Starting phenix.real_space_refine
on Tue Mar  3 11:27:35 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wth_32786/03_2026/7wth_32786.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wth_32786/03_2026/7wth_32786.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wth_32786/03_2026/7wth_32786.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wth_32786/03_2026/7wth_32786.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wth_32786/03_2026/7wth_32786.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wth_32786/03_2026/7wth_32786.map"
  }
  resolution = 4.3
  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=   0.001
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      16      5.16       5
     C    2084      2.51       5
     N     543      2.21       5
     O     614      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 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: 3257
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "E"
      Number of atoms: 1573
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 197, 1573
          Classifications: {'peptide': 197}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 12, 'TRANS': 184}
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 10
          Planarities with less than four sites: {'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "L"
      Number of atoms: 772
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 772
          Classifications: {'peptide': 106}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 6, 'TRANS': 99}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 7
          Planarities with less than four sites: {'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "H"
      Number of atoms: 912
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 118, 912
          Classifications: {'peptide': 118}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 6, 'TRANS': 111}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
  Time building chain proxies: 0.78, per 1000 atoms: 0.24
  Number of scatterers: 3257
  At special positions: 0
  Unit cell: (77.04, 77.04, 94.16, 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      16     16.00
     O     614      8.00
     N     543      7.00
     C    2084      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS E 336 " - pdb=" SG  CYS E 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 379 " - pdb=" SG  CYS E 432 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E 391 " - pdb=" SG  CYS E 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 480 " - pdb=" SG  CYS E 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  22 " - pdb=" SG  CYS L  90 " distance=2.04
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  97 " 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: 0.18
  Conformation dependent library (CDL) restraints added in 80.6 milliseconds
  

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  774

  Finding SS restraints...
    Secondary structure from input PDB file:
      6 helices and 8 sheets defined
      7.8% alpha, 21.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.10
  Creating SS restraints...
    Processing helix  chain 'E' and resid 337 through 342
      removed outlier: 3.931A  pdb=" N   VAL E 341 " --> pdb=" O   PRO E 337 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 366 through 371
      removed outlier: 3.672A  pdb=" N   TYR E 369 " --> pdb=" O   SER E 366 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 386 through 390
      removed outlier: 3.966A  pdb=" N   LEU E 390 " --> pdb=" O   LEU E 387 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 403 through 410
      removed outlier: 4.019A  pdb=" N   VAL E 407 " --> pdb=" O   GLY E 404 " (cutoff:3.500A)
      removed outlier: 4.105A  pdb=" N   ARG E 408 " --> pdb=" O   ASP E 405 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 65 through 67
      No H-bonds generated for 'chain 'H' and resid 65 through 67'
    Processing helix  chain 'H' and resid 88 through 92
      removed outlier: 3.593A  pdb=" N   THR H  92 " --> pdb=" O   PRO H  89 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'E' and resid 356 through 358
      removed outlier: 3.706A  pdb=" N   ALA E 397 " --> pdb=" O   LYS E 356 " (cutoff:3.500A)
      removed outlier: 3.988A  pdb=" N   VAL E 395 " --> pdb=" O   ILE E 358 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'E' and resid 361 through 362
      removed outlier: 7.179A  pdb=" N   CYS E 361 " --> pdb=" O   CYS E 525 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'E' and resid 374 through 376
      removed outlier: 3.772A  pdb=" N   THR E 376 " --> pdb=" O   ALA E 435 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'E' and resid 452 through 454
      removed outlier: 3.621A  pdb=" N   ARG E 493 " --> pdb=" O   TYR E 453 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'L' and resid 19 through 23
      removed outlier: 3.667A  pdb=" N   VAL L  20 " --> pdb=" O   LEU L  75 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'L' and resid 44 through 50
      removed outlier: 5.328A  pdb=" N   ALA L  45 " --> pdb=" O   HIS L  41 " (cutoff:3.500A)
      removed outlier: 5.448A  pdb=" N   HIS L  41 " --> pdb=" O   ALA L  45 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   LYS L  47 " --> pdb=" O   GLN L  39 " (cutoff:3.500A)
      removed outlier: 6.840A  pdb=" N   TRP L  37 " --> pdb=" O   LEU L  49 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   ASP L  87 " --> pdb=" O   HIS L  40 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'H' and resid 3 through 7
      removed outlier: 4.404A  pdb=" N   THR H   3 " --> pdb=" O   SER H  25 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'H' and resid 11 through 12
      removed outlier: 3.661A  pdb=" N   THR H 113 " --> pdb=" O   TYR H  95 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   THR H  94 " --> pdb=" O   GLN H  41 " (cutoff:3.500A)
      removed outlier: 3.950A  pdb=" N   ALA H  51 " --> pdb=" O   TRP H  38 " (cutoff:3.500A)
      removed outlier: 7.017A  pdb=" N   ARG H  40 " --> pdb=" O   TRP H  49 " (cutoff:3.500A)
      removed outlier: 6.119A  pdb=" N   TRP H  49 " --> pdb=" O   ARG H  40 " (cutoff:3.500A)

