight residual
     113.80  122.07   -8.27 1.00e+00 1.00e+00 6.84e+01
  angle pdb=" CA  PHE B 609 "
        pdb=" CB  PHE B 609 "
        pdb=" CG  PHE B 609 "
      ideal   model   delta    sigma   weight residual
     113.80  122.06   -8.26 1.00e+00 1.00e+00 6.83e+01
  angle pdb=" C   PHE B 609 "
        pdb=" CA  PHE B 609 "
        pdb=" CB  PHE B 609 "
      ideal   model   delta    sigma   weight residual
     109.99   97.53   12.46 2.09e+00 2.29e-01 3.55e+01
  angle pdb=" C   PHE A 609 "
        pdb=" CA  PHE A 609 "
        pdb=" CB  PHE A 609 "
      ideal   model   delta    sigma   weight residual
     109.99   97.53   12.46 2.09e+00 2.29e-01 3.55e+01
  angle pdb=" CA  PHE B 610 "
        pdb=" CB  PHE B 610 "
        pdb=" CG  PHE B 610 "
      ideal   model   delta    sigma   weight residual
     113.80  119.72   -5.92 1.00e+00 1.00e+00 3.50e+01
  ... (remaining 8859 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.05: 3195
       17.05 -    34.10: 360
       34.10 -    51.16: 89
       51.16 -    68.21: 20
       68.21 -    85.26: 8
  Dihedral angle restraints: 3672
    sinusoidal: 1450
      harmonic: 2222
  Sorted by residual:
  dihedral pdb=" C   PHE A 609 "
           pdb=" N   PHE A 609 "
           pdb=" CA  PHE A 609 "
           pdb=" CB  PHE A 609 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -110.00  -12.60     0      2.50e+00 1.60e-01 2.54e+01
  dihedral pdb=" C   PHE B 609 "
           pdb=" N   PHE B 609 "
           pdb=" CA  PHE B 609 "
           pdb=" CB  PHE B 609 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -110.05  -12.55     0      2.50e+00 1.60e-01 2.52e+01
  dihedral pdb=" CA  ASN B 544 "
           pdb=" C   ASN B 544 "
           pdb=" N   THR B 545 "
           pdb=" CA  THR B 545 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.09  -20.91     0      5.00e+00 4.00e-02 1.75e+01
  ... (remaining 3669 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 660
       0.041 -    0.081: 260
       0.081 -    0.122: 44
       0.122 -    0.162: 0
       0.162 -    0.203: 4
  Chirality restraints: 968
  Sorted by residual:
  chirality pdb=" CA  PHE A 610 "
            pdb=" N   PHE A 610 "
            pdb=" C   PHE A 610 "
            pdb=" CB  PHE A 610 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 1.03e+00
  chirality pdb=" CA  PHE B 610 "
            pdb=" N   PHE B 610 "
            pdb=" C   PHE B 610 "
            pdb=" CB  PHE B 610 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 9.99e-01
  chirality pdb=" CA  PHE A 609 "
            pdb=" N   PHE A 609 "
            pdb=" C   PHE A 609 "
            pdb=" CB  PHE A 609 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.69   -0.18 2.00e-01 2.50e+01 8.37e-01
  ... (remaining 965 not shown)

  Planarity restraints: 1070
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN B 608 "   -0.017 2.00e-02 2.50e+03   3.22e-02 1.04e+01
        pdb=" C   ASN B 608 "    0.056 2.00e-02 2.50e+03
        pdb=" O   ASN B 608 "   -0.020 2.00e-02 2.50e+03
        pdb=" N   PHE B 609 "   -0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN A 608 "    0.017 2.00e-02 2.50e+03   3.16e-02 1.00e+01
        pdb=" C   ASN A 608 "   -0.055 2.00e-02 2.50e+03
        pdb=" O   ASN A 608 "    0.019 2.00e-02 2.50e+03
        pdb=" N   PHE A 609 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A 610 "   -0.013 2.00e-02 2.50e+03   2.65e-02 7.02e+00
        pdb=" C   PHE A 610 "    0.046 2.00e-02 2.50e+03
        pdb=" O   PHE A 610 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   ARG A 611 "   -0.016 2.00e-02 2.50e+03
  ... (remaining 1067 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 229
        2.71 -     3.26: 6719
        3.26 -     3.80: 10647
        3.80 -     4.35: 12896
        4.35 -     4.90: 21424
  Nonbonded interactions: 51915
  Sorted by model distance:
  nonbonded pdb=" O   LEU B 284 "
            pdb=" CE1 PHE B 605 "
     model   vdw
     2.160 3.340
  nonbonded pdb=" O   LEU A 284 "
            pdb=" CE1 PHE A 605 "
     model   vdw
     2.161 3.340
  nonbonded pdb=" O   ILE B 271 "
            pdb=" OH  TYR B 352 "
     model   vdw
     2.178 3.040
  nonbonded pdb=" O   ILE A 271 "
            pdb=" OH  TYR A 352 "
     model   vdw
     2.178 3.040
  nonbonded pdb=" O   CYS B 440 "
            pdb=" ND1 HIS B 441 "
     model   vdw
     2.243 3.120
  ... (remaining 51910 not shown)

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

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:             0.980
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     6.360
  Find NCS groups from input model:        0.030
  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:1.190
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.670
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7697
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      :  0.006   0.084   6520  Z= 0.292
  Angle     :  0.769  12.460   8868  Z= 0.476
  Chirality :  0.043   0.203    968
  Planarity :  0.005   0.045   1070
  Dihedral  : 16.268  85.261   2234
  Min Nonbonded Distance : 2.160

