Starting phenix.real_space_refine
on Tue Mar  3 15:54:14 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7x8w_33059/03_2026/7x8w_33059_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7x8w_33059/03_2026/7x8w_33059.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7x8w_33059/03_2026/7x8w_33059.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7x8w_33059/03_2026/7x8w_33059.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7x8w_33059/03_2026/7x8w_33059_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7x8w_33059/03_2026/7x8w_33059_trim.cif"
  }
  resolution = 3.1
  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=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      18      5.16       5
     C    2186      2.51       5
     N     574      2.21       5
     O     682      1.98       5
     H    3214      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6674
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 3065
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 198, 3065
          Classifications: {'peptide': 198}
          Link IDs: {'PTRANS': 11, 'TRANS': 186}
    Chain: "H"
      Number of atoms: 1883
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 124, 1883
          Classifications: {'peptide': 124}
          Link IDs: {'PTRANS': 3, 'TRANS': 120}
    Chain: "L"
      Number of atoms: 1627
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 113, 1627
          Classifications: {'peptide': 113}
          Link IDs: {'PTRANS': 8, 'TRANS': 104}
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "C"
      Number of atoms: 71
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 71
          Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 2}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 18
          Unresolved non-hydrogen chiralities: 6
  Time building chain proxies: 1.39, per 1000 atoms: 0.21
  Number of scatterers: 6674
  At special positions: 0
  Unit cell: (94.506, 63.004, 99.48, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      18     16.00
     O     682      8.00
     N     574      7.00
     C    2186      6.00
     H    3214      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 336 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 379 " - pdb=" SG  CYS A 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 391 " - pdb=" SG  CYS A 525 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 480 " - pdb=" SG  CYS A 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  22 " - pdb=" SG  CYS L  90 " 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
  Links applied
    ALPHA1-3
      " BMA C   3 " - " MAN C   4 "
    ALPHA1-6
      " BMA C   3 " - " MAN C   5 "
    BETA1-4
      " NAG B   1 " - " NAG B   2 "
      " NAG C   1 " - " NAG C   2 "
      " NAG C   2 " - " BMA C   3 "
    BETA1-6
      " NAG C   1 " - " FUC C   6 "
       ~> Even though FUC is an alpha isomer, a beta linkage is required...
    NAG-ASN
      " NAG B   1 " - " ASN A 343 "
      " NAG C   1 " - " ASN H  59 "
  Time building additional restraints: 0.57
  Conformation dependent library (CDL) restraints added in 306.7 milliseconds
  

  858 Ramachandran restraints generated.
    429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  788

  Finding SS restraints...
    Secondary structure from input PDB file:
      8 helices and 9 sheets defined
      10.1% alpha, 33.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.13
  Creating SS restraints...
    Processing helix  chain 'A' and resid 338 through 343
    Processing helix  chain 'A' and resid 349 through 353
    Processing helix  chain 'A' and resid 365 through 370
    Processing helix  chain 'A' and resid 405 through 411
      removed outlier: 4.329A  pdb=" N   ARG A 408 " --> pdb=" O   ASP A 405 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   ALA A 411 " --> pdb=" O   ARG A 408 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 417 through 422
      removed outlier: 3.694A  pdb=" N   TYR A 421 " --> pdb=" O   LYS A 417 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 502 through 505
    Processing helix  chain 'H' and resid 87 through 91
      removed outlier: 4.059A  pdb=" N   THR H  91 " --> pdb=" O   SER H  88 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 81 through 85
      removed outlier: 4.044A  pdb=" N   GLU L  85 " --> pdb=" O   ALA L  82 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 355 through 358
    Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454
    Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 474
    Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 6
    Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 12
      removed outlier: 6.906A  pdb=" N   MET H  34 " --> pdb=" O   TRP H  50 " (cutoff:3.500A)
      removed outlier: 4.723A  pdb=" N   TRP H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 6.727A  pdb=" N   TRP H  36 " --> pdb=" O   MET H  48 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'H' and resid 10 through 12
      removed outlier: 3.871A  pdb=" N   TYR H 111 " --> pdb=" O   ARG H  98 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'L' and resid 9 through 11
      removed outlier: 6.697A  pdb=" N   ALA L  10 " --> pdb=" O   THR L 108 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   ALA L  86 " --> pdb=" O   VAL L 107 " (cutoff:3.500A)
      removed outlier: 6.637A  pdb=" N   TRP L  37 " --> pdb=" O   MET L  49 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'L' and resid 9 through 11
      removed outlier: 6.697A  pdb=" N   ALA L  10 " --> pdb=" O   THR L 108 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   ALA L  86 " --> pdb=" O   VAL L 107 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'L' and resid 18 through 23

    109 hydrogen bonds defined for protein.
    258 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: 1.37

