Starting phenix.real_space_refine
on Wed Mar  5 18:23:33 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wth_32786/03_2025/7wth_32786.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wth_32786/03_2025/7wth_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wth_32786/03_2025/7wth_32786.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wth_32786/03_2025/7wth_32786.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wth_32786/03_2025/7wth_32786.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wth_32786/03_2025/7wth_32786.cif"
  }
  resolution = 4.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 3.31, per 1000 atoms: 1.02
  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: 0.77
  Conformation dependent library (CDL) restraints added in 411.2 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: 0.38
  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: 0.72

  Time building geometry restraints manager: 0.92 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:             3.010
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     13.540
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  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:2.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.720
-------------------------------------------------------------------------------
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   3345  Z= 0.256
  Angle     :  0.778   8.712   4559  Z= 0.455
  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 : 9.08
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  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
 TRP   0.011   0.002   TRP H  49 
 HIS   0.001   0.000   HIS L  41 
 PHE   0.008   0.001   PHE H 106 
 TYR   0.021   0.001   TYR H  61 
 ARG   0.003   0.000   ARG H  60 

*********************** 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  : 0.370 
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: 0.7854 (mm) cc_final: 0.7439 (mm)
  outliers start: 3
  outliers final: 0
  residues processed: 85
  average time/residue: 0.1468
  time to fit residues: 15.4016
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  : 0.374 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 33 optimal weight:    0.6980
   chunk 30 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9980
   chunk 20 optimal weight:    1.9990
   chunk 31 optimal weight:    0.8980
   chunk 12 optimal weight:    1.9990
   chunk 19 optimal weight:    0.8980
   chunk 23 optimal weight:    0.7980
   chunk 36 optimal weight:    0.1980
   chunk 11 optimal weight:    0.5980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.3558 r_free = 0.3558 target = 0.107389 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.090101 restraints weight = 8046.003|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.092098 restraints weight = 5442.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.093508 restraints weight = 4066.494|
|-----------------------------------------------------------------------------|
r_work (final): 0.3325
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7140
moved from start:          0.1904

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   3345  Z= 0.271
  Angle     :  0.681   7.078   4559  Z= 0.359
  Chirality :  0.046   0.139    501
  Planarity :  0.005   0.051    584
  Dihedral  :  5.159  23.212    462
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 9.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.60 %
    Favored  : 89.40 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.80 %
    Favored  : 93.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.24 (0.41), residues: 415
  helix: -4.77 (0.50), residues: 20
  sheet:  0.17 (0.55), residues: 105
  loop : -2.04 (0.35), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP E 436 
 HIS   0.005   0.001   HIS H 100 
 PHE   0.016   0.002   PHE E 464 
 TYR   0.012   0.002   TYR H  61 
 ARG   0.002   0.000   ARG H  40 

*********************** 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
  75 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 75
  time to evaluate  : 0.386 
Fit side-chains
REVERT: L   51 TYR cc_start: 0.6657 (p90) cc_final: 0.6451 (p90)
REVERT: H   18 LEU cc_start: 0.7171 (mm) cc_final: 0.6831 (mm)
REVERT: H   45 LYS cc_start: 0.8813 (ttpp) cc_final: 0.8521 (mptt)
  outliers start: 0
  outliers final: 0
  residues processed: 75
  average time/residue: 0.1630
  time to fit residues: 14.8197
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  : 0.383 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 14 optimal weight:    0.6980
   chunk 3 optimal weight:    0.7980
   chunk 19 optimal weight:    2.9990
   chunk 13 optimal weight:    0.8980
   chunk 35 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9980
   chunk 23 optimal weight:    1.9990
   chunk 17 optimal weight:    0.7980
   chunk 11 optimal weight:    1.9990
   chunk 5 optimal weight:    0.0070
   chunk 33 optimal weight:    0.9990
   overall best weight:    0.6398

-------------------------------------------------------------------------------
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 = 0.3553 r_free = 0.3553 target = 0.106404 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.087989 restraints weight = 8165.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.089939 restraints weight = 5515.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.091395 restraints weight = 4151.027|
|-----------------------------------------------------------------------------|
r_work (final): 0.3297
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7149
moved from start:          0.2578