    61 hydrogen bonds defined for protein.
    141 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: 0.35

  Time building geometry restraints manager: 0.24 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 1027
        1.35 -     1.47: 867
        1.47 -     1.58: 1432
        1.58 -     1.70: 0
        1.70 -     1.82: 19
  Bond restraints: 3345
  Sorted by residual:
  bond pdb=" N   ILE E 418 "
       pdb=" CA  ILE E 418 "
    ideal  model  delta    sigma   weight residual
    1.462  1.498 -0.036 1.17e-02 7.31e+03 9.28e+00
  bond pdb=" N   GLY E 447 "
       pdb=" CA  GLY E 447 "
    ideal  model  delta    sigma   weight residual
    1.447  1.478 -0.032 1.09e-02 8.42e+03 8.54e+00
  bond pdb=" CA  SER E 438 "
       pdb=" CB  SER E 438 "
    ideal  model  delta    sigma   weight residual
    1.528  1.490  0.038 1.34e-02 5.57e+03 8.07e+00
  bond pdb=" N   GLY E 416 "
       pdb=" CA  GLY E 416 "
    ideal  model  delta    sigma   weight residual
    1.447  1.475 -0.028 1.03e-02 9.43e+03 7.45e+00
  bond pdb=" N   ASN E 437 "
       pdb=" CA  ASN E 437 "
    ideal  model  delta    sigma   weight residual
    1.456  1.488 -0.032 1.22e-02 6.72e+03 6.75e+00
  ... (remaining 3340 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.74: 4362
        1.74 -     3.48: 165
        3.48 -     5.23: 25
        5.23 -     6.97: 4
        6.97 -     8.71: 3
  Bond angle restraints: 4559
  Sorted by residual:
  angle pdb=" CA  GLY E 447 "
        pdb=" C   GLY E 447 "
        pdb=" O   GLY E 447 "
      ideal   model   delta    sigma   weight residual
     122.29  118.53    3.76 8.10e-01 1.52e+00 2.15e+01
  angle pdb=" CA  PRO H   9 "
        pdb=" CB  PRO H   9 "
        pdb=" CG  PRO H   9 "
      ideal   model   delta    sigma   weight residual
     104.50   96.46    8.04 1.90e+00 2.77e-01 1.79e+01
  angle pdb=" N   PRO H   9 "
        pdb=" CD  PRO H   9 "
        pdb=" CG  PRO H   9 "
      ideal   model   delta    sigma   weight residual
     103.20   97.15    6.05 1.50e+00 4.44e-01 1.62e+01
  angle pdb=" N   GLY E 404 "
        pdb=" CA  GLY E 404 "
        pdb=" C   GLY E 404 "
      ideal   model   delta    sigma   weight residual
     111.02  118.30   -7.28 1.86e+00 2.89e-01 1.53e+01
  angle pdb=" N   ILE E 418 "
        pdb=" CA  ILE E 418 "
        pdb=" C   ILE E 418 "
      ideal   model   delta    sigma   weight residual
     113.07  108.39    4.68 1.36e+00 5.41e-01 1.19e+01
  ... (remaining 4554 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.35: 1742
       15.35 -    30.70: 177
       30.70 -    46.06: 34
       46.06 -    61.41: 10
       61.41 -    76.76: 5
  Dihedral angle restraints: 1968
    sinusoidal: 749
      harmonic: 1219
  Sorted by residual:
  dihedral pdb=" CB  CYS E 336 "
           pdb=" SG  CYS E 336 "
           pdb=" SG  CYS E 361 "
           pdb=" CB  CYS E 361 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   18.13   74.87     1      1.00e+01 1.00e-02 7.09e+01
  dihedral pdb=" CB  CYS H  22 "
           pdb=" SG  CYS H  22 "
           pdb=" SG  CYS H  97 "
           pdb=" CB  CYS H  97 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  147.18  -54.18     1      1.00e+01 1.00e-02 3.98e+01
  dihedral pdb=" CA  CYS E 432 "
           pdb=" C   CYS E 432 "
           pdb=" N   VAL E 433 "
           pdb=" CA  VAL E 433 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.78  -20.22     0      5.00e+00 4.00e-02 1.64e+01
  ... (remaining 1965 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 349
       0.042 -    0.083: 96
       0.083 -    0.125: 50
       0.125 -    0.166: 4
       0.166 -    0.208: 2
  Chirality restraints: 501
  Sorted by residual:
  chirality pdb=" CA  VAL E 445 "
            pdb=" N   VAL E 445 "
            pdb=" C   VAL E 445 "
            pdb=" CB  VAL E 445 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.65   -0.21 2.00e-01 2.50e+01 1.08e+00
  chirality pdb=" CA  SER E 446 "
            pdb=" N   SER E 446 "
            pdb=" C   SER E 446 "
            pdb=" CB  SER E 446 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 9.77e-01
  chirality pdb=" CA  ILE H  39 "
            pdb=" N   ILE H  39 "
            pdb=" C   ILE H  39 "
            pdb=" CB  ILE H  39 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.16 2.00e-01 2.50e+01 6.79e-01
  ... (remaining 498 not shown)

