Starting phenix.real_space_refine
on Fri Aug 22 13:16:35 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xv2_38691/08_2025/8xv2_38691.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xv2_38691/08_2025/8xv2_38691.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xv2_38691/08_2025/8xv2_38691.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xv2_38691/08_2025/8xv2_38691.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xv2_38691/08_2025/8xv2_38691.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xv2_38691/08_2025/8xv2_38691.map"
  }
  resolution = 3.7
  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=   0.017
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      17      5.16       5
     C    2112      2.51       5
     N     470      2.21       5
     O     529      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3128
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3110
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 388, 3110
          Classifications: {'peptide': 388}
          Link IDs: {'PTRANS': 14, 'TRANS': 373}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 18
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 18
          Unusual residues: {'VIB': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.04, per 1000 atoms: 0.33
  Number of scatterers: 3128
  At special positions: 0
  Unit cell: (69.55, 58.85, 79.18, 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      17     16.00
     O     529      8.00
     N     470      7.00
     C    2112      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.28
  Conformation dependent library (CDL) restraints added in 117.0 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  736

  Finding SS restraints...
    Secondary structure from input PDB file:
      18 helices and 0 sheets defined
      84.5% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.10
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 28
    Processing helix  chain 'A' and resid 34 through 40
    Processing helix  chain 'A' and resid 47 through 55
      removed outlier: 3.880A  pdb=" N   ILE A  55 " --> pdb=" O   ILE A  51 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 56 through 66
      removed outlier: 4.013A  pdb=" N   THR A  60 " --> pdb=" O   PHE A  56 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   LEU A  66 " --> pdb=" O   SER A  62 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 67 through 76
      removed outlier: 3.532A  pdb=" N   PHE A  71 " --> pdb=" O   LEU A  67 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   VAL A  72 " --> pdb=" O   LEU A  68 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   TYR A  76 " --> pdb=" O   VAL A  72 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 80 through 100
    Processing helix  chain 'A' and resid 104 through 126
      removed outlier: 3.540A  pdb=" N   VAL A 108 " --> pdb=" O   LYS A 104 " (cutoff:3.500A)
      removed outlier: 4.508A  pdb=" N   VAL A 121 " --> pdb=" O   THR A 117 " (cutoff:3.500A)
      removed outlier: 4.377A  pdb=" N   ALA A 122 " --> pdb=" O   ALA A 118 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 126 through 131
    Processing helix  chain 'A' and resid 132 through 134
      No H-bonds generated for 'chain 'A' and resid 132 through 134'
    Processing helix  chain 'A' and resid 135 through 166
      removed outlier: 4.002A  pdb=" N   SER A 140 " --> pdb=" O   TYR A 136 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   ASN A 166 " --> pdb=" O   VAL A 162 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 168 through 188
      removed outlier: 3.644A  pdb=" N   LEU A 172 " --> pdb=" O   SER A 168 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   LEU A 188 " --> pdb=" O   PHE A 184 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 268 through 273
      removed outlier: 3.587A  pdb=" N   CYS A 272 " --> pdb=" O   ASP A 268 " (cutoff:3.500A)
      removed outlier: 4.015A  pdb=" N   TYR A 273 " --> pdb=" O   LEU A 269 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 268 through 273'
    Processing helix  chain 'A' and resid 275 through 307
      removed outlier: 4.500A  pdb=" N   TYR A 280 " --> pdb=" O   LYS A 276 " (cutoff:3.500A)
      removed outlier: 5.411A  pdb=" N   TRP A 281 " --> pdb=" O   ARG A 277 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   SER A 282 " --> pdb=" O   LEU A 278 " (cutoff:3.500A)
      removed outlier: 5.408A  pdb=" N   GLN A 300 " --> pdb=" O   LEU A 296 " (cutoff:3.500A)
      removed outlier: 4.930A  pdb=" N   ILE A 301 " --> pdb=" O   ASN A 297 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 315 through 335
      removed outlier: 3.993A  pdb=" N   GLY A 335 " --> pdb=" O   ALA A 331 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 340 through 366
      removed outlier: 4.167A  pdb=" N   GLU A 346 " --> pdb=" O   ASP A 342 " (cutoff:3.500A)
      removed outlier: 4.434A  pdb=" N   LEU A 347 " --> pdb=" O   LEU A 343 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   LEU A 349 " --> pdb=" O   GLY A 345 " (cutoff:3.500A)
      removed outlier: 5.008A  pdb=" N   VAL A 350 " --> pdb=" O   GLU A 346 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   PHE A 352 " --> pdb=" O   ALA A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 368 through 396
      removed outlier: 3.914A  pdb=" N   VAL A 396 " --> pdb=" O   PHE A 392 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 400 through 426
      removed outlier: 3.571A  pdb=" N   ALA A 404 " --> pdb=" O   VAL A 400 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   LEU A 405 " --> pdb=" O   GLU A 401 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 434 through 458
      removed outlier: 3.621A  pdb=" N   GLN A 438 " --> pdb=" O   PRO A 434 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   PHE A 439 " --> pdb=" O   VAL A 435 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   LEU A 440 " --> pdb=" O   SER A 436 " (cutoff:3.500A)

    225 hydrogen bonds defined for protein.
    675 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: 0.49