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   3345  Z= 0.264
  Angle     :  0.667   6.178   4559  Z= 0.351
  Chirality :  0.047   0.175    501
  Planarity :  0.005   0.056    584
  Dihedral  :  5.379  25.378    462
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 9.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.84 %
    Favored  : 89.16 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.95 %
    Favored  : 94.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.37 (0.40), residues: 415
  helix: -5.23 (0.26), residues: 14
  sheet:  0.03 (0.54), residues: 104
  loop : -2.16 (0.34), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP E 436 
 HIS   0.005   0.001   HIS H 100 
 PHE   0.020   0.002   PHE L 102 
 TYR   0.014   0.002   TYR H  61 
 ARG   0.005   0.001   ARG H  60 

*********************** 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
  68 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 68
  time to evaluate  : 0.343 
Fit side-chains
   revert: symmetry clash
REVERT: E  340 GLU cc_start: 0.7749 (mm-30) cc_final: 0.7324 (mm-30)
REVERT: E  359 SER cc_start: 0.7812 (p) cc_final: 0.7555 (p)
REVERT: E  516 GLU cc_start: 0.7234 (tp30) cc_final: 0.6979 (tp30)
REVERT: L   51 TYR cc_start: 0.6710 (p90) cc_final: 0.6475 (p90)
REVERT: H   18 LEU cc_start: 0.7115 (mm) cc_final: 0.6766 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 68
  average time/residue: 0.1441
  time to fit residues: 12.1209
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  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 38 optimal weight:    3.9990
   chunk 37 optimal weight:    0.9980
   chunk 34 optimal weight:    0.9990
   chunk 19 optimal weight:    0.4980
   chunk 39 optimal weight:    0.3980
   chunk 2 optimal weight:    0.0870
   chunk 26 optimal weight:    2.9990
   chunk 1 optimal weight:    0.7980
   chunk 13 optimal weight:    0.8980
   chunk 22 optimal weight:    0.9990
   chunk 17 optimal weight:    0.7980
   overall best weight:    0.5158

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.107365 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.089057 restraints weight = 8110.470|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.091106 restraints weight = 5378.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.092594 restraints weight = 3976.908|
|-----------------------------------------------------------------------------|
r_work (final): 0.3314
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7117
moved from start:          0.2918

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3345  Z= 0.228
  Angle     :  0.649   5.579   4559  Z= 0.339
  Chirality :  0.045   0.166    501
  Planarity :  0.005   0.053    584
  Dihedral  :  5.290  25.698    462
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 9.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.36 %
    Favored  : 89.64 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.95 %
    Favored  : 94.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.41 (0.39), residues: 415
  helix: -5.23 (0.25), residues: 14
  sheet:  0.00 (0.54), residues: 104
  loop : -2.19 (0.33), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP H  55 
 HIS   0.002   0.001   HIS H 100 
 PHE   0.016   0.002   PHE L 102 
 TYR   0.013   0.001   TYR H  61 
 ARG   0.004   0.000   ARG H  60 

*********************** 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
  72 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 72
  time to evaluate  : 0.346 
Fit side-chains
   revert: symmetry clash
REVERT: E  340 GLU cc_start: 0.7775 (mm-30) cc_final: 0.7507 (mm-30)
REVERT: E  516 GLU cc_start: 0.7171 (tp30) cc_final: 0.6962 (tp30)
REVERT: L   53 VAL cc_start: 0.5596 (t) cc_final: 0.5362 (t)
REVERT: L   87 ASP cc_start: 0.8547 (m-30) cc_final: 0.8327 (m-30)
REVERT: H   18 LEU cc_start: 0.7189 (mm) cc_final: 0.6947 (mm)
REVERT: H   29 LEU cc_start: 0.7827 (mm) cc_final: 0.7572 (mm)
REVERT: H   45 LYS cc_start: 0.8780 (ttpt) cc_final: 0.8476 (mptt)
REVERT: H   95 TYR cc_start: 0.7658 (m-80) cc_final: 0.7443 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 72
  average time/residue: 0.1457
  time to fit residues: 12.9603
Evaluate side-chains
  59 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 59
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 2 optimal weight:    0.1980
   chunk 37 optimal weight:    0.9990
   chunk 3 optimal weight:    0.8980
   chunk 7 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9990
   chunk 9 optimal weight:    0.9990
   chunk 26 optimal weight:    3.9990
   chunk 12 optimal weight:    0.9990
   chunk 27 optimal weight:    0.8980
   chunk 28 optimal weight:    0.4980
   chunk 10 optimal weight:    0.9980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.3538 r_free = 0.3538 target = 0.105630 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.087699 restraints weight = 8236.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.089557 restraints weight = 5657.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.090892 restraints weight = 4302.944|
|-----------------------------------------------------------------------------|
r_work (final): 0.3294
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7175
moved from start:          0.3284