  Planarity restraints: 584
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA E 419 "   -0.012 2.00e-02 2.50e+03   2.44e-02 5.97e+00
        pdb=" C   ALA E 419 "    0.042 2.00e-02 2.50e+03
        pdb=" O   ALA E 419 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   ASP E 420 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS E 440 "    0.009 2.00e-02 2.50e+03   1.73e-02 2.99e+00
        pdb=" C   LYS E 440 "   -0.030 2.00e-02 2.50e+03
        pdb=" O   LYS E 440 "    0.011 2.00e-02 2.50e+03
        pdb=" N   LEU E 441 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE L  98 "   -0.028 5.00e-02 4.00e+02   4.20e-02 2.82e+00
        pdb=" N   PRO L  99 "    0.073 5.00e-02 4.00e+02
        pdb=" CA  PRO L  99 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO L  99 "   -0.023 5.00e-02 4.00e+02
  ... (remaining 581 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.71: 153
        2.71 -     3.26: 3186
        3.26 -     3.81: 4694
        3.81 -     4.35: 5739
        4.35 -     4.90: 9754
  Nonbonded interactions: 23526
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP H  74 "
            pdb=" OG  SER H  76 "
     model   vdw
     2.169 3.040
  nonbonded pdb=" OG1 THR H   3 "
            pdb=" OG  SER H  25 "
     model   vdw
     2.291 3.040
  nonbonded pdb=" NZ  LYS H  45 "
            pdb=" O   ALA H  46 "
     model   vdw
     2.311 3.120
  nonbonded pdb=" N   GLU H   6 "
            pdb=" OE1 GLU H   6 "
     model   vdw
     2.334 3.120
  nonbonded pdb=" NZ  LYS H   5 "
            pdb=" O   GLU H   6 "
     model   vdw
     2.409 3.120
  ... (remaining 23521 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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.590
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.000
  Process input model:                     4.390
  Find NCS groups from input model:        0.010
  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:1.270
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.350
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7016
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   0.061   3351  Z= 0.250
  Angle     :  0.778   8.712   4571  Z= 0.454
  Chirality :  0.048   0.208    501
  Planarity :  0.005   0.042    584
  Dihedral  : 12.973  76.758   1176
  Min Nonbonded Distance : 2.169

Molprobity Statistics.
  All-atom Clashscore : 8.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.95 %
    Favored  : 92.05 %
  Rotamer:
    Outliers :  0.85 %
    Allowed  :  0.57 %
    Favored  : 98.58 %
  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: -2.03 (0.40), residues: 415
  helix: -4.34 (0.65), residues: 26
  sheet:  0.36 (0.54), residues: 104
  loop : -1.85 (0.35), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H  60 
 TYR   0.021   0.001   TYR H  61 
 PHE   0.008   0.001   PHE H 106 
 TRP   0.011   0.002   TRP H  49 
 HIS   0.001   0.000   HIS L  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00388 ( 3345)
  covalent geometry    : angle       0.77756 ( 4559)
  SS BOND              : bond        0.00374 (    6)
  SS BOND              : angle       0.77543 (   12)
  hydrogen bonds       : bond        0.33519 (   61)
  hydrogen bonds       : angle       9.72676 (  141)

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 84
  time to evaluate  : 0.106 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  359 SER cc_start: 0.8534 (p) cc_final: 0.8255 (p)
REVERT: H   29 LEU cc_start: 0.7855 (mm) cc_final: 0.7439 (mm)
  outliers start: 3
  outliers final: 0
  residues processed: 85
  average time/residue: 0.0579
  time to fit residues: 6.1987
Evaluate side-chains
  57 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 0.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 24 optimal weight:    0.0470
   chunk 26 optimal weight:    3.9990
   chunk 2 optimal weight:    0.0770
   chunk 16 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9990
   chunk 31 optimal weight:    2.9990
   chunk 25 optimal weight:    0.8980
   chunk 19 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 22 optimal weight:    0.6980
   chunk 37 optimal weight:    0.0370
   overall best weight:    0.3514

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

Flipped N/Q/H residues before XYZ refinement:
E 439 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.110586 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.093215 restraints weight = 8029.766|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.095322 restraints weight = 5335.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.096818 restraints weight = 3943.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.097818 restraints weight = 3147.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.098665 restraints weight = 2668.744|
|-----------------------------------------------------------------------------|
r_work (final): 0.3416
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7031
moved from start:          0.1514