  Time building geometry restraints manager: 0.79 seconds

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

  Histogram of bond lengths:
        0.84 -     1.04: 3214
        1.04 -     1.23: 82
        1.23 -     1.43: 1488
        1.43 -     1.62: 1954
        1.62 -     1.82: 24
  Bond restraints: 6762
  Sorted by residual:
  bond pdb=" C1  NAG B   2 "
       pdb=" O5  NAG B   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.447 -0.041 2.00e-02 2.50e+03 4.18e+00
  bond pdb=" C1  MAN C   5 "
       pdb=" C2  MAN C   5 "
    ideal  model  delta    sigma   weight residual
    1.526  1.562 -0.036 2.00e-02 2.50e+03 3.33e+00
  bond pdb=" N   GLN L   1 "
       pdb=" CA  GLN L   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 3.05e+00
  bond pdb=" N   GLN H   1 "
       pdb=" CA  GLN H   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.84e+00
  bond pdb=" N   GLN L   1 "
       pdb=" H   GLN L   1 "
    ideal  model  delta    sigma   weight residual
    0.860  0.890 -0.030 2.00e-02 2.50e+03 2.29e+00
  ... (remaining 6757 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.32: 11672
        1.32 -     2.64: 358
        2.64 -     3.96: 37
        3.96 -     5.28: 8
        5.28 -     6.60: 5
  Bond angle restraints: 12080
  Sorted by residual:
  angle pdb=" C3  BMA C   3 "
        pdb=" C2  BMA C   3 "
        pdb=" O2  BMA C   3 "
      ideal   model   delta    sigma   weight residual
     112.95  106.35    6.60 3.00e+00 1.11e-01 4.85e+00
  angle pdb=" C3  MAN C   5 "
        pdb=" C2  MAN C   5 "
        pdb=" O2  MAN C   5 "
      ideal   model   delta    sigma   weight residual
     111.77  105.37    6.40 3.00e+00 1.11e-01 4.55e+00
  angle pdb=" C3  MAN C   4 "
        pdb=" C2  MAN C   4 "
        pdb=" O2  MAN C   4 "
      ideal   model   delta    sigma   weight residual
     111.77  105.65    6.12 3.00e+00 1.11e-01 4.16e+00
  angle pdb=" C4  FUC C   6 "
        pdb=" C3  FUC C   6 "
        pdb=" O3  FUC C   6 "
      ideal   model   delta    sigma   weight residual
     113.24  107.38    5.86 3.00e+00 1.11e-01 3.82e+00
  angle pdb=" C1  BMA C   3 "
        pdb=" O5  BMA C   3 "
        pdb=" C5  BMA C   3 "
      ideal   model   delta    sigma   weight residual
     118.82  113.51    5.31 3.00e+00 1.11e-01 3.14e+00
  ... (remaining 12075 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.68: 3140
       21.68 -    43.35: 166
       43.35 -    65.03: 54
       65.03 -    86.71: 16
       86.71 -   108.39: 5
  Dihedral angle restraints: 3381
    sinusoidal: 1856
      harmonic: 1525
  Sorted by residual:
  dihedral pdb=" O4  BMA C   3 "
           pdb=" C4  BMA C   3 "
           pdb=" C5  BMA C   3 "
           pdb=" O5  BMA C   3 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -71.29 -179.68  108.39     1      3.00e+01 1.11e-03 1.40e+01
  dihedral pdb=" C3  BMA C   3 "
           pdb=" C4  BMA C   3 "
           pdb=" C5  BMA C   3 "
           pdb=" O5  BMA C   3 "
      ideal   model   delta sinusoidal    sigma   weight residual
      47.62  -58.69  106.31     1      3.00e+01 1.11e-03 1.37e+01
  dihedral pdb=" C6  BMA C   3 "
           pdb=" C4  BMA C   3 "
           pdb=" C5  BMA C   3 "
           pdb=" O4  BMA C   3 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -163.34  -60.53 -102.81     1      3.00e+01 1.11e-03 1.30e+01
  ... (remaining 3378 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.055: 459
       0.055 -    0.110: 68
       0.110 -    0.164: 12
       0.164 -    0.219: 0
       0.219 -    0.273: 2
  Chirality restraints: 541
  Sorted by residual:
  chirality pdb=" C5  BMA C   3 "
            pdb=" C4  BMA C   3 "
            pdb=" C6  BMA C   3 "
            pdb=" O5  BMA C   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.55    0.27 2.00e-01 2.50e+01 1.87e+00
  chirality pdb=" C1  NAG C   1 "
            pdb=" ND2 ASN H  59 "
            pdb=" C2  NAG C   1 "
            pdb=" O5  NAG C   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.17   -0.23 2.00e-01 2.50e+01 1.37e+00
  chirality pdb=" CA  ILE L  20 "
            pdb=" N   ILE L  20 "
            pdb=" C   ILE L  20 "
            pdb=" CB  ILE L  20 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.57e-01
  ... (remaining 538 not shown)

  Planarity restraints: 1023
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG H 106 "   -0.128 9.50e-02 1.11e+02   4.30e-02 2.23e+00
        pdb=" NE  ARG H 106 "    0.010 2.00e-02 2.50e+03
        pdb=" CZ  ARG H 106 "   -0.007 2.00e-02 2.50e+03
        pdb=" NH1 ARG H 106 "   -0.000 2.00e-02 2.50e+03
        pdb=" NH2 ARG H 106 "    0.000 2.00e-02 2.50e+03
        pdb="HH11 ARG H 106 "    0.004 2.00e-02 2.50e+03
        pdb="HH12 ARG H 106 "   -0.000 2.00e-02 2.50e+03
        pdb="HH21 ARG H 106 "   -0.000 2.00e-02 2.50e+03
        pdb="HH22 ARG H 106 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 520 "   -0.024 5.00e-02 4.00e+02   3.71e-02 2.20e+00
        pdb=" N   PRO A 521 "    0.064 5.00e-02 4.00e+02
        pdb=" CA  PRO A 521 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A 521 "   -0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A 400 "   -0.004 2.00e-02 2.50e+03   7.44e-03 5.54e-01
        pdb=" C   PHE A 400 "    0.013 2.00e-02 2.50e+03
        pdb=" O   PHE A 400 "   -0.005 2.00e-02 2.50e+03
        pdb=" N   VAL A 401 "   -0.004 2.00e-02 2.50e+03
  ... (remaining 1020 not shown)