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   3345  Z= 0.283
  Angle     :  0.696   7.574   4559  Z= 0.364
  Chirality :  0.047   0.149    501
  Planarity :  0.006   0.060    584
  Dihedral  :  5.609  25.413    462
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 10.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.57 %
    Favored  : 88.43 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.59 (0.38), residues: 415
  helix: -5.22 (0.26), residues: 15
  sheet: -0.18 (0.53), residues: 104
  loop : -2.29 (0.33), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP H  55 
 HIS   0.006   0.001   HIS H 100 
 PHE   0.017   0.002   PHE L 102 
 TYR   0.011   0.002   TYR E 489 
 ARG   0.004   0.001   ARG H  40 

*********************** 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
  77 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.395 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   53 VAL cc_start: 0.5894 (t) cc_final: 0.5692 (t)
REVERT: L   87 ASP cc_start: 0.8557 (m-30) cc_final: 0.8295 (m-30)
REVERT: H   18 LEU cc_start: 0.7124 (mm) cc_final: 0.6846 (mm)
REVERT: H   29 LEU cc_start: 0.7852 (mm) cc_final: 0.7571 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 77
  average time/residue: 0.1450
  time to fit residues: 13.8452
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  : 0.389 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 18 optimal weight:    0.8980
   chunk 30 optimal weight:    0.8980
   chunk 39 optimal weight:    0.9980
   chunk 26 optimal weight:    0.4980
   chunk 22 optimal weight:    0.8980
   chunk 16 optimal weight:    0.7980
   chunk 24 optimal weight:    0.9990
   chunk 15 optimal weight:    2.9990
   chunk 28 optimal weight:    0.8980
   chunk 10 optimal weight:    0.1980
   chunk 13 optimal weight:    0.1980
   overall best weight:    0.5180

-------------------------------------------------------------------------------
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 = 0.3547 r_free = 0.3547 target = 0.105988 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.088060 restraints weight = 8317.511|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.090043 restraints weight = 5551.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.091472 restraints weight = 4144.347|
|-----------------------------------------------------------------------------|
r_work (final): 0.3303
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7170
moved from start:          0.3401

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   3345  Z= 0.233
  Angle     :  0.666   7.329   4559  Z= 0.346
  Chirality :  0.046   0.144    501
  Planarity :  0.005   0.055    584
  Dihedral  :  5.558  26.295    462
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 9.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.12 %
    Favored  : 89.88 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.47 (0.39), residues: 415
  helix: -4.65 (0.59), residues: 14
  sheet: -0.11 (0.53), residues: 104
  loop : -2.24 (0.33), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP E 436 
 HIS   0.002   0.001   HIS H  99 
 PHE   0.016   0.002   PHE L 102 
 TYR   0.011   0.001   TYR H  95 
 ARG   0.003   0.000   ARG H  60 

*********************** 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
  71 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 71
  time to evaluate  : 0.352 
Fit side-chains
   revert: symmetry clash
REVERT: L   53 VAL cc_start: 0.5985 (t) cc_final: 0.5716 (t)
REVERT: L   87 ASP cc_start: 0.8522 (m-30) cc_final: 0.8316 (m-30)
REVERT: H   18 LEU cc_start: 0.6950 (mm) cc_final: 0.6729 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 71
  average time/residue: 0.1487
  time to fit residues: 13.0962
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  : 0.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 15 optimal weight:    0.7980
   chunk 36 optimal weight:    0.0670
   chunk 17 optimal weight:    0.7980
   chunk 4 optimal weight:    0.9990
   chunk 37 optimal weight:    0.1980
   chunk 23 optimal weight:    0.8980
   chunk 19 optimal weight:    0.6980
   chunk 9 optimal weight:    0.6980
   chunk 25 optimal weight:    0.7980
   chunk 5 optimal weight:    0.9980
   chunk 8 optimal weight:    0.2980
   overall best weight:    0.3918