Molprobity Statistics.
  All-atom Clashscore : 14.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.36 %
    Favored  : 91.64 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 17.66 %
    Favored  : 82.34 %
  Cbeta Deviations :  0.28 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    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 are not related in a simple way.
  whole: -3.00 (0.26), residues: 742
  helix: -1.19 (0.19), residues: 560
  sheet:  None (None), residues: 0
  loop : -4.24 (0.34), residues: 182

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 270 
 TYR   0.012   0.002   TYR B 272 
 PHE   0.042   0.002   PHE A 609 
 TRP   0.009   0.001   TRP A 514 
 HIS   0.003   0.001   HIS B 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00649 ( 6518)
  covalent geometry    : angle       0.76918 ( 8864)
  SS BOND              : bond        0.00027 (    2)
  SS BOND              : angle       0.32912 (    4)
  hydrogen bonds       : bond        0.12058 (  414)
  hydrogen bonds       : angle       5.05255 ( 1236)

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

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

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 136
  time to evaluate  : 0.139 
Fit side-chains
REVERT: A  364 LYS cc_start: 0.8158 (mmtp) cc_final: 0.7846 (mmmt)
REVERT: A  369 LYS cc_start: 0.5802 (tmtt) cc_final: 0.4652 (pttp)
REVERT: B  364 LYS cc_start: 0.8243 (mmtp) cc_final: 0.7910 (mmmt)
REVERT: B  369 LYS cc_start: 0.5861 (tmtt) cc_final: 0.4693 (pttp)
  outliers start: 0
  outliers final: 0
  residues processed: 136
  average time/residue: 0.1042
  time to fit residues: 17.3593
Evaluate side-chains
  85 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.164 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 53 optimal weight:    0.7980
   chunk 5 optimal weight:    0.5980
   chunk 33 optimal weight:    0.1980
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.7980
   chunk 38 optimal weight:    0.6980
   chunk 61 optimal weight:    0.7980
   chunk 45 optimal weight:    0.6980
   chunk 27 optimal weight:    0.5980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
A 288 ASN
A 399 GLN
B 288 ASN
** B 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 399 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4047 r_free = 0.4047 target = 0.171960 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.136202 restraints weight = 7424.906|
|-----------------------------------------------------------------------------|
r_work (start): 0.3639 rms_B_bonded: 2.40
r_work: 0.3497 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work (final): 0.3497
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7530
moved from start:          0.1843

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   6520  Z= 0.145
  Angle     :  0.590   7.578   8868  Z= 0.306
  Chirality :  0.040   0.213    968
  Planarity :  0.004   0.035   1070
  Dihedral  :  4.315  18.972    830
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 7.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.66 %
    Favored  : 94.34 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 19.76 %
    Favored  : 77.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    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 are not related in a simple way.
  whole: -0.90 (0.30), residues: 742
  helix:  0.37 (0.21), residues: 562
  sheet:  None (None), residues: 0
  loop : -3.69 (0.38), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 371 
 TYR   0.008   0.001   TYR A 352 
 PHE   0.024   0.001   PHE A 605 
 TRP   0.008   0.001   TRP B 528 
 HIS   0.004   0.001   HIS B 441 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 6518)
  covalent geometry    : angle       0.59022 ( 8864)
  SS BOND              : bond        0.00254 (    2)
  SS BOND              : angle       0.70668 (    4)
  hydrogen bonds       : bond        0.04554 (  414)
  hydrogen bonds       : angle       3.96970 ( 1236)

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

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

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 78
  time to evaluate  : 0.164 
Fit side-chains
REVERT: A  369 LYS cc_start: 0.5542 (tmtt) cc_final: 0.4118 (pttp)
REVERT: A  398 ASP cc_start: 0.8193 (OUTLIER) cc_final: 0.7549 (m-30)
REVERT: A  613 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.8279 (tm-30)
REVERT: A  618 ASN cc_start: 0.8165 (m-40) cc_final: 0.7945 (m-40)
REVERT: B  369 LYS cc_start: 0.5454 (tmtt) cc_final: 0.4086 (pttp)
REVERT: B  398 ASP cc_start: 0.8259 (OUTLIER) cc_final: 0.7644 (m-30)
REVERT: B  452 GLN cc_start: 0.8477 (tp40) cc_final: 0.8205 (tp40)
REVERT: B  550 GLU cc_start: 0.8068 (pm20) cc_final: 0.7338 (tt0)
REVERT: B  613 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.8193 (tm-30)
  outliers start: 18
  outliers final: 11
  residues processed: 88
  average time/residue: 0.0614
  time to fit residues: 7.3629
Evaluate side-chains
  80 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 65
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  304 GLU
Chi-restraints excluded: chain A residue  312 SER
Chi-restraints excluded: chain A residue  370 SER
Chi-restraints excluded: chain A residue  398 ASP
Chi-restraints excluded: chain A residue  513 LEU
Chi-restraints excluded: chain A residue  613 GLU
Chi-restraints excluded: chain B residue  301 LEU
Chi-restraints excluded: chain B residue  304 GLU
Chi-restraints excluded: chain B residue  312 SER
Chi-restraints excluded: chain B residue  370 SER
Chi-restraints excluded: chain B residue  398 ASP
Chi-restraints excluded: chain B residue  513 LEU
Chi-restraints excluded: chain B residue  583 THR
Chi-restraints excluded: chain B residue  613 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 69 optimal weight:    0.9990
   chunk 4 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9990
   chunk 52 optimal weight:    0.0020
   chunk 35 optimal weight:    0.5980
   chunk 12 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9990
   chunk 23 optimal weight:    0.2980
   chunk 15 optimal weight:    0.0040
   chunk 19 optimal weight:    5.9990
   chunk 70 optimal weight:    0.9990
   overall best weight:    0.3802