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3351  Z= 0.127
  Angle     :  0.628   5.667   4571  Z= 0.329
  Chirality :  0.045   0.136    501
  Planarity :  0.005   0.049    584
  Dihedral  :  4.746  21.873    462
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 7.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.43 %
    Favored  : 91.57 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.25 %
    Favored  : 95.75 %
  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: -2.07 (0.40), residues: 415
  helix: -4.73 (0.52), residues: 20
  sheet:  0.39 (0.56), residues: 104
  loop : -1.94 (0.34), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H  40 
 TYR   0.012   0.001   TYR H  61 
 PHE   0.015   0.001   PHE L 102 
 TRP   0.006   0.001   TRP H  49 
 HIS   0.003   0.001   HIS H 100 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 3345)
  covalent geometry    : angle       0.62770 ( 4559)
  SS BOND              : bond        0.00475 (    6)
  SS BOND              : angle       0.80064 (   12)
  hydrogen bonds       : bond        0.04576 (   61)
  hydrogen bonds       : angle       7.07684 (  141)

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 0.120 
Fit side-chains
REVERT: E  359 SER cc_start: 0.8162 (p) cc_final: 0.7869 (p)
REVERT: E  389 ASP cc_start: 0.8261 (t0) cc_final: 0.8001 (t0)
REVERT: H   18 LEU cc_start: 0.7039 (mm) cc_final: 0.6797 (mm)
REVERT: H   45 LYS cc_start: 0.8781 (ttpp) cc_final: 0.8530 (mptt)
  outliers start: 0
  outliers final: 0
  residues processed: 84
  average time/residue: 0.0647
  time to fit residues: 6.6252
Evaluate side-chains
  56 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 56
  time to evaluate  : 0.119 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 13 optimal weight:    0.9980
   chunk 1 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 39 optimal weight:    0.7980
   chunk 38 optimal weight:    2.9990
   chunk 11 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 20 optimal weight:    0.0010
   chunk 37 optimal weight:    2.9990
   chunk 27 optimal weight:    0.8980
   chunk 36 optimal weight:    0.2980
   overall best weight:    0.5986

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

Flipped N/Q/H residues before XYZ refinement:
E 439 ASN
H  99 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.106976 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.088633 restraints weight = 8066.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.090748 restraints weight = 5303.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.092222 restraints weight = 3890.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.093271 restraints weight = 3104.700|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.094037 restraints weight = 2631.495|
|-----------------------------------------------------------------------------|
r_work (final): 0.3338
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7104
moved from start:          0.2450

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   3351  Z= 0.165
  Angle     :  0.667   6.138   4571  Z= 0.350
  Chirality :  0.047   0.150    501
  Planarity :  0.005   0.058    584
  Dihedral  :  5.271  24.563    462
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 9.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.12 %
    Favored  : 89.88 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  7.37 %
    Favored  : 92.63 %
  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: -2.23 (0.40), residues: 415
  helix: -5.28 (0.24), residues: 14
  sheet:  0.18 (0.55), residues: 104
  loop : -2.08 (0.34), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG H  60 
 TYR   0.015   0.002   TYR H  61 
 PHE   0.018   0.002   PHE L 102 
 TRP   0.008   0.001   TRP H 109 
 HIS   0.005   0.001   HIS H 100 

Details of bonding type rmsd
  covalent geometry    : bond        0.00382 ( 3345)
  covalent geometry    : angle       0.66597 ( 4559)
  SS BOND              : bond        0.00614 (    6)
  SS BOND              : angle       1.05768 (   12)
  hydrogen bonds       : bond        0.04415 (   61)
  hydrogen bonds       : angle       6.83578 (  141)

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 74
  time to evaluate  : 0.132 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  516 GLU cc_start: 0.7144 (tp30) cc_final: 0.6913 (tp30)
REVERT: L   87 ASP cc_start: 0.8553 (m-30) cc_final: 0.8349 (m-30)
REVERT: H   18 LEU cc_start: 0.7081 (mm) cc_final: 0.6745 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 74
  average time/residue: 0.0621
  time to fit residues: 5.6857
Evaluate side-chains
  54 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 0.129 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 6 optimal weight:    0.9980
   chunk 29 optimal weight:    2.9990
   chunk 1 optimal weight:    0.1980
   chunk 30 optimal weight:    0.6980
   chunk 22 optimal weight:    0.7980
   chunk 16 optimal weight:    0.7980
   chunk 27 optimal weight:    0.2980
   chunk 11 optimal weight:    0.7980
   chunk 2 optimal weight:    0.8980
   chunk 33 optimal weight:    1.9990
   chunk 10 optimal weight:    0.2980
   overall best weight:    0.4580

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

Flipped N/Q/H residues before XYZ refinement:
E 439 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.108171 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.090196 restraints weight = 8024.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.092194 restraints weight = 5406.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.093633 restraints weight = 4038.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.094667 restraints weight = 3248.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.095352 restraints weight = 2764.347|
|-----------------------------------------------------------------------------|
r_work (final): 0.3369
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7078
moved from start:          0.2709