  Histogram of nonbonded interaction distances:
        1.62 -     2.22: 616
        2.22 -     2.81: 13564
        2.81 -     3.41: 16199
        3.41 -     4.00: 23473
        4.00 -     4.60: 35091
  Nonbonded interactions: 88943
  Sorted by model distance:
  nonbonded pdb=" O   GLY H  31 "
            pdb=" H   SER H 103 "
     model   vdw
     1.624 2.450
  nonbonded pdb=" O   THR A 345 "
            pdb="HH22 ARG A 509 "
     model   vdw
     1.651 2.450
  nonbonded pdb=" OD1 ASN A 360 "
            pdb=" HG1 THR A 523 "
     model   vdw
     1.655 2.450
  nonbonded pdb="HH21 ARG A 454 "
            pdb=" O   ASP A 467 "
     model   vdw
     1.674 2.450
  nonbonded pdb="HH11 ARG A 457 "
            pdb=" O   SER A 459 "
     model   vdw
     1.704 2.450
  ... (remaining 88938 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: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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:             0.320
  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:             0.040
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.110
  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:1.230
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.900
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8411
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      :  0.004   0.041   3562  Z= 0.191
  Angle     :  0.624   8.805   4861  Z= 0.285
  Chirality :  0.045   0.273    541
  Planarity :  0.004   0.056    611
  Dihedral  : 16.079 108.387   1376
  Min Nonbonded Distance : 2.257

Molprobity Statistics.
  All-atom Clashscore : 4.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.83 %
    Favored  : 94.17 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.27 %
    Favored  : 99.73 %
  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 are not related in a simple way.
  whole: -1.35 (0.40), residues: 429
  helix: -3.61 (0.73), residues: 27
  sheet:  0.25 (0.44), residues: 146
  loop : -1.32 (0.38), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG H 106 
 TYR   0.008   0.001   TYR L  51 
 PHE   0.009   0.001   PHE A 347 
 TRP   0.007   0.001   TRP H  36 
 HIS   0.001   0.001   HIS L  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00406 ( 3548)
  covalent geometry    : angle       0.60092 ( 4825)
  SS BOND              : bond        0.00279 (    6)
  SS BOND              : angle       0.85455 (   12)
  hydrogen bonds       : bond        0.11363 (   99)
  hydrogen bonds       : angle       7.74662 (  258)
  link_ALPHA1-3        : bond        0.00197 (    1)
  link_ALPHA1-3        : angle       2.07110 (    3)
  link_ALPHA1-6        : bond        0.00703 (    1)
  link_ALPHA1-6        : angle       1.25012 (    3)
  link_BETA1-4         : bond        0.01299 (    3)
  link_BETA1-4         : angle       3.42673 (    9)
  link_BETA1-6         : bond        0.00616 (    1)
  link_BETA1-6         : angle       1.90046 (    3)
  link_NAG-ASN         : bond        0.00113 (    2)
  link_NAG-ASN         : angle       1.14619 (    6)

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

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

  858 Ramachandran restraints generated.
    429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  858 Ramachandran restraints generated.
    429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 69
  time to evaluate  : 0.149 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 69
  average time/residue: 0.2208
  time to fit residues: 17.5341
Evaluate side-chains
  58 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 0.172 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 24 optimal weight:    4.9990
   chunk 26 optimal weight:    2.9990
   chunk 2 optimal weight:    3.9990
   chunk 16 optimal weight:    3.9990
   chunk 32 optimal weight:    0.7980
   chunk 31 optimal weight:    0.2980
   chunk 25 optimal weight:    0.8980
   chunk 19 optimal weight:    5.9990
   chunk 30 optimal weight:    4.9990
   chunk 22 optimal weight:    5.9990
   chunk 37 optimal weight:    0.6980
   overall best weight:    1.1382

-------------------------------------------------------------------------------
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 = 0.3188 r_free = 0.3188 target = 0.086457 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2905 r_free = 0.2905 target = 0.069835 restraints weight = 18776.359|
|-----------------------------------------------------------------------------|
r_work (start): 0.2864 rms_B_bonded: 3.34
r_work: 0.2750 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work (final): 0.2750
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8221
moved from start:          0.0796

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3562  Z= 0.112
  Angle     :  0.537   5.736   4861  Z= 0.260
  Chirality :  0.042   0.162    541
  Planarity :  0.004   0.039    611
  Dihedral  :  9.840  66.592    637
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 3.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.59 %
    Favored  : 94.41 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  5.75 %
    Favored  : 93.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -1.32 (0.40), residues: 429
  helix: -3.88 (0.65), residues: 32
  sheet:  0.63 (0.47), residues: 131
  loop : -1.33 (0.37), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG H 106 
 TYR   0.009   0.001   TYR A 369 
 PHE   0.005   0.001   PHE L 101 
 TRP   0.005   0.001   TRP H  50 
 HIS   0.002   0.001   HIS L  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 ( 3548)
  covalent geometry    : angle       0.52042 ( 4825)
  SS BOND              : bond        0.00203 (    6)
  SS BOND              : angle       1.37014 (   12)
  hydrogen bonds       : bond        0.02555 (   99)
  hydrogen bonds       : angle       6.11643 (  258)
  link_ALPHA1-3        : bond        0.00775 (    1)
  link_ALPHA1-3        : angle       2.03919 (    3)
  link_ALPHA1-6        : bond        0.00772 (    1)
  link_ALPHA1-6        : angle       1.53486 (    3)
  link_BETA1-4         : bond        0.00649 (    3)
  link_BETA1-4         : angle       2.18235 (    9)
  link_BETA1-6         : bond        0.00343 (    1)
  link_BETA1-6         : angle       1.53925 (    3)
  link_NAG-ASN         : bond        0.00285 (    2)
  link_NAG-ASN         : angle       0.77284 (    6)