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

Flipped N/Q/H residues before XYZ refinement:
B 299 HIS
** B 310 ASN ** 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 = 0.4080 r_free = 0.4080 target = 0.173953 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.138819 restraints weight = 7312.514|
|-----------------------------------------------------------------------------|
r_work (start): 0.3693 rms_B_bonded: 2.31
r_work: 0.3555 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.3407 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.3407
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7474
moved from start:          0.2494

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   6520  Z= 0.122
  Angle     :  0.545   7.261   8868  Z= 0.277
  Chirality :  0.038   0.187    968
  Planarity :  0.003   0.034   1070
  Dihedral  :  3.956  17.597    830
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 6.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 20.66 %
    Favored  : 76.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    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 are not related in a simple way.
  whole:  0.12 (0.31), residues: 742
  helix:  1.08 (0.22), residues: 560
  sheet:  None (None), residues: 0
  loop : -3.20 (0.41), residues: 182

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 380 
 TYR   0.008   0.001   TYR A 559 
 PHE   0.016   0.001   PHE A 609 
 TRP   0.008   0.001   TRP B 573 
 HIS   0.005   0.001   HIS B 441 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 6518)
  covalent geometry    : angle       0.54464 ( 8864)
  SS BOND              : bond        0.00289 (    2)
  SS BOND              : angle       0.95996 (    4)
  hydrogen bonds       : bond        0.04036 (  414)
  hydrogen bonds       : angle       3.75788 ( 1236)

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

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

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 70
  time to evaluate  : 0.149 
Fit side-chains
REVERT: A  369 LYS cc_start: 0.5360 (tmtt) cc_final: 0.3913 (pttp)
REVERT: A  387 HIS cc_start: 0.8363 (m-70) cc_final: 0.7846 (m-70)
REVERT: A  388 LYS cc_start: 0.7924 (OUTLIER) cc_final: 0.7666 (ttpp)
REVERT: A  398 ASP cc_start: 0.8275 (OUTLIER) cc_final: 0.7511 (m-30)
REVERT: A  454 ILE cc_start: 0.8021 (OUTLIER) cc_final: 0.7803 (tt)
REVERT: A  472 ARG cc_start: 0.8474 (mtm-85) cc_final: 0.8059 (ttp-110)
REVERT: B  369 LYS cc_start: 0.5166 (tmtt) cc_final: 0.3793 (tptp)
REVERT: B  398 ASP cc_start: 0.8245 (OUTLIER) cc_final: 0.7576 (m-30)
REVERT: B  454 ILE cc_start: 0.7926 (OUTLIER) cc_final: 0.7523 (tt)
REVERT: B  472 ARG cc_start: 0.8611 (mtm-85) cc_final: 0.8240 (ttp-110)
  outliers start: 17
  outliers final: 6
  residues processed: 84
  average time/residue: 0.0636
  time to fit residues: 7.3942
Evaluate side-chains
  75 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 64
  time to evaluate  : 0.231 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  312 SER
Chi-restraints excluded: chain A residue  388 LYS
Chi-restraints excluded: chain A residue  398 ASP
Chi-restraints excluded: chain A residue  454 ILE
Chi-restraints excluded: chain A residue  513 LEU
Chi-restraints excluded: chain A residue  581 SER
Chi-restraints excluded: chain B residue  398 ASP
Chi-restraints excluded: chain B residue  454 ILE
Chi-restraints excluded: chain B residue  513 LEU
Chi-restraints excluded: chain B residue  581 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 9 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   chunk 51 optimal weight:    0.6980
   chunk 23 optimal weight:    0.9990
   chunk 59 optimal weight:    1.9990
   chunk 4 optimal weight:    0.7980
   chunk 56 optimal weight:    0.9990
   chunk 28 optimal weight:    0.9990
   chunk 69 optimal weight:    1.9990
   chunk 29 optimal weight:    5.9990
   chunk 0 optimal weight:    2.9990
   overall best weight:    0.8986

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

Flipped N/Q/H residues before XYZ refinement:
A 387 HIS
** B 310 ASN ** 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 = 0.4022 r_free = 0.4022 target = 0.170291 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.134163 restraints weight = 7413.886|
|-----------------------------------------------------------------------------|
r_work (start): 0.3612 rms_B_bonded: 2.43
r_work: 0.3467 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.3467
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7517
moved from start:          0.2590

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   6520  Z= 0.174
  Angle     :  0.572   7.304   8868  Z= 0.294
  Chirality :  0.040   0.154    968
  Planarity :  0.003   0.034   1070
  Dihedral  :  4.091  17.898    830
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 7.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.60 %
    Favored  : 93.40 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 20.81 %
    Favored  : 75.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    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 are not related in a simple way.
  whole:  0.20 (0.31), residues: 742
  helix:  1.09 (0.21), residues: 562
  sheet:  None (None), residues: 0
  loop : -2.98 (0.42), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 380 
 TYR   0.011   0.001   TYR A 553 
 PHE   0.018   0.001   PHE A 605 
 TRP   0.006   0.001   TRP B 514 
 HIS   0.005   0.001   HIS B 441 

Details of bonding type rmsd
  covalent geometry    : bond        0.00411 ( 6518)
  covalent geometry    : angle       0.57189 ( 8864)
  SS BOND              : bond        0.00292 (    2)
  SS BOND              : angle       0.79208 (    4)
  hydrogen bonds       : bond        0.04493 (  414)
  hydrogen bonds       : angle       3.78372 ( 1236)