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3351  Z= 0.135
  Angle     :  0.628   5.390   4571  Z= 0.326
  Chirality :  0.046   0.168    501
  Planarity :  0.005   0.056    584
  Dihedral  :  5.153  24.149    462
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 8.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.40 %
    Favored  : 90.60 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.10 %
    Favored  : 94.90 %
  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: -2.28 (0.40), residues: 415
  helix: -5.23 (0.20), residues: 20
  sheet:  0.15 (0.55), residues: 104
  loop : -2.02 (0.34), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG H  60 
 TYR   0.013   0.001   TYR H  61 
 PHE   0.015   0.002   PHE L 102 
 TRP   0.007   0.001   TRP H  49 
 HIS   0.003   0.001   HIS H 100 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 3345)
  covalent geometry    : angle       0.62598 ( 4559)
  SS BOND              : bond        0.00483 (    6)
  SS BOND              : angle       1.07534 (   12)
  hydrogen bonds       : bond        0.03543 (   61)
  hydrogen bonds       : angle       6.44067 (  141)

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 74
  time to evaluate  : 0.126 
Fit side-chains
   revert: symmetry clash
REVERT: E  508 TYR cc_start: 0.7219 (m-10) cc_final: 0.6962 (m-10)
REVERT: E  516 GLU cc_start: 0.7178 (tp30) cc_final: 0.6973 (tp30)
REVERT: L   87 ASP cc_start: 0.8537 (m-30) cc_final: 0.8321 (m-30)
REVERT: H   18 LEU cc_start: 0.6957 (mm) cc_final: 0.6695 (mm)
REVERT: H   45 LYS cc_start: 0.8752 (ttpt) cc_final: 0.8473 (mptt)
  outliers start: 0
  outliers final: 0
  residues processed: 74
  average time/residue: 0.0547
  time to fit residues: 5.0832
Evaluate side-chains
  53 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 53
  time to evaluate  : 0.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 24 optimal weight:    0.3980
   chunk 16 optimal weight:    0.9980
   chunk 22 optimal weight:    0.9980
   chunk 33 optimal weight:    0.5980
   chunk 38 optimal weight:    1.9990
   chunk 21 optimal weight:    4.9990
   chunk 8 optimal weight:    1.9990
   chunk 9 optimal weight:    0.0980
   chunk 7 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9990
   chunk 17 optimal weight:    0.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** E 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 422 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.106967 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.089110 restraints weight = 7958.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.090884 restraints weight = 5563.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.092174 restraints weight = 4281.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.093100 restraints weight = 3525.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.093582 restraints weight = 3046.475|
|-----------------------------------------------------------------------------|
r_work (final): 0.3338
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7145
moved from start:          0.3139

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   3351  Z= 0.166
  Angle     :  0.672   7.209   4571  Z= 0.348
  Chirality :  0.046   0.147    501
  Planarity :  0.006   0.061    584
  Dihedral  :  5.354  24.519    462
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 8.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.33 %
    Favored  : 88.67 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  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: -2.36 (0.39), residues: 415
  helix: -5.35 (0.22), residues: 14
  sheet:  0.03 (0.54), residues: 104
  loop : -2.14 (0.34), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG H  60 
 TYR   0.011   0.002   TYR H  61 
 PHE   0.015   0.002   PHE L 102 
 TRP   0.008   0.001   TRP E 436 
 HIS   0.004   0.001   HIS H 100 

Details of bonding type rmsd
  covalent geometry    : bond        0.00387 ( 3345)
  covalent geometry    : angle       0.67068 ( 4559)
  SS BOND              : bond        0.00431 (    6)
  SS BOND              : angle       1.11971 (   12)
  hydrogen bonds       : bond        0.03695 (   61)
  hydrogen bonds       : angle       6.56450 (  141)

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 75
  time to evaluate  : 0.106 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  340 GLU cc_start: 0.7676 (mm-30) cc_final: 0.7334 (mm-30)
REVERT: L   87 ASP cc_start: 0.8487 (m-30) cc_final: 0.8257 (m-30)
REVERT: H   18 LEU cc_start: 0.6933 (mm) cc_final: 0.6691 (mm)
REVERT: H   29 LEU cc_start: 0.8268 (mm) cc_final: 0.7598 (mp)
  outliers start: 0
  outliers final: 0
  residues processed: 75
  average time/residue: 0.0617
  time to fit residues: 5.6869
Evaluate side-chains
  53 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 53
  time to evaluate  : 0.104 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 3 optimal weight:    0.4980
   chunk 34 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 26 optimal weight:    0.8980
   chunk 2 optimal weight:    0.3980
   chunk 18 optimal weight:    0.8980
   chunk 36 optimal weight:    0.7980
   chunk 17 optimal weight:    0.3980
   chunk 0 optimal weight:    0.5980
   chunk 8 optimal weight:    0.7980
   overall best weight:    0.5380