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

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

  858 Ramachandran restraints generated.
    429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  858 Ramachandran restraints generated.
    429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 60
  time to evaluate  : 0.134 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 1
  outliers final: 1
  residues processed: 60
  average time/residue: 0.2252
  time to fit residues: 15.5743
Evaluate side-chains
  59 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 58
  time to evaluate  : 0.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  398 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 6 optimal weight:    3.9990
   chunk 23 optimal weight:    3.9990
   chunk 26 optimal weight:    5.9990
   chunk 14 optimal weight:    0.0570
   chunk 17 optimal weight:    0.9980
   chunk 25 optimal weight:    3.9990
   chunk 32 optimal weight:    4.9990
   chunk 22 optimal weight:    2.9990
   chunk 36 optimal weight:    0.0970
   chunk 9 optimal weight:    2.9990
   chunk 5 optimal weight:    3.9990
   overall best weight:    1.4300

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

Flipped N/Q/H residues before XYZ refinement:
L  98 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.086110 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2885 r_free = 0.2885 target = 0.068920 restraints weight = 18708.634|
|-----------------------------------------------------------------------------|
r_work (start): 0.2864 rms_B_bonded: 3.43
r_work: 0.2746 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work (final): 0.2746
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8208
moved from start:          0.0927

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3562  Z= 0.120
  Angle     :  0.516   6.636   4861  Z= 0.249
  Chirality :  0.042   0.172    541
  Planarity :  0.004   0.051    611
  Dihedral  :  8.953  59.404    637
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 2.96
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  5.36 %
    Favored  : 94.41 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  8.22 %
    Favored  : 91.51 %
  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 are not related in a simple way.
  whole: -1.36 (0.40), residues: 429
  helix: -3.78 (0.70), residues: 32
  sheet:  0.27 (0.45), residues: 145
  loop : -1.24 (0.38), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG H 106 
 TYR   0.009   0.001   TYR A 369 
 PHE   0.005   0.001   PHE L 101 
 TRP   0.006   0.001   TRP H  50 
 HIS   0.001   0.001   HIS L  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 3548)
  covalent geometry    : angle       0.50299 ( 4825)
  SS BOND              : bond        0.00337 (    6)
  SS BOND              : angle       1.19663 (   12)
  hydrogen bonds       : bond        0.02503 (   99)
  hydrogen bonds       : angle       5.82855 (  258)
  link_ALPHA1-3        : bond        0.01051 (    1)
  link_ALPHA1-3        : angle       1.27612 (    3)
  link_ALPHA1-6        : bond        0.00594 (    1)
  link_ALPHA1-6        : angle       1.79731 (    3)
  link_BETA1-4         : bond        0.00640 (    3)
  link_BETA1-4         : angle       1.77689 (    9)
  link_BETA1-6         : bond        0.00499 (    1)
  link_BETA1-6         : angle       1.58300 (    3)
  link_NAG-ASN         : bond        0.00232 (    2)
  link_NAG-ASN         : angle       0.85826 (    6)

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

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

  858 Ramachandran restraints generated.
    429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  858 Ramachandran restraints generated.
    429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 60
  time to evaluate  : 0.177 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   73 ASP cc_start: 0.7357 (t0) cc_final: 0.7094 (t0)
  outliers start: 1
  outliers final: 1
  residues processed: 60
  average time/residue: 0.2342
  time to fit residues: 16.1748
Evaluate side-chains
  60 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 59
  time to evaluate  : 0.193 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  398 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 38 optimal weight:    4.9990
   chunk 34 optimal weight:    4.9990
   chunk 9 optimal weight:    4.9990
   chunk 10 optimal weight:    2.9990
   chunk 22 optimal weight:    5.9990
   chunk 21 optimal weight:    0.9980
   chunk 1 optimal weight:    2.9990
   chunk 31 optimal weight:    3.9990
   chunk 30 optimal weight:    3.9990
   chunk 12 optimal weight:    3.9990
   chunk 4 optimal weight:    0.8980
   overall best weight:    2.3786

-------------------------------------------------------------------------------
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 = 0.3167 r_free = 0.3167 target = 0.085398 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2874 r_free = 0.2874 target = 0.068342 restraints weight = 18811.567|
|-----------------------------------------------------------------------------|
r_work (start): 0.2836 rms_B_bonded: 3.36
r_work: 0.2720 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work (final): 0.2720
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8246
moved from start:          0.1047

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   3562  Z= 0.171
  Angle     :  0.529   6.793   4861  Z= 0.256
  Chirality :  0.042   0.211    541
  Planarity :  0.004   0.051    611
  Dihedral  :  8.040  58.035    637
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 2.96
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  5.13 %
    Favored  : 94.64 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  9.04 %
    Favored  : 90.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.50 (0.41), residues: 429
  helix: -3.80 (0.70), residues: 32
  sheet:  0.02 (0.43), residues: 155
  loop : -1.29 (0.39), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG H 106 
 TYR   0.008   0.001   TYR A 369 
 PHE   0.007   0.001   PHE A 347 
 TRP   0.006   0.001   TRP A 436 
 HIS   0.001   0.001   HIS L  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00393 ( 3548)
  covalent geometry    : angle       0.51751 ( 4825)
  SS BOND              : bond        0.00306 (    6)
  SS BOND              : angle       1.01591 (   12)
  hydrogen bonds       : bond        0.02527 (   99)
  hydrogen bonds       : angle       5.72507 (  258)
  link_ALPHA1-3        : bond        0.01045 (    1)
  link_ALPHA1-3        : angle       1.17998 (    3)
  link_ALPHA1-6        : bond        0.00445 (    1)
  link_ALPHA1-6        : angle       1.98606 (    3)
  link_BETA1-4         : bond        0.00588 (    3)
  link_BETA1-4         : angle       1.65788 (    9)
  link_BETA1-6         : bond        0.00361 (    1)
  link_BETA1-6         : angle       1.83486 (    3)
  link_NAG-ASN         : bond        0.00245 (    2)
  link_NAG-ASN         : angle       0.89469 (    6)