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

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

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 73
  time to evaluate  : 0.241 
Fit side-chains
REVERT: A  369 LYS cc_start: 0.5304 (tmtt) cc_final: 0.3971 (pttm)
REVERT: A  388 LYS cc_start: 0.7766 (OUTLIER) cc_final: 0.7482 (ttpp)
REVERT: A  398 ASP cc_start: 0.8185 (OUTLIER) cc_final: 0.7482 (m-30)
REVERT: A  472 ARG cc_start: 0.8532 (mtm-85) cc_final: 0.8261 (ttp-170)
REVERT: B  369 LYS cc_start: 0.5174 (tmtt) cc_final: 0.3753 (tptp)
REVERT: B  398 ASP cc_start: 0.8308 (OUTLIER) cc_final: 0.7814 (m-30)
REVERT: B  472 ARG cc_start: 0.8653 (mtm-85) cc_final: 0.8416 (ttp-170)
  outliers start: 24
  outliers final: 12
  residues processed: 89
  average time/residue: 0.0718
  time to fit residues: 8.7046
Evaluate side-chains
  84 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 69
  time to evaluate  : 0.182 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  312 SER
Chi-restraints excluded: chain A residue  370 SER
Chi-restraints excluded: chain A residue  383 THR
Chi-restraints excluded: chain A residue  388 LYS
Chi-restraints excluded: chain A residue  398 ASP
Chi-restraints excluded: chain A residue  513 LEU
Chi-restraints excluded: chain B residue  297 VAL
Chi-restraints excluded: chain B residue  301 LEU
Chi-restraints excluded: chain B residue  312 SER
Chi-restraints excluded: chain B residue  370 SER
Chi-restraints excluded: chain B residue  398 ASP
Chi-restraints excluded: chain B residue  513 LEU
Chi-restraints excluded: chain B residue  577 ILE
Chi-restraints excluded: chain B residue  581 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 29 optimal weight:    0.1980
   chunk 68 optimal weight:    0.5980
   chunk 5 optimal weight:    0.5980
   chunk 50 optimal weight:    0.6980
   chunk 23 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9990
   chunk 45 optimal weight:    0.5980
   chunk 64 optimal weight:    0.8980
   chunk 24 optimal weight:    2.9990
   chunk 28 optimal weight:    0.8980
   chunk 67 optimal weight:    0.5980
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
** B 310 ASN ** 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 = 0.4052 r_free = 0.4052 target = 0.171453 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.135848 restraints weight = 7386.126|
|-----------------------------------------------------------------------------|
r_work (start): 0.3652 rms_B_bonded: 2.39
r_work: 0.3510 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work (final): 0.3510
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7607
moved from start:          0.2826

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   6520  Z= 0.131
  Angle     :  0.547   8.903   8868  Z= 0.281
  Chirality :  0.039   0.160    968
  Planarity :  0.003   0.034   1070
  Dihedral  :  4.016  17.462    830
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 6.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.53 %
    Favored  : 94.47 %
  Rotamer:
    Outliers :  4.19 %
    Allowed  : 21.26 %
    Favored  : 74.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    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 are not related in a simple way.
  whole:  0.56 (0.31), residues: 742
  helix:  1.33 (0.22), residues: 560
  sheet:  None (None), residues: 0
  loop : -2.75 (0.43), residues: 182

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 380 
 TYR   0.010   0.001   TYR B 443 
 PHE   0.015   0.001   PHE A 605 
 TRP   0.006   0.001   TRP B 514 
 HIS   0.006   0.001   HIS B 441 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 6518)
  covalent geometry    : angle       0.54674 ( 8864)
  SS BOND              : bond        0.00355 (    2)
  SS BOND              : angle       0.89162 (    4)
  hydrogen bonds       : bond        0.04145 (  414)
  hydrogen bonds       : angle       3.66455 ( 1236)

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

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

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 69
  time to evaluate  : 0.181 
Fit side-chains
   revert: symmetry clash
REVERT: A  369 LYS cc_start: 0.5365 (tmtt) cc_final: 0.4022 (pttp)
REVERT: A  388 LYS cc_start: 0.7790 (OUTLIER) cc_final: 0.7542 (ttpp)
REVERT: A  398 ASP cc_start: 0.8292 (OUTLIER) cc_final: 0.7514 (m-30)
REVERT: A  452 GLN cc_start: 0.8238 (tp40) cc_final: 0.8016 (tp40)
REVERT: A  472 ARG cc_start: 0.8679 (mtm-85) cc_final: 0.8447 (ttp-170)
REVERT: B  369 LYS cc_start: 0.5416 (tmtt) cc_final: 0.3858 (tptp)
REVERT: B  398 ASP cc_start: 0.8265 (OUTLIER) cc_final: 0.7840 (m-30)
REVERT: B  472 ARG cc_start: 0.8673 (mtm-85) cc_final: 0.8452 (ttp-170)
  outliers start: 28
  outliers final: 14
  residues processed: 88
  average time/residue: 0.0680
  time to fit residues: 8.3354
Evaluate side-chains
  87 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 70
  time to evaluate  : 0.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  312 SER
Chi-restraints excluded: chain A residue  335 PHE
Chi-restraints excluded: chain A residue  370 SER
Chi-restraints excluded: chain A residue  383 THR
Chi-restraints excluded: chain A residue  388 LYS
Chi-restraints excluded: chain A residue  398 ASP
Chi-restraints excluded: chain A residue  469 ASP
Chi-restraints excluded: chain A residue  513 LEU
Chi-restraints excluded: chain A residue  581 SER
Chi-restraints excluded: chain B residue  301 LEU
Chi-restraints excluded: chain B residue  312 SER
Chi-restraints excluded: chain B residue  370 SER
Chi-restraints excluded: chain B residue  398 ASP
Chi-restraints excluded: chain B residue  463 CYS
Chi-restraints excluded: chain B residue  513 LEU
Chi-restraints excluded: chain B residue  581 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 53 optimal weight:    0.2980
   chunk 23 optimal weight:    0.0970
   chunk 14 optimal weight:    0.8980
   chunk 48 optimal weight:    0.8980
   chunk 52 optimal weight:    0.8980
   chunk 45 optimal weight:    0.5980
   chunk 46 optimal weight:    0.9980
   chunk 10 optimal weight:    0.0670
   chunk 32 optimal weight:    0.7980
   chunk 18 optimal weight:    0.6980
   chunk 1 optimal weight:    0.5980
   overall best weight:    0.3316