-------------------------------------------------------------------------------
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 = 0.3554 r_free = 0.3554 target = 0.106561 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.088573 restraints weight = 8031.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.090479 restraints weight = 5432.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.091883 restraints weight = 4099.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.092800 restraints weight = 3312.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.093545 restraints weight = 2847.808|
|-----------------------------------------------------------------------------|
r_work (final): 0.3338
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7117
moved from start:          0.3261

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   3351  Z= 0.152
  Angle     :  0.653   5.855   4571  Z= 0.339
  Chirality :  0.046   0.144    501
  Planarity :  0.005   0.055    584
  Dihedral  :  5.438  26.604    462
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 8.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.08 %
    Favored  : 88.92 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  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: -2.32 (0.39), residues: 415
  helix: -5.38 (0.22), residues: 14
  sheet: -0.01 (0.53), residues: 104
  loop : -2.08 (0.33), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H  60 
 TYR   0.010   0.002   TYR L  93 
 PHE   0.008   0.002   PHE E 486 
 TRP   0.006   0.001   TRP E 436 
 HIS   0.004   0.001   HIS H 100 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 ( 3345)
  covalent geometry    : angle       0.65017 ( 4559)
  SS BOND              : bond        0.00448 (    6)
  SS BOND              : angle       1.31915 (   12)
  hydrogen bonds       : bond        0.03478 (   61)
  hydrogen bonds       : angle       6.40822 (  141)

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 76
  time to evaluate  : 0.128 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  340 GLU cc_start: 0.7683 (mm-30) cc_final: 0.7328 (mm-30)
REVERT: E  508 TYR cc_start: 0.7279 (m-10) cc_final: 0.7013 (m-10)
REVERT: L   87 ASP cc_start: 0.8527 (m-30) cc_final: 0.8307 (m-30)
REVERT: H   18 LEU cc_start: 0.7014 (mm) cc_final: 0.6766 (mm)
REVERT: H   29 LEU cc_start: 0.8341 (mm) cc_final: 0.7665 (mp)
  outliers start: 0
  outliers final: 0
  residues processed: 76
  average time/residue: 0.0532
  time to fit residues: 5.1296
Evaluate side-chains
  56 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 56
  time to evaluate  : 0.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 17 optimal weight:    0.4980
   chunk 10 optimal weight:    0.8980
   chunk 38 optimal weight:    2.9990
   chunk 32 optimal weight:    0.5980
   chunk 3 optimal weight:    0.9980
   chunk 20 optimal weight:    0.0060
   chunk 19 optimal weight:    0.1980
   chunk 9 optimal weight:    0.7980
   chunk 18 optimal weight:    0.8980
   chunk 34 optimal weight:    0.9980
   chunk 22 optimal weight:    1.9990
   overall best weight:    0.4196

-------------------------------------------------------------------------------
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 = 0.3555 r_free = 0.3555 target = 0.106699 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.088588 restraints weight = 8203.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.090519 restraints weight = 5541.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.091904 restraints weight = 4168.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.092819 restraints weight = 3378.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.093555 restraints weight = 2906.261|
|-----------------------------------------------------------------------------|
r_work (final): 0.3336
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7104
moved from start:          0.3328

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3351  Z= 0.133
  Angle     :  0.649   7.013   4571  Z= 0.333
  Chirality :  0.046   0.153    501
  Planarity :  0.005   0.053    584
  Dihedral  :  5.333  25.354    462
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 9.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.12 %
    Favored  : 89.88 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.70 %
    Favored  : 98.30 %
  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: -2.25 (0.40), residues: 415
  helix: -5.37 (0.21), residues: 14
  sheet:  0.11 (0.54), residues: 104
  loop : -2.06 (0.34), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H  60 
 TYR   0.011   0.001   TYR H  95 
 PHE   0.016   0.002   PHE L 102 
 TRP   0.006   0.001   TRP E 436 
 HIS   0.003   0.001   HIS H 100 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 3345)
  covalent geometry    : angle       0.64761 ( 4559)
  SS BOND              : bond        0.00413 (    6)
  SS BOND              : angle       1.07447 (   12)
  hydrogen bonds       : bond        0.03260 (   61)
  hydrogen bonds       : angle       6.34784 (  141)