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

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

  858 Ramachandran restraints generated.
    429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  858 Ramachandran restraints generated.
    429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 60
  time to evaluate  : 0.180 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   73 ASP cc_start: 0.7437 (t0) cc_final: 0.7115 (t0)
  outliers start: 1
  outliers final: 1
  residues processed: 60
  average time/residue: 0.2405
  time to fit residues: 16.5015
Evaluate side-chains
  59 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 58
  time to evaluate  : 0.132 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  398 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 32 optimal weight:    7.9990
   chunk 12 optimal weight:    4.9990
   chunk 31 optimal weight:    0.6980
   chunk 25 optimal weight:    0.9980
   chunk 13 optimal weight:    0.6980
   chunk 10 optimal weight:    4.9990
   chunk 21 optimal weight:    5.9990
   chunk 38 optimal weight:    0.5980
   chunk 35 optimal weight:    5.9990
   chunk 36 optimal weight:    0.0010
   chunk 19 optimal weight:    0.8980
   overall best weight:    0.5786

-------------------------------------------------------------------------------
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 = 0.3186 r_free = 0.3186 target = 0.086789 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2899 r_free = 0.2899 target = 0.069704 restraints weight = 18736.779|
|-----------------------------------------------------------------------------|
r_work (start): 0.2876 rms_B_bonded: 3.41
r_work: 0.2759 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.2759
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8183
moved from start:          0.1133

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   3562  Z= 0.085
  Angle     :  0.508   6.784   4861  Z= 0.246
  Chirality :  0.042   0.209    541
  Planarity :  0.004   0.056    611
  Dihedral  :  7.389  57.788    637
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 2.81
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  3.73 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  0.55 %
    Allowed  :  9.59 %
    Favored  : 89.86 %
  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 are not related in a simple way.
  whole: -1.29 (0.41), residues: 429
  helix: -3.79 (0.69), residues: 32
  sheet:  0.64 (0.47), residues: 131
  loop : -1.31 (0.38), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG H 106 
 TYR   0.009   0.001   TYR A 369 
 PHE   0.005   0.000   PHE L 101 
 TRP   0.006   0.001   TRP A 436 
 HIS   0.001   0.001   HIS L  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00201 ( 3548)
  covalent geometry    : angle       0.49753 ( 4825)
  SS BOND              : bond        0.00352 (    6)
  SS BOND              : angle       0.85978 (   12)
  hydrogen bonds       : bond        0.02292 (   99)
  hydrogen bonds       : angle       5.56799 (  258)
  link_ALPHA1-3        : bond        0.00930 (    1)
  link_ALPHA1-3        : angle       1.15447 (    3)
  link_ALPHA1-6        : bond        0.00474 (    1)
  link_ALPHA1-6        : angle       2.05119 (    3)
  link_BETA1-4         : bond        0.00652 (    3)
  link_BETA1-4         : angle       1.66659 (    9)
  link_BETA1-6         : bond        0.00582 (    1)
  link_BETA1-6         : angle       1.36249 (    3)
  link_NAG-ASN         : bond        0.00286 (    2)
  link_NAG-ASN         : angle       0.73038 (    6)

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

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

  858 Ramachandran restraints generated.
    429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  858 Ramachandran restraints generated.
    429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 62
  time to evaluate  : 0.180 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   60 TYR cc_start: 0.9061 (OUTLIER) cc_final: 0.8093 (m-10)
  outliers start: 2
  outliers final: 1
  residues processed: 62
  average time/residue: 0.2198
  time to fit residues: 15.6859
Evaluate side-chains
  59 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 57
  time to evaluate  : 0.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  398 ASP
Chi-restraints excluded: chain H residue   60 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 18 optimal weight:    2.9990
   chunk 26 optimal weight:    5.9990
   chunk 30 optimal weight:    6.9990
   chunk 34 optimal weight:    3.9990
   chunk 35 optimal weight:    2.9990
   chunk 22 optimal weight:    5.9990
   chunk 27 optimal weight:    0.8980
   chunk 8 optimal weight:    1.9990
   chunk 38 optimal weight:    5.9990
   chunk 5 optimal weight:    3.9990
   chunk 24 optimal weight:    0.6980
   overall best weight:    1.9186

-------------------------------------------------------------------------------
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 = 0.3167 r_free = 0.3167 target = 0.085693 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2872 r_free = 0.2872 target = 0.068348 restraints weight = 18940.832|
|-----------------------------------------------------------------------------|
r_work (start): 0.2852 rms_B_bonded: 3.45
r_work: 0.2736 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.2736
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8224
moved from start:          0.1300

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3562  Z= 0.142
  Angle     :  0.515   6.806   4861  Z= 0.249
  Chirality :  0.042   0.204    541
  Planarity :  0.004   0.057    611
  Dihedral  :  7.045  56.991    637
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 3.40
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  5.13 %
    Favored  : 94.64 %
  Rotamer:
    Outliers :  0.55 %
    Allowed  : 11.51 %
    Favored  : 87.95 %
  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 are not related in a simple way.
  whole: -1.39 (0.41), residues: 429
  helix: -3.78 (0.70), residues: 32
  sheet:  0.17 (0.44), residues: 152
  loop : -1.24 (0.40), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG H 106 
 TYR   0.009   0.001   TYR A 369 
 PHE   0.006   0.001   PHE A 347 
 TRP   0.005   0.001   TRP A 436 
 HIS   0.001   0.001   HIS L  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 3548)
  covalent geometry    : angle       0.50426 ( 4825)
  SS BOND              : bond        0.00441 (    6)
  SS BOND              : angle       0.85287 (   12)
  hydrogen bonds       : bond        0.02429 (   99)
  hydrogen bonds       : angle       5.54182 (  258)
  link_ALPHA1-3        : bond        0.01055 (    1)
  link_ALPHA1-3        : angle       1.14027 (    3)
  link_ALPHA1-6        : bond        0.00311 (    1)
  link_ALPHA1-6        : angle       2.05232 (    3)
  link_BETA1-4         : bond        0.00543 (    3)
  link_BETA1-4         : angle       1.56737 (    9)
  link_BETA1-6         : bond        0.00399 (    1)
  link_BETA1-6         : angle       1.68290 (    3)
  link_NAG-ASN         : bond        0.00203 (    2)
  link_NAG-ASN         : angle       0.84040 (    6)