-------------------------------------------------------------------------------
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 = 0.4077 r_free = 0.4077 target = 0.175679 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.139746 restraints weight = 7444.284|
|-----------------------------------------------------------------------------|
r_work (start): 0.3690 rms_B_bonded: 2.43
r_work: 0.3547 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work (final): 0.3547
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7531
moved from start:          0.3113

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6520  Z= 0.116
  Angle     :  0.533   8.546   8868  Z= 0.274
  Chirality :  0.038   0.162    968
  Planarity :  0.003   0.034   1070
  Dihedral  :  3.873  16.741    830
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 6.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.66 %
    Favored  : 94.34 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 21.86 %
    Favored  : 74.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    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 are not related in a simple way.
  whole:  0.89 (0.31), residues: 742
  helix:  1.60 (0.22), residues: 558
  sheet:  None (None), residues: 0
  loop : -2.73 (0.43), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 380 
 TYR   0.011   0.001   TYR B 443 
 PHE   0.016   0.001   PHE A 609 
 TRP   0.006   0.001   TRP A 528 
 HIS   0.007   0.001   HIS B 441 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 6518)
  covalent geometry    : angle       0.53282 ( 8864)
  SS BOND              : bond        0.00361 (    2)
  SS BOND              : angle       0.86602 (    4)
  hydrogen bonds       : bond        0.03896 (  414)
  hydrogen bonds       : angle       3.56374 ( 1236)

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

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

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 75
  time to evaluate  : 0.145 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  369 LYS cc_start: 0.5337 (tmtt) cc_final: 0.3988 (tttm)
REVERT: A  387 HIS cc_start: 0.8266 (m90) cc_final: 0.7887 (m-70)
REVERT: A  388 LYS cc_start: 0.7915 (OUTLIER) cc_final: 0.7658 (ttpp)
REVERT: A  398 ASP cc_start: 0.8242 (OUTLIER) cc_final: 0.7455 (m-30)
REVERT: A  463 CYS cc_start: 0.8278 (OUTLIER) cc_final: 0.8075 (m)
REVERT: A  472 ARG cc_start: 0.8684 (mtm-85) cc_final: 0.8365 (ttp-170)
REVERT: B  311 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8327 (tp)
REVERT: B  369 LYS cc_start: 0.5317 (tmtt) cc_final: 0.4013 (tttm)
REVERT: B  387 HIS cc_start: 0.8350 (m-70) cc_final: 0.7728 (m-70)
REVERT: B  472 ARG cc_start: 0.8650 (mtm-85) cc_final: 0.8317 (ttp-170)
REVERT: B  550 GLU cc_start: 0.8075 (pm20) cc_final: 0.7287 (tt0)
  outliers start: 23
  outliers final: 11
  residues processed: 94
  average time/residue: 0.0724
  time to fit residues: 9.1415
Evaluate side-chains
  85 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 70
  time to evaluate  : 0.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  335 PHE
Chi-restraints excluded: chain A residue  370 SER
Chi-restraints excluded: chain A residue  383 THR
Chi-restraints excluded: chain A residue  388 LYS
Chi-restraints excluded: chain A residue  398 ASP
Chi-restraints excluded: chain A residue  463 CYS
Chi-restraints excluded: chain A residue  513 LEU
Chi-restraints excluded: chain A residue  581 SER
Chi-restraints excluded: chain B residue  301 LEU
Chi-restraints excluded: chain B residue  311 LEU
Chi-restraints excluded: chain B residue  312 SER
Chi-restraints excluded: chain B residue  463 CYS
Chi-restraints excluded: chain B residue  513 LEU
Chi-restraints excluded: chain B residue  581 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 60 optimal weight:    0.6980
   chunk 5 optimal weight:    0.5980
   chunk 27 optimal weight:    0.7980
   chunk 9 optimal weight:    0.5980
   chunk 64 optimal weight:    0.9990
   chunk 62 optimal weight:    6.9990
   chunk 41 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9990
   chunk 18 optimal weight:    0.0770
   chunk 17 optimal weight:    0.5980
   chunk 13 optimal weight:    0.7980
   overall best weight:    0.5138

-------------------------------------------------------------------------------
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 = 0.4064 r_free = 0.4064 target = 0.172620 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.137172 restraints weight = 7371.902|
|-----------------------------------------------------------------------------|
r_work (start): 0.3669 rms_B_bonded: 2.36
r_work: 0.3526 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work (final): 0.3526
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7584
moved from start:          0.3152

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   6520  Z= 0.129
  Angle     :  0.536   7.759   8868  Z= 0.276
  Chirality :  0.038   0.166    968
  Planarity :  0.003   0.034   1070
  Dihedral  :  3.893  16.517    830
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 7.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.99 %
    Favored  : 95.01 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 22.01 %
    Favored  : 75.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    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 are not related in a simple way.
  whole:  0.97 (0.31), residues: 742
  helix:  1.63 (0.22), residues: 558
  sheet:  None (None), residues: 0
  loop : -2.59 (0.44), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 380 
 TYR   0.010   0.001   TYR B 443 
 PHE   0.014   0.001   PHE A 605 
 TRP   0.006   0.001   TRP B 514 
 HIS   0.007   0.001   HIS B 441 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 6518)
  covalent geometry    : angle       0.53556 ( 8864)
  SS BOND              : bond        0.00348 (    2)
  SS BOND              : angle       0.88648 (    4)
  hydrogen bonds       : bond        0.04048 (  414)
  hydrogen bonds       : angle       3.58694 ( 1236)