-------------------------------------------------------------------------------
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 = 0.3552 r_free = 0.3552 target = 0.106240 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.088339 restraints weight = 7989.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.090271 restraints weight = 5426.667|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.091676 restraints weight = 4083.603|
|-----------------------------------------------------------------------------|
r_work (final): 0.3306
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7147
moved from start:          0.3394

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3345  Z= 0.203
  Angle     :  0.647   5.678   4559  Z= 0.337
  Chirality :  0.046   0.159    501
  Planarity :  0.005   0.053    584
  Dihedral  :  5.412  24.924    462
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 9.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.40 %
    Favored  : 90.60 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.39 (0.39), residues: 415
  helix: -3.71 (1.16), residues: 14
  sheet: -0.04 (0.54), residues: 104
  loop : -2.24 (0.32), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP E 353 
 HIS   0.002   0.001   HIS H 100 
 PHE   0.013   0.001   PHE E 490 
 TYR   0.012   0.001   TYR E 489 
 ARG   0.003   0.000   ARG H  60 

*********************** 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
  71 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 71
  time to evaluate  : 0.349 
Fit side-chains
REVERT: H   18 LEU cc_start: 0.6931 (mm) cc_final: 0.6729 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 71
  average time/residue: 0.1407
  time to fit residues: 12.4498
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  : 0.401 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 6 optimal weight:    0.8980
   chunk 17 optimal weight:    1.9990
   chunk 2 optimal weight:    0.0870
   chunk 11 optimal weight:    0.5980
   chunk 26 optimal weight:    2.9990
   chunk 35 optimal weight:    1.9990
   chunk 27 optimal weight:    0.7980
   chunk 10 optimal weight:    0.0970
   chunk 16 optimal weight:    0.7980
   chunk 29 optimal weight:    2.9990
   chunk 39 optimal weight:    0.0980
   overall best weight:    0.3356

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.108107 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.090223 restraints weight = 7999.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.092244 restraints weight = 5341.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.093649 restraints weight = 3988.820|
|-----------------------------------------------------------------------------|
r_work (final): 0.3334
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7095
moved from start:          0.3504

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3345  Z= 0.198
  Angle     :  0.670   6.593   4559  Z= 0.344
  Chirality :  0.047   0.213    501
  Planarity :  0.005   0.049    584
  Dihedral  :  5.383  26.791    462
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 9.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.92 %
    Favored  : 91.08 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.24 (0.39), residues: 415
  helix: -3.70 (1.16), residues: 14
  sheet:  0.08 (0.55), residues: 104
  loop : -2.13 (0.33), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP E 436 
 HIS   0.002   0.001   HIS H 100 
 PHE   0.013   0.002   PHE L 102 
 TYR   0.011   0.001   TYR H  61 
 ARG   0.003   0.000   ARG H  60 

*********************** 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
  76 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 76
  time to evaluate  : 0.431 
Fit side-chains
REVERT: L   67 SER cc_start: 0.8626 (t) cc_final: 0.8392 (p)
REVERT: H    5 LYS cc_start: 0.8298 (tptp) cc_final: 0.7714 (tptp)
REVERT: H   18 LEU cc_start: 0.7014 (mm) cc_final: 0.6687 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 76
  average time/residue: 0.1428
  time to fit residues: 13.6409
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  : 0.401 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 3 optimal weight:    0.9980
   chunk 16 optimal weight:    0.8980
   chunk 29 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9990
   chunk 12 optimal weight:    0.7980
   chunk 31 optimal weight:    0.6980
   chunk 17 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9990
   chunk 13 optimal weight:    0.0470
   chunk 39 optimal weight:    0.0770
   chunk 1 optimal weight:    0.9990
   overall best weight:    0.5036

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.106149 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.087979 restraints weight = 8046.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.090014 restraints weight = 5239.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.091445 restraints weight = 3861.775|
|-----------------------------------------------------------------------------|
r_work (final): 0.3297
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7132
moved from start:          0.3627

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   3345  Z= 0.235
  Angle     :  0.671   7.641   4559  Z= 0.348
  Chirality :  0.048   0.193    501
  Planarity :  0.005   0.056    584
  Dihedral  :  5.492  27.316    462
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 9.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.33 %
    Favored  : 88.67 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.85 %
    Favored  : 99.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.33 (0.39), residues: 415
  helix: -3.76 (1.12), residues: 14
  sheet: -0.05 (0.54), residues: 104
  loop : -2.16 (0.33), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP H 109 
 HIS   0.003   0.001   HIS H 100 
 PHE   0.010   0.002   PHE E 490 
 TYR   0.012   0.001   TYR H  95 
 ARG   0.002   0.000   ARG H  60 