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

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

  858 Ramachandran restraints generated.
    429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  858 Ramachandran restraints generated.
    429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 59
  time to evaluate  : 0.281 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   60 TYR cc_start: 0.9098 (OUTLIER) cc_final: 0.8156 (m-10)
REVERT: H   73 ASP cc_start: 0.7345 (t0) cc_final: 0.7090 (t0)
  outliers start: 2
  outliers final: 1
  residues processed: 59
  average time/residue: 0.2262
  time to fit residues: 15.4138
Evaluate side-chains
  61 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 59
  time to evaluate  : 0.171 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  398 ASP
Chi-restraints excluded: chain H residue   60 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 27 optimal weight:    4.9990
   chunk 34 optimal weight:    4.9990
   chunk 23 optimal weight:    0.9980
   chunk 4 optimal weight:    4.9990
   chunk 19 optimal weight:    4.9990
   chunk 12 optimal weight:    5.9990
   chunk 5 optimal weight:    2.9990
   chunk 32 optimal weight:    0.0070
   chunk 29 optimal weight:    2.9990
   chunk 20 optimal weight:    4.9990
   chunk 18 optimal weight:    0.9990
   overall best weight:    1.6004

-------------------------------------------------------------------------------
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 = 0.3169 r_free = 0.3169 target = 0.085848 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2876 r_free = 0.2876 target = 0.068563 restraints weight = 18748.464|
|-----------------------------------------------------------------------------|
r_work (start): 0.2856 rms_B_bonded: 3.43
r_work: 0.2740 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.2740
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8224
moved from start:          0.1347

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3562  Z= 0.121
  Angle     :  0.505   6.491   4861  Z= 0.247
  Chirality :  0.042   0.186    541
  Planarity :  0.004   0.062    611
  Dihedral  :  6.759  56.425    637
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 3.70
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  4.20 %
    Favored  : 95.57 %
  Rotamer:
    Outliers :  0.55 %
    Allowed  : 11.78 %
    Favored  : 87.67 %
  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 are not related in a simple way.
  whole: -1.36 (0.41), residues: 429
  helix: -3.77 (0.70), residues: 32
  sheet:  0.17 (0.44), residues: 152
  loop : -1.20 (0.40), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG H 106 
 TYR   0.009   0.001   TYR A 369 
 PHE   0.005   0.001   PHE A 347 
 TRP   0.006   0.001   TRP A 436 
 HIS   0.001   0.001   HIS L  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 3548)
  covalent geometry    : angle       0.49508 ( 4825)
  SS BOND              : bond        0.00272 (    6)
  SS BOND              : angle       0.81532 (   12)
  hydrogen bonds       : bond        0.02361 (   99)
  hydrogen bonds       : angle       5.49994 (  258)
  link_ALPHA1-3        : bond        0.01053 (    1)
  link_ALPHA1-3        : angle       1.07704 (    3)
  link_ALPHA1-6        : bond        0.00312 (    1)
  link_ALPHA1-6        : angle       1.98156 (    3)
  link_BETA1-4         : bond        0.00526 (    3)
  link_BETA1-4         : angle       1.53398 (    9)
  link_BETA1-6         : bond        0.00468 (    1)
  link_BETA1-6         : angle       1.55960 (    3)
  link_NAG-ASN         : bond        0.00244 (    2)
  link_NAG-ASN         : angle       0.82313 (    6)

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

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

  858 Ramachandran restraints generated.
    429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  858 Ramachandran restraints generated.
    429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 60
  time to evaluate  : 0.170 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   60 TYR cc_start: 0.9097 (OUTLIER) cc_final: 0.8156 (m-10)
REVERT: H   73 ASP cc_start: 0.7355 (t0) cc_final: 0.7096 (t0)
  outliers start: 2
  outliers final: 1
  residues processed: 60
  average time/residue: 0.2293
  time to fit residues: 15.7107
Evaluate side-chains
  61 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 59
  time to evaluate  : 0.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  398 ASP
Chi-restraints excluded: chain H residue   60 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 20 optimal weight:    0.8980
   chunk 7 optimal weight:    1.9990
   chunk 22 optimal weight:    5.9990
   chunk 33 optimal weight:    4.9990
   chunk 29 optimal weight:    3.9990
   chunk 21 optimal weight:    1.9990
   chunk 32 optimal weight:    6.9990
   chunk 19 optimal weight:    0.9990
   chunk 24 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9980
   chunk 10 optimal weight:    2.9990
   overall best weight:    1.3786

-------------------------------------------------------------------------------
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 = 0.3179 r_free = 0.3179 target = 0.086425 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2884 r_free = 0.2884 target = 0.069030 restraints weight = 18691.043|
|-----------------------------------------------------------------------------|
r_work (start): 0.2863 rms_B_bonded: 3.44
r_work: 0.2747 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.2747
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8222
moved from start:          0.1424