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

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

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 75
  time to evaluate  : 0.157 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  369 LYS cc_start: 0.5441 (tmtt) cc_final: 0.4082 (tttm)
REVERT: A  387 HIS cc_start: 0.8314 (m90) cc_final: 0.8004 (m-70)
REVERT: A  388 LYS cc_start: 0.7900 (OUTLIER) cc_final: 0.7662 (ttpp)
REVERT: A  472 ARG cc_start: 0.8649 (mtm-85) cc_final: 0.8339 (ttp-170)
REVERT: A  549 GLU cc_start: 0.8374 (tm-30) cc_final: 0.7986 (tm-30)
REVERT: B  311 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8340 (tp)
REVERT: B  369 LYS cc_start: 0.5366 (tmtt) cc_final: 0.4076 (tttm)
REVERT: B  398 ASP cc_start: 0.8278 (OUTLIER) cc_final: 0.7851 (m-30)
REVERT: B  472 ARG cc_start: 0.8639 (mtm-85) cc_final: 0.8319 (ttp-170)
  outliers start: 20
  outliers final: 12
  residues processed: 90
  average time/residue: 0.0822
  time to fit residues: 9.7848
Evaluate side-chains
  91 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 76
  time to evaluate  : 0.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  335 PHE
Chi-restraints excluded: chain A residue  370 SER
Chi-restraints excluded: chain A residue  383 THR
Chi-restraints excluded: chain A residue  388 LYS
Chi-restraints excluded: chain A residue  469 ASP
Chi-restraints excluded: chain A residue  513 LEU
Chi-restraints excluded: chain A residue  581 SER
Chi-restraints excluded: chain B residue  301 LEU
Chi-restraints excluded: chain B residue  311 LEU
Chi-restraints excluded: chain B residue  312 SER
Chi-restraints excluded: chain B residue  370 SER
Chi-restraints excluded: chain B residue  398 ASP
Chi-restraints excluded: chain B residue  513 LEU
Chi-restraints excluded: chain B residue  581 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 65 optimal weight:    0.9990
   chunk 3 optimal weight:    0.9990
   chunk 49 optimal weight:    2.9990
   chunk 64 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9980
   chunk 34 optimal weight:    0.1980
   chunk 61 optimal weight:    0.5980
   chunk 56 optimal weight:    0.3980
   chunk 20 optimal weight:    0.6980
   chunk 48 optimal weight:    0.9980
   chunk 70 optimal weight:    7.9990
   overall best weight:    0.5780

-------------------------------------------------------------------------------
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 = 0.4062 r_free = 0.4062 target = 0.172047 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.136555 restraints weight = 7440.344|
|-----------------------------------------------------------------------------|
r_work (start): 0.3658 rms_B_bonded: 2.38
r_work: 0.3516 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work (final): 0.3516
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7547
moved from start:          0.3231

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   6520  Z= 0.139
  Angle     :  0.555   7.929   8868  Z= 0.286
  Chirality :  0.039   0.163    968
  Planarity :  0.003   0.045   1070
  Dihedral  :  3.916  16.110    830
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 6.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.39 %
    Favored  : 94.61 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 21.86 %
    Favored  : 74.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    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 are not related in a simple way.
  whole:  1.00 (0.31), residues: 742
  helix:  1.65 (0.22), residues: 558
  sheet:  None (None), residues: 0
  loop : -2.55 (0.43), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 380 
 TYR   0.010   0.001   TYR B 443 
 PHE   0.015   0.001   PHE A 609 
 TRP   0.006   0.001   TRP B 514 
 HIS   0.007   0.001   HIS B 441 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 6518)
  covalent geometry    : angle       0.55452 ( 8864)
  SS BOND              : bond        0.00347 (    2)
  SS BOND              : angle       0.86682 (    4)
  hydrogen bonds       : bond        0.04137 (  414)
  hydrogen bonds       : angle       3.61229 ( 1236)

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

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

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 78
  time to evaluate  : 0.142 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  369 LYS cc_start: 0.5279 (tmtt) cc_final: 0.3894 (tttm)
REVERT: A  387 HIS cc_start: 0.8261 (m90) cc_final: 0.7891 (m-70)
REVERT: A  388 LYS cc_start: 0.7935 (OUTLIER) cc_final: 0.7662 (ttpp)
REVERT: A  398 ASP cc_start: 0.8288 (OUTLIER) cc_final: 0.7480 (m-30)
REVERT: A  472 ARG cc_start: 0.8612 (mtm-85) cc_final: 0.8296 (ttp-170)
REVERT: A  549 GLU cc_start: 0.8414 (tm-30) cc_final: 0.8020 (tm-30)
REVERT: B  311 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8327 (tp)
REVERT: B  369 LYS cc_start: 0.5300 (tmtt) cc_final: 0.4013 (tttm)
REVERT: B  387 HIS cc_start: 0.8141 (m90) cc_final: 0.7794 (m170)
REVERT: B  398 ASP cc_start: 0.8279 (OUTLIER) cc_final: 0.7830 (m-30)
REVERT: B  472 ARG cc_start: 0.8639 (mtm-85) cc_final: 0.8320 (ttp-170)
  outliers start: 23
  outliers final: 15
  residues processed: 94
  average time/residue: 0.0768
  time to fit residues: 9.6551
Evaluate side-chains
  93 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 74
  time to evaluate  : 0.138 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  312 SER
Chi-restraints excluded: chain A residue  335 PHE
Chi-restraints excluded: chain A residue  370 SER
Chi-restraints excluded: chain A residue  383 THR
Chi-restraints excluded: chain A residue  388 LYS
Chi-restraints excluded: chain A residue  398 ASP
Chi-restraints excluded: chain A residue  469 ASP
Chi-restraints excluded: chain A residue  513 LEU
Chi-restraints excluded: chain A residue  581 SER
Chi-restraints excluded: chain A residue  605 PHE
Chi-restraints excluded: chain B residue  301 LEU
Chi-restraints excluded: chain B residue  311 LEU
Chi-restraints excluded: chain B residue  312 SER
Chi-restraints excluded: chain B residue  370 SER
Chi-restraints excluded: chain B residue  398 ASP
Chi-restraints excluded: chain B residue  513 LEU
Chi-restraints excluded: chain B residue  581 SER
Chi-restraints excluded: chain B residue  605 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 16 optimal weight:    0.6980
   chunk 43 optimal weight:    0.6980
   chunk 59 optimal weight:    6.9990
   chunk 61 optimal weight:    0.8980
   chunk 19 optimal weight:    5.9990
   chunk 11 optimal weight:    0.9980
   chunk 68 optimal weight:    0.9980
   chunk 50 optimal weight:    0.9990
   chunk 65 optimal weight:    0.6980
   chunk 4 optimal weight:    0.9980
   chunk 26 optimal weight:    4.9990
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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 = 0.4031 r_free = 0.4031 target = 0.169207 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.133823 restraints weight = 7525.328|
|-----------------------------------------------------------------------------|
r_work (start): 0.3624 rms_B_bonded: 2.37
r_work: 0.3480 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work (final): 0.3480
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7575
moved from start:          0.3216