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 74
  time to evaluate  : 0.087 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  340 GLU cc_start: 0.7616 (mm-30) cc_final: 0.7255 (mm-30)
REVERT: L   53 VAL cc_start: 0.5771 (t) cc_final: 0.5489 (t)
REVERT: L   87 ASP cc_start: 0.8533 (m-30) cc_final: 0.8291 (m-30)
REVERT: H   18 LEU cc_start: 0.6926 (mm) cc_final: 0.6723 (mm)
REVERT: H   29 LEU cc_start: 0.8322 (mm) cc_final: 0.7781 (mp)
REVERT: H   45 LYS cc_start: 0.8645 (ttpt) cc_final: 0.8341 (mptt)
  outliers start: 0
  outliers final: 0
  residues processed: 74
  average time/residue: 0.0631
  time to fit residues: 5.7404
Evaluate side-chains
  55 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 55
  time to evaluate  : 0.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 37 optimal weight:    1.9990
   chunk 30 optimal weight:    0.7980
   chunk 27 optimal weight:    0.9990
   chunk 36 optimal weight:    0.6980
   chunk 35 optimal weight:    0.8980
   chunk 6 optimal weight:    0.1980
   chunk 26 optimal weight:    3.9990
   chunk 17 optimal weight:    0.9980
   chunk 39 optimal weight:    0.9990
   chunk 11 optimal weight:    1.9990
   chunk 25 optimal weight:    0.4980
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 = 0.3526 r_free = 0.3526 target = 0.104828 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.087398 restraints weight = 8254.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.089218 restraints weight = 5628.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.090492 restraints weight = 4264.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.091436 restraints weight = 3477.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.091989 restraints weight = 2990.694|
|-----------------------------------------------------------------------------|
r_work (final): 0.3310
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7152
moved from start:          0.3602

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   3351  Z= 0.170
  Angle     :  0.681   6.178   4571  Z= 0.356
  Chirality :  0.047   0.143    501
  Planarity :  0.005   0.060    584
  Dihedral  :  5.616  26.058    462
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 9.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.57 %
    Favored  : 88.43 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  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: -2.34 (0.39), residues: 415
  helix: -5.38 (0.22), residues: 14
  sheet:  0.07 (0.55), residues: 104
  loop : -2.13 (0.33), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H  40 
 TYR   0.015   0.002   TYR H  95 
 PHE   0.012   0.002   PHE E 490 
 TRP   0.008   0.001   TRP E 436 
 HIS   0.003   0.001   HIS H 100 

Details of bonding type rmsd
  covalent geometry    : bond        0.00395 ( 3345)
  covalent geometry    : angle       0.67869 ( 4559)
  SS BOND              : bond        0.00408 (    6)
  SS BOND              : angle       1.22435 (   12)
  hydrogen bonds       : bond        0.03564 (   61)
  hydrogen bonds       : angle       6.49944 (  141)

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.133 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  340 GLU cc_start: 0.7653 (mm-30) cc_final: 0.7195 (mm-30)
REVERT: H   18 LEU cc_start: 0.6811 (mm) cc_final: 0.6592 (mm)
REVERT: H   29 LEU cc_start: 0.8339 (mm) cc_final: 0.7757 (mp)
  outliers start: 0
  outliers final: 0
  residues processed: 77
  average time/residue: 0.0573
  time to fit residues: 5.5781
Evaluate side-chains
  55 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 55
  time to evaluate  : 0.130 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 24 optimal weight:    0.0000
   chunk 38 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 29 optimal weight:    0.6980
   chunk 12 optimal weight:    0.7980
   chunk 37 optimal weight:    0.6980
   chunk 14 optimal weight:    2.9990
   chunk 11 optimal weight:    1.9990
   chunk 2 optimal weight:    0.7980
   chunk 21 optimal weight:    0.5980
   chunk 7 optimal weight:    0.9990
   overall best weight:    0.5584

-------------------------------------------------------------------------------
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 = 0.3526 r_free = 0.3526 target = 0.104889 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.087124 restraints weight = 8262.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.088960 restraints weight = 5605.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.090288 restraints weight = 4243.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.091173 restraints weight = 3452.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.091898 restraints weight = 2970.066|
|-----------------------------------------------------------------------------|
r_work (final): 0.3308
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7151
moved from start:          0.3820

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   3351  Z= 0.160
  Angle     :  0.690   7.131   4571  Z= 0.357
  Chirality :  0.048   0.231    501
  Planarity :  0.005   0.056    584
  Dihedral  :  5.615  28.465    462
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 10.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.12 %
    Favored  : 89.88 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.13 %
    Favored  : 98.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.37 (0.39), residues: 415
  helix: -5.39 (0.22), residues: 14
  sheet:  0.01 (0.55), residues: 104
  loop : -2.14 (0.33), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H  60 
 TYR   0.012   0.002   TYR H  95 
 PHE   0.012   0.002   PHE E 490 
 TRP   0.007   0.001   TRP H 109 
 HIS   0.002   0.001   HIS H 100 

Details of bonding type rmsd
  covalent geometry    : bond        0.00372 ( 3345)
  covalent geometry    : angle       0.68687 ( 4559)
  SS BOND              : bond        0.00354 (    6)
  SS BOND              : angle       1.46738 (   12)
  hydrogen bonds       : bond        0.03254 (   61)
  hydrogen bonds       : angle       6.49186 (  141)