*********************** 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
  71 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 71
  time to evaluate  : 0.388 
Fit side-chains
REVERT: L   87 ASP cc_start: 0.8603 (m-30) cc_final: 0.8366 (m-30)
REVERT: H   18 LEU cc_start: 0.6998 (mm) cc_final: 0.6159 (mm)
REVERT: H   29 LEU cc_start: 0.8087 (mm) cc_final: 0.7866 (mp)
REVERT: H   84 MET cc_start: 0.7434 (ptm) cc_final: 0.6697 (ptm)
REVERT: H   87 MET cc_start: 0.4793 (tpt) cc_final: 0.4026 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 71
  average time/residue: 0.1405
  time to fit residues: 12.5196
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  : 0.383 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 13 optimal weight:    0.5980
   chunk 26 optimal weight:    0.9980
   chunk 15 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9990
   chunk 16 optimal weight:    0.4980
   chunk 18 optimal weight:    0.9990
   chunk 22 optimal weight:    3.9990
   chunk 20 optimal weight:    0.8980
   chunk 33 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9980
   chunk 34 optimal weight:    0.7980
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.104196 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.086585 restraints weight = 8002.965|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.088294 restraints weight = 5546.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.089517 restraints weight = 4279.974|
|-----------------------------------------------------------------------------|
r_work (final): 0.3269
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7223
moved from start:          0.3945

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   3345  Z= 0.316
  Angle     :  0.751   9.730   4559  Z= 0.388
  Chirality :  0.050   0.184    501
  Planarity :  0.006   0.063    584
  Dihedral  :  5.878  28.738    462
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 11.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.29 %
    Favored  : 87.71 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.47 (0.39), residues: 415
  helix: -3.68 (1.17), residues: 14
  sheet: -0.11 (0.53), residues: 104
  loop : -2.30 (0.33), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP H  55 
 HIS   0.002   0.001   HIS H 100 
 PHE   0.011   0.002   PHE E 400 
 TYR   0.015   0.002   TYR H 104 
 ARG   0.003   0.000   ARG H  40 

********************** 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
  66 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 66
  time to evaluate  : 0.332 
Fit side-chains
   revert: symmetry clash
REVERT: L   87 ASP cc_start: 0.8551 (m-30) cc_final: 0.8301 (m-30)
REVERT: H   18 LEU cc_start: 0.6602 (mm) cc_final: 0.6326 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 66
  average time/residue: 0.1367
  time to fit residues: 11.3641
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  : 0.357 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 38 optimal weight:    2.9990
   chunk 6 optimal weight:    0.3980
   chunk 37 optimal weight:    0.9980
   chunk 35 optimal weight:    0.9990
   chunk 39 optimal weight:    0.7980
   chunk 16 optimal weight:    0.9980
   chunk 24 optimal weight:    0.0970
   chunk 18 optimal weight:    0.9990
   chunk 4 optimal weight:    0.0970
   chunk 3 optimal weight:    0.4980
   chunk 14 optimal weight:    0.8980
   overall best weight:    0.3776

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.106890 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.088760 restraints weight = 7836.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.090716 restraints weight = 5278.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.092059 restraints weight = 3968.250|
|-----------------------------------------------------------------------------|
r_work (final): 0.3308
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7142
moved from start:          0.3859

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3345  Z= 0.206
  Angle     :  0.665   7.929   4559  Z= 0.342
  Chirality :  0.046   0.159    501
  Planarity :  0.005   0.057    584
  Dihedral  :  5.430  25.449    462
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 9.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.36 %
    Favored  : 89.64 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.85 %
    Favored  : 99.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.32 (0.40), residues: 415
  helix: -3.61 (1.21), residues: 14
  sheet: -0.09 (0.53), residues: 104
  loop : -2.15 (0.34), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP L  37 
 HIS   0.001   0.001   HIS H 100 
 PHE   0.009   0.002   PHE L 102 
 TYR   0.011   0.001   TYR H 104 
 ARG   0.003   0.000   ARG H  60 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1515.19 seconds
wall clock time: 26 minutes 59.43 seconds (1619.43 seconds total)