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   3562  Z= 0.114
  Angle     :  0.506   5.965   4861  Z= 0.246
  Chirality :  0.041   0.169    541
  Planarity :  0.004   0.063    611
  Dihedral  :  6.543  56.066    637
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 3.99
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  4.66 %
    Favored  : 95.10 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  : 12.33 %
    Favored  : 86.85 %
  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 are not related in a simple way.
  whole: -1.33 (0.41), residues: 429
  helix: -3.75 (0.71), residues: 32
  sheet:  0.17 (0.44), residues: 152
  loop : -1.17 (0.40), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG H  72 
 TYR   0.009   0.001   TYR A 369 
 PHE   0.005   0.001   PHE A 400 
 TRP   0.006   0.001   TRP A 436 
 HIS   0.001   0.001   HIS L  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 3548)
  covalent geometry    : angle       0.49680 ( 4825)
  SS BOND              : bond        0.00418 (    6)
  SS BOND              : angle       0.80030 (   12)
  hydrogen bonds       : bond        0.02357 (   99)
  hydrogen bonds       : angle       5.47188 (  258)
  link_ALPHA1-3        : bond        0.01070 (    1)
  link_ALPHA1-3        : angle       1.06240 (    3)
  link_ALPHA1-6        : bond        0.00290 (    1)
  link_ALPHA1-6        : angle       1.91851 (    3)
  link_BETA1-4         : bond        0.00516 (    3)
  link_BETA1-4         : angle       1.53302 (    9)
  link_BETA1-6         : bond        0.00466 (    1)
  link_BETA1-6         : angle       1.50322 (    3)
  link_NAG-ASN         : bond        0.00220 (    2)
  link_NAG-ASN         : angle       0.82304 (    6)

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

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

  858 Ramachandran restraints generated.
    429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  858 Ramachandran restraints generated.
    429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 59
  time to evaluate  : 0.181 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   60 TYR cc_start: 0.9109 (OUTLIER) cc_final: 0.8292 (m-80)
REVERT: H   73 ASP cc_start: 0.7370 (t0) cc_final: 0.7094 (t0)
  outliers start: 3
  outliers final: 1
  residues processed: 60
  average time/residue: 0.2081
  time to fit residues: 14.4559
Evaluate side-chains
  61 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 59
  time to evaluate  : 0.178 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  398 ASP
Chi-restraints excluded: chain H residue   60 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 13 optimal weight:    4.9990
   chunk 22 optimal weight:    5.9990
   chunk 16 optimal weight:    0.8980
   chunk 4 optimal weight:    4.9990
   chunk 25 optimal weight:    3.9990
   chunk 21 optimal weight:    0.8980
   chunk 12 optimal weight:    0.9980
   chunk 7 optimal weight:    0.8980
   chunk 15 optimal weight:    0.3980
   chunk 36 optimal weight:    0.9980
   chunk 14 optimal weight:    0.8980
   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 = 0.3198 r_free = 0.3198 target = 0.087420 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2908 r_free = 0.2908 target = 0.070262 restraints weight = 18719.193|
|-----------------------------------------------------------------------------|
r_work (start): 0.2878 rms_B_bonded: 3.43
r_work: 0.2761 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.2761
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8207
moved from start:          0.1468

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   3562  Z= 0.092
  Angle     :  0.501   5.768   4861  Z= 0.245
  Chirality :  0.041   0.156    541
  Planarity :  0.004   0.066    611
  Dihedral  :  6.372  55.931    637
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 3.70
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  3.96 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  0.55 %
    Allowed  : 12.60 %
    Favored  : 86.85 %
  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 are not related in a simple way.
  whole: -1.24 (0.41), residues: 429
  helix: -3.75 (0.70), residues: 32
  sheet:  0.41 (0.46), residues: 142
  loop : -1.17 (0.39), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG H  72 
 TYR   0.009   0.001   TYR A 369 
 PHE   0.005   0.001   PHE A 338 
 TRP   0.006   0.001   TRP A 436 
 HIS   0.001   0.000   HIS L  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00215 ( 3548)
  covalent geometry    : angle       0.49191 ( 4825)
  SS BOND              : bond        0.00426 (    6)
  SS BOND              : angle       0.79620 (   12)
  hydrogen bonds       : bond        0.02319 (   99)
  hydrogen bonds       : angle       5.42920 (  258)
  link_ALPHA1-3        : bond        0.01066 (    1)
  link_ALPHA1-3        : angle       1.06146 (    3)
  link_ALPHA1-6        : bond        0.00299 (    1)
  link_ALPHA1-6        : angle       1.85451 (    3)
  link_BETA1-4         : bond        0.00512 (    3)
  link_BETA1-4         : angle       1.53482 (    9)
  link_BETA1-6         : bond        0.00531 (    1)
  link_BETA1-6         : angle       1.33566 (    3)
  link_NAG-ASN         : bond        0.00248 (    2)
  link_NAG-ASN         : angle       0.76844 (    6)

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

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

  858 Ramachandran restraints generated.
    429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  858 Ramachandran restraints generated.
    429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 61
  time to evaluate  : 0.189 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   60 TYR cc_start: 0.9101 (OUTLIER) cc_final: 0.8301 (m-80)
REVERT: H   73 ASP cc_start: 0.7338 (t0) cc_final: 0.7089 (t0)
  outliers start: 2
  outliers final: 1
  residues processed: 61
  average time/residue: 0.2479
  time to fit residues: 17.2141
Evaluate side-chains
  61 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 59
  time to evaluate  : 0.181 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  392 PHE
Chi-restraints excluded: chain H residue   60 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 29 optimal weight:    3.9990
   chunk 13 optimal weight:    4.9990
   chunk 23 optimal weight:    2.9990
   chunk 21 optimal weight:    4.9990
   chunk 33 optimal weight:    3.9990
   chunk 24 optimal weight:    0.5980
   chunk 27 optimal weight:    5.9990
   chunk 11 optimal weight:    4.9990
   chunk 4 optimal weight:    4.9990
   chunk 15 optimal weight:    0.8980
   chunk 40 optimal weight:    0.8980
   overall best weight:    1.8784