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   6520  Z= 0.165
  Angle     :  0.581   7.392   8868  Z= 0.300
  Chirality :  0.039   0.169    968
  Planarity :  0.003   0.045   1070
  Dihedral  :  4.014  16.902    830
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 6.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.66 %
    Favored  : 94.34 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 22.90 %
    Favored  : 73.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    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 are not related in a simple way.
  whole:  0.89 (0.31), residues: 742
  helix:  1.54 (0.22), residues: 560
  sheet:  None (None), residues: 0
  loop : -2.54 (0.44), residues: 182

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 380 
 TYR   0.009   0.001   TYR B 443 
 PHE   0.016   0.001   PHE A 605 
 TRP   0.008   0.001   TRP B 514 
 HIS   0.007   0.001   HIS B 441 

Details of bonding type rmsd
  covalent geometry    : bond        0.00391 ( 6518)
  covalent geometry    : angle       0.58130 ( 8864)
  SS BOND              : bond        0.00339 (    2)
  SS BOND              : angle       0.85332 (    4)
  hydrogen bonds       : bond        0.04406 (  414)
  hydrogen bonds       : angle       3.70603 ( 1236)

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

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

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 87
  time to evaluate  : 0.235 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  369 LYS cc_start: 0.5217 (tmtt) cc_final: 0.3792 (pttm)
REVERT: A  388 LYS cc_start: 0.7923 (OUTLIER) cc_final: 0.7645 (ttpp)
REVERT: A  398 ASP cc_start: 0.8284 (OUTLIER) cc_final: 0.7507 (m-30)
REVERT: A  472 ARG cc_start: 0.8589 (mtm-85) cc_final: 0.8274 (ttp-170)
REVERT: A  549 GLU cc_start: 0.8463 (tm-30) cc_final: 0.8046 (tm-30)
REVERT: B  311 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8223 (tp)
REVERT: B  369 LYS cc_start: 0.5290 (tmtt) cc_final: 0.3975 (tttm)
REVERT: B  398 ASP cc_start: 0.8322 (OUTLIER) cc_final: 0.7818 (m-30)
REVERT: B  472 ARG cc_start: 0.8624 (mtm-85) cc_final: 0.8302 (ttp-170)
  outliers start: 22
  outliers final: 16
  residues processed: 102
  average time/residue: 0.0746
  time to fit residues: 10.2211
Evaluate side-chains
  99 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 79
  time to evaluate  : 0.192 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  312 SER
Chi-restraints excluded: chain A residue  335 PHE
Chi-restraints excluded: chain A residue  370 SER
Chi-restraints excluded: chain A residue  383 THR
Chi-restraints excluded: chain A residue  388 LYS
Chi-restraints excluded: chain A residue  398 ASP
Chi-restraints excluded: chain A residue  469 ASP
Chi-restraints excluded: chain A residue  513 LEU
Chi-restraints excluded: chain A residue  581 SER
Chi-restraints excluded: chain A residue  605 PHE
Chi-restraints excluded: chain B residue  301 LEU
Chi-restraints excluded: chain B residue  311 LEU
Chi-restraints excluded: chain B residue  312 SER
Chi-restraints excluded: chain B residue  335 PHE
Chi-restraints excluded: chain B residue  370 SER
Chi-restraints excluded: chain B residue  398 ASP
Chi-restraints excluded: chain B residue  513 LEU
Chi-restraints excluded: chain B residue  581 SER
Chi-restraints excluded: chain B residue  605 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 44 optimal weight:    0.0020
   chunk 50 optimal weight:    0.9990
   chunk 49 optimal weight:    0.8980
   chunk 9 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9980
   chunk 20 optimal weight:    2.9990
   chunk 70 optimal weight:    1.9990
   chunk 60 optimal weight:    0.9990
   chunk 15 optimal weight:    2.9990
   chunk 62 optimal weight:    0.0170
   chunk 27 optimal weight:    0.9990
   overall best weight:    0.5828

-------------------------------------------------------------------------------
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 = 0.4051 r_free = 0.4051 target = 0.170937 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.135719 restraints weight = 7374.774|
|-----------------------------------------------------------------------------|
r_work (start): 0.3652 rms_B_bonded: 2.36
r_work: 0.3512 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work (final): 0.3512
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7604
moved from start:          0.3339