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 69
  time to evaluate  : 0.132 
Fit side-chains
   revert: symmetry clash
REVERT: E  340 GLU cc_start: 0.7592 (mm-30) cc_final: 0.7168 (mm-30)
REVERT: H   18 LEU cc_start: 0.6843 (mm) cc_final: 0.6641 (mm)
REVERT: H   29 LEU cc_start: 0.8355 (mm) cc_final: 0.7761 (mp)
  outliers start: 0
  outliers final: 0
  residues processed: 69
  average time/residue: 0.0546
  time to fit residues: 4.7708
Evaluate side-chains
  52 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 52
  time to evaluate  : 0.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 10 optimal weight:    0.1980
   chunk 31 optimal weight:    0.5980
   chunk 25 optimal weight:    0.9990
   chunk 8 optimal weight:    0.6980
   chunk 4 optimal weight:    0.7980
   chunk 7 optimal weight:    0.0870
   chunk 28 optimal weight:    0.0980
   chunk 15 optimal weight:    0.0040
   chunk 6 optimal weight:    0.7980
   chunk 33 optimal weight:    0.8980
   chunk 1 optimal weight:    0.5980
   overall best weight:    0.1970

-------------------------------------------------------------------------------
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 = 0.3582 r_free = 0.3582 target = 0.108389 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.090494 restraints weight = 8041.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.092475 restraints weight = 5448.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.093811 restraints weight = 4085.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.094814 restraints weight = 3325.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.095602 restraints weight = 2848.428|
|-----------------------------------------------------------------------------|
r_work (final): 0.3370
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7075
moved from start:          0.3688

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   3351  Z= 0.107
  Angle     :  0.641   6.368   4571  Z= 0.328
  Chirality :  0.046   0.167    501
  Planarity :  0.005   0.051    584
  Dihedral  :  5.121  25.245    462
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 7.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.95 %
    Favored  : 92.05 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.28 %
    Favored  : 99.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.29 (0.39), residues: 415
  helix: -5.36 (0.22), residues: 14
  sheet:  0.06 (0.54), residues: 104
  loop : -2.08 (0.33), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H  60 
 TYR   0.011   0.001   TYR H  61 
 PHE   0.011   0.001   PHE L 102 
 TRP   0.011   0.001   TRP H  55 
 HIS   0.001   0.001   HIS H  99 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 ( 3345)
  covalent geometry    : angle       0.63965 ( 4559)
  SS BOND              : bond        0.00371 (    6)
  SS BOND              : angle       1.09875 (   12)
  hydrogen bonds       : bond        0.03069 (   61)
  hydrogen bonds       : angle       6.19784 (  141)

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 73
  time to evaluate  : 0.118 
Fit side-chains
REVERT: E  340 GLU cc_start: 0.7471 (mm-30) cc_final: 0.7029 (mm-30)
REVERT: H   18 LEU cc_start: 0.6850 (mm) cc_final: 0.6084 (mm)
REVERT: H   29 LEU cc_start: 0.8242 (mm) cc_final: 0.7740 (mp)
REVERT: H   87 MET cc_start: 0.4628 (tpt) cc_final: 0.3956 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 73
  average time/residue: 0.0588
  time to fit residues: 5.3365
Evaluate side-chains
  58 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 0.083 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 19 optimal weight:    0.0670
   chunk 20 optimal weight:    4.9990
   chunk 32 optimal weight:    0.2980
   chunk 25 optimal weight:    1.9990
   chunk 5 optimal weight:    0.5980
   chunk 21 optimal weight:    0.8980
   chunk 38 optimal weight:    0.6980
   chunk 24 optimal weight:    0.9980
   chunk 14 optimal weight:    1.9990
   chunk 9 optimal weight:    0.6980
   chunk 7 optimal weight:    0.9980
   overall best weight:    0.4718

-------------------------------------------------------------------------------
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 = 0.3553 r_free = 0.3553 target = 0.106566 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.088684 restraints weight = 8359.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.090527 restraints weight = 5764.686|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.091828 restraints weight = 4372.082|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.092733 restraints weight = 3573.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.093201 restraints weight = 3075.627|
|-----------------------------------------------------------------------------|
r_work (final): 0.3329
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7127
moved from start:          0.3834

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3351  Z= 0.142
  Angle     :  0.666   7.432   4571  Z= 0.343
  Chirality :  0.047   0.155    501
  Planarity :  0.005   0.056    584
  Dihedral  :  5.359  26.448    462
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 9.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.08 %
    Favored  : 88.92 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.28 %
    Favored  : 99.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.38 (0.39), residues: 415
  helix: -5.37 (0.22), residues: 14
  sheet:  0.10 (0.54), residues: 104
  loop : -2.19 (0.33), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H  40 
 TYR   0.013   0.001   TYR H  95 
 PHE   0.010   0.002   PHE E 490 
 TRP   0.007   0.001   TRP E 436 
 HIS   0.003   0.001   HIS H 100 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 3345)
  covalent geometry    : angle       0.66300 ( 4559)
  SS BOND              : bond        0.00365 (    6)
  SS BOND              : angle       1.35940 (   12)
  hydrogen bonds       : bond        0.03090 (   61)
  hydrogen bonds       : angle       6.28826 (  141)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 783.88 seconds
wall clock time: 14 minutes 9.63 seconds (849.63 seconds total)