-------------------------------------------------------------------------------
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 = 0.3173 r_free = 0.3173 target = 0.086071 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2877 r_free = 0.2877 target = 0.068606 restraints weight = 18789.647|
|-----------------------------------------------------------------------------|
r_work (start): 0.2858 rms_B_bonded: 3.45
r_work: 0.2742 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.2742
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8227
moved from start:          0.1527

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3562  Z= 0.141
  Angle     :  0.511   5.412   4861  Z= 0.250
  Chirality :  0.041   0.161    541
  Planarity :  0.005   0.067    611
  Dihedral  :  6.343  55.515    637
  Min Nonbonded Distance : 2.395

Molprobity Statistics.
  All-atom Clashscore : 4.14
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  4.66 %
    Favored  : 95.10 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  : 12.33 %
    Favored  : 86.85 %
  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 are not related in a simple way.
  whole: -1.37 (0.41), residues: 429
  helix: -3.81 (0.70), residues: 32
  sheet:  0.16 (0.44), residues: 152
  loop : -1.20 (0.40), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG H  72 
 TYR   0.009   0.001   TYR A 369 
 PHE   0.007   0.001   PHE A 347 
 TRP   0.005   0.001   TRP A 436 
 HIS   0.001   0.001   HIS L  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 3548)
  covalent geometry    : angle       0.50145 ( 4825)
  SS BOND              : bond        0.00380 (    6)
  SS BOND              : angle       0.84418 (   12)
  hydrogen bonds       : bond        0.02404 (   99)
  hydrogen bonds       : angle       5.44103 (  258)
  link_ALPHA1-3        : bond        0.01094 (    1)
  link_ALPHA1-3        : angle       1.05354 (    3)
  link_ALPHA1-6        : bond        0.00296 (    1)
  link_ALPHA1-6        : angle       1.84639 (    3)
  link_BETA1-4         : bond        0.00492 (    3)
  link_BETA1-4         : angle       1.48652 (    9)
  link_BETA1-6         : bond        0.00378 (    1)
  link_BETA1-6         : angle       1.60882 (    3)
  link_NAG-ASN         : bond        0.00190 (    2)
  link_NAG-ASN         : angle       0.84335 (    6)

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

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

  858 Ramachandran restraints generated.
    429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2.
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Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  858 Ramachandran restraints generated.
    429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2.
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Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 59
  time to evaluate  : 0.173 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   60 TYR cc_start: 0.9124 (OUTLIER) cc_final: 0.8316 (m-80)
REVERT: H   73 ASP cc_start: 0.7400 (t0) cc_final: 0.7106 (t0)
  outliers start: 3
  outliers final: 2
  residues processed: 60
  average time/residue: 0.2228
  time to fit residues: 15.3719
Evaluate side-chains
  62 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 59
  time to evaluate  : 0.170 
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Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  392 PHE
Chi-restraints excluded: chain A residue  525 CYS
Chi-restraints excluded: chain H residue   60 TYR
Rotamers are restrained with sigma=1.00
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XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 41 optimal weight:    4.9990
   chunk 13 optimal weight:    0.4980
   chunk 30 optimal weight:    3.9990
   chunk 18 optimal weight:    0.9990
   chunk 20 optimal weight:    3.9990
   chunk 5 optimal weight:    0.0670
   chunk 37 optimal weight:    0.6980
   chunk 1 optimal weight:    0.7980
   chunk 4 optimal weight:    2.9990
   chunk 31 optimal weight:    2.9990
   chunk 34 optimal weight:    5.9990
   overall best weight:    0.6120

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

No N/Q/H corrections needed this macrocycle
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ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.087399 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2907 r_free = 0.2907 target = 0.070129 restraints weight = 18603.602|
|-----------------------------------------------------------------------------|
r_work (start): 0.2886 rms_B_bonded: 3.45
r_work: 0.2770 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work (final): 0.2770
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8201
moved from start:          0.1579

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   3562  Z= 0.087
  Angle     :  0.494   4.828   4861  Z= 0.244
  Chirality :  0.041   0.152    541
  Planarity :  0.005   0.067    611
  Dihedral  :  6.163  55.528    637
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 3.70
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  3.50 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  : 12.33 %
    Favored  : 86.85 %
  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 are not related in a simple way.
  whole: -1.22 (0.41), residues: 429
  helix: -3.78 (0.70), residues: 32
  sheet:  0.44 (0.46), residues: 142
  loop : -1.16 (0.39), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG H  72 
 TYR   0.010   0.001   TYR A 369 
 PHE   0.005   0.001   PHE A 400 
 TRP   0.007   0.001   TRP A 436 
 HIS   0.001   0.000   HIS L  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00203 ( 3548)
  covalent geometry    : angle       0.48551 ( 4825)
  SS BOND              : bond        0.00384 (    6)
  SS BOND              : angle       0.79014 (   12)
  hydrogen bonds       : bond        0.02272 (   99)
  hydrogen bonds       : angle       5.35915 (  258)
  link_ALPHA1-3        : bond        0.01092 (    1)
  link_ALPHA1-3        : angle       1.08660 (    3)
  link_ALPHA1-6        : bond        0.00313 (    1)
  link_ALPHA1-6        : angle       1.74913 (    3)
  link_BETA1-4         : bond        0.00506 (    3)
  link_BETA1-4         : angle       1.53505 (    9)
  link_BETA1-6         : bond        0.00528 (    1)
  link_BETA1-6         : angle       1.26813 (    3)
  link_NAG-ASN         : bond        0.00276 (    2)
  link_NAG-ASN         : angle       0.75312 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2000.10 seconds
wall clock time: 34 minutes 32.61 seconds (2072.61 seconds total)