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   6520  Z= 0.141
  Angle     :  0.563   7.341   8868  Z= 0.293
  Chirality :  0.039   0.171    968
  Planarity :  0.003   0.045   1070
  Dihedral  :  3.992  16.766    830
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 7.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.53 %
    Favored  : 94.47 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 22.75 %
    Favored  : 74.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    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 are not related in a simple way.
  whole:  0.98 (0.31), residues: 742
  helix:  1.63 (0.22), residues: 558
  sheet:  None (None), residues: 0
  loop : -2.53 (0.44), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 380 
 TYR   0.011   0.001   TYR B 483 
 PHE   0.019   0.001   PHE B 372 
 TRP   0.007   0.001   TRP A 528 
 HIS   0.008   0.001   HIS B 441 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 6518)
  covalent geometry    : angle       0.56335 ( 8864)
  SS BOND              : bond        0.00346 (    2)
  SS BOND              : angle       0.82211 (    4)
  hydrogen bonds       : bond        0.04211 (  414)
  hydrogen bonds       : angle       3.64257 ( 1236)

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

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

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 75
  time to evaluate  : 0.146 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  369 LYS cc_start: 0.5365 (tmtt) cc_final: 0.3949 (tttm)
REVERT: A  388 LYS cc_start: 0.7974 (OUTLIER) cc_final: 0.7694 (ttpm)
REVERT: A  398 ASP cc_start: 0.8308 (OUTLIER) cc_final: 0.7502 (m-30)
REVERT: A  472 ARG cc_start: 0.8613 (mtm-85) cc_final: 0.8307 (ttp-170)
REVERT: A  549 GLU cc_start: 0.8491 (tm-30) cc_final: 0.8079 (tm-30)
REVERT: A  590 ASP cc_start: 0.7544 (m-30) cc_final: 0.7145 (m-30)
REVERT: B  311 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8237 (tp)
REVERT: B  369 LYS cc_start: 0.5758 (tmtt) cc_final: 0.4397 (tttm)
REVERT: B  398 ASP cc_start: 0.8283 (OUTLIER) cc_final: 0.7844 (m-30)
REVERT: B  472 ARG cc_start: 0.8656 (mtm-85) cc_final: 0.8347 (ttp-170)
  outliers start: 21
  outliers final: 17
  residues processed: 90
  average time/residue: 0.0754
  time to fit residues: 8.8662
Evaluate side-chains
  94 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 73
  time to evaluate  : 0.146 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  312 SER
Chi-restraints excluded: chain A residue  335 PHE
Chi-restraints excluded: chain A residue  370 SER
Chi-restraints excluded: chain A residue  383 THR
Chi-restraints excluded: chain A residue  388 LYS
Chi-restraints excluded: chain A residue  398 ASP
Chi-restraints excluded: chain A residue  469 ASP
Chi-restraints excluded: chain A residue  513 LEU
Chi-restraints excluded: chain A residue  581 SER
Chi-restraints excluded: chain A residue  605 PHE
Chi-restraints excluded: chain B residue  301 LEU
Chi-restraints excluded: chain B residue  311 LEU
Chi-restraints excluded: chain B residue  312 SER
Chi-restraints excluded: chain B residue  335 PHE
Chi-restraints excluded: chain B residue  370 SER
Chi-restraints excluded: chain B residue  398 ASP
Chi-restraints excluded: chain B residue  513 LEU
Chi-restraints excluded: chain B residue  532 MET
Chi-restraints excluded: chain B residue  581 SER
Chi-restraints excluded: chain B residue  605 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 28 optimal weight:    1.9990
   chunk 55 optimal weight:    0.7980
   chunk 51 optimal weight:    0.7980
   chunk 56 optimal weight:    0.7980
   chunk 44 optimal weight:    0.0270
   chunk 40 optimal weight:    0.8980
   chunk 14 optimal weight:    0.9980
   chunk 30 optimal weight:    0.9990
   chunk 45 optimal weight:    0.5980
   chunk 64 optimal weight:    0.5980
   chunk 48 optimal weight:    0.9980
   overall best weight:    0.5638

-------------------------------------------------------------------------------
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 = 0.4052 r_free = 0.4052 target = 0.172974 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.136824 restraints weight = 7512.914|
|-----------------------------------------------------------------------------|
r_work (start): 0.3647 rms_B_bonded: 2.48
r_work: 0.3502 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.3502
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7495
moved from start:          0.3431

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   6520  Z= 0.139
  Angle     :  0.559   7.337   8868  Z= 0.289
  Chirality :  0.038   0.171    968
  Planarity :  0.003   0.045   1070
  Dihedral  :  3.937  16.333    830
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 7.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.39 %
    Favored  : 94.61 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 22.75 %
    Favored  : 74.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    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 are not related in a simple way.
  whole:  1.06 (0.31), residues: 742
  helix:  1.69 (0.22), residues: 556
  sheet:  None (None), residues: 0
  loop : -2.45 (0.44), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 380 
 TYR   0.010   0.001   TYR B 443 
 PHE   0.015   0.001   PHE A 609 
 TRP   0.007   0.001   TRP B 528 
 HIS   0.008   0.001   HIS B 441 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 6518)
  covalent geometry    : angle       0.55913 ( 8864)
  SS BOND              : bond        0.00355 (    2)
  SS BOND              : angle       0.78876 (    4)
  hydrogen bonds       : bond        0.04146 (  414)
  hydrogen bonds       : angle       3.62884 ( 1236)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1199.30 seconds
wall clock time: 21 minutes 16.01 seconds (1276.01 seconds total)