  Time building geometry restraints manager: 0.36 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 885
        1.34 -     1.46: 853
        1.46 -     1.58: 1459
        1.58 -     1.69: 0
        1.69 -     1.81: 28
  Bond restraints: 3225
  Sorted by residual:
  bond pdb=" C5  VIB A 501 "
       pdb=" S1  VIB A 501 "
    ideal  model  delta    sigma   weight residual
    1.721  1.507  0.214 2.00e-02 2.50e+03 1.14e+02
  bond pdb=" C2  VIB A 501 "
       pdb=" S1  VIB A 501 "
    ideal  model  delta    sigma   weight residual
    1.670  1.541  0.129 2.00e-02 2.50e+03 4.16e+01
  bond pdb=" C2  VIB A 501 "
       pdb=" N3  VIB A 501 "
    ideal  model  delta    sigma   weight residual
    1.315  1.420 -0.105 2.00e-02 2.50e+03 2.78e+01
  bond pdb=" C4A VIB A 501 "
       pdb=" N4A VIB A 501 "
    ideal  model  delta    sigma   weight residual
    1.347  1.449 -0.102 2.00e-02 2.50e+03 2.60e+01
  bond pdb=" C4  VIB A 501 "
       pdb=" C5  VIB A 501 "
    ideal  model  delta    sigma   weight residual
    1.358  1.446 -0.088 2.00e-02 2.50e+03 1.92e+01
  ... (remaining 3220 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.49: 4279
        2.49 -     4.98: 102
        4.98 -     7.47: 18
        7.47 -     9.95: 4
        9.95 -    12.44: 3
  Bond angle restraints: 4406
  Sorted by residual:
  angle pdb=" C2  VIB A 501 "
        pdb=" S1  VIB A 501 "
        pdb=" C5  VIB A 501 "
      ideal   model   delta    sigma   weight residual
      91.25  103.69  -12.44 3.00e+00 1.11e-01 1.72e+01
  angle pdb=" C   VAL A  77 "
        pdb=" N   ARG A  78 "
        pdb=" CA  ARG A  78 "
      ideal   model   delta    sigma   weight residual
     122.46  127.56   -5.10 1.41e+00 5.03e-01 1.31e+01
  angle pdb=" C6A VIB A 501 "
        pdb=" C5A VIB A 501 "
        pdb=" C7A VIB A 501 "
      ideal   model   delta    sigma   weight residual
     121.49  111.43   10.06 3.00e+00 1.11e-01 1.13e+01
  angle pdb=" CA  TRP A 284 "
        pdb=" CB  TRP A 284 "
        pdb=" CG  TRP A 284 "
      ideal   model   delta    sigma   weight residual
     113.60  107.61    5.99 1.90e+00 2.77e-01 9.96e+00
  angle pdb=" N   PHE A  56 "
        pdb=" CA  PHE A  56 "
        pdb=" C   PHE A  56 "
      ideal   model   delta    sigma   weight residual
     113.16  117.60   -4.44 1.42e+00 4.96e-01 9.77e+00
  ... (remaining 4401 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.74: 1716
       14.74 -    29.47: 87
       29.47 -    44.20: 16
       44.20 -    58.94: 0
       58.94 -    73.67: 2
  Dihedral angle restraints: 1821
    sinusoidal: 669
      harmonic: 1152
  Sorted by residual:
  dihedral pdb=" CA  ARG A  78 "
           pdb=" C   ARG A  78 "
           pdb=" N   TYR A  79 "
           pdb=" CA  TYR A  79 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.93   23.07     0      5.00e+00 4.00e-02 2.13e+01
  dihedral pdb=" CA  TRP A  12 "
           pdb=" C   TRP A  12 "
           pdb=" N   ILE A  13 "
           pdb=" CA  ILE A  13 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.74  -20.26     0      5.00e+00 4.00e-02 1.64e+01
  dihedral pdb=" CA  VAL A 426 "
           pdb=" C   VAL A 426 "
           pdb=" N   ASP A 427 "
           pdb=" CA  ASP A 427 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.73  -19.27     0      5.00e+00 4.00e-02 1.48e+01
  ... (remaining 1818 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 285
       0.040 -    0.081: 156
       0.081 -    0.121: 42
       0.121 -    0.161: 12
       0.161 -    0.202: 7
  Chirality restraints: 502
  Sorted by residual:
  chirality pdb=" CA  PHE A  56 "
            pdb=" N   PHE A  56 "
            pdb=" C   PHE A  56 "
            pdb=" CB  PHE A  56 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 1.02e+00
  chirality pdb=" CB  VAL A 435 "
            pdb=" CA  VAL A 435 "
            pdb=" CG1 VAL A 435 "
            pdb=" CG2 VAL A 435 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.43   -0.20 2.00e-01 2.50e+01 9.56e-01
  chirality pdb=" CA  TRP A  94 "
            pdb=" N   TRP A  94 "
            pdb=" C   TRP A  94 "
            pdb=" CB  TRP A  94 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 9.39e-01
  ... (remaining 499 not shown)

  Planarity restraints: 528
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A  63 "    0.020 2.00e-02 2.50e+03   2.31e-02 1.07e+01
        pdb=" CG  TYR A  63 "   -0.057 2.00e-02 2.50e+03
        pdb=" CD1 TYR A  63 "    0.022 2.00e-02 2.50e+03
        pdb=" CD2 TYR A  63 "    0.011 2.00e-02 2.50e+03
        pdb=" CE1 TYR A  63 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE2 TYR A  63 "    0.007 2.00e-02 2.50e+03
        pdb=" CZ  TYR A  63 "    0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR A  63 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 373 "    0.025 2.00e-02 2.50e+03   2.04e-02 8.35e+00
        pdb=" CG  TYR A 373 "   -0.050 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 373 "    0.010 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 373 "    0.004 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 373 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 373 "    0.007 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 373 "    0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR A 373 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR A  61 "    0.013 2.00e-02 2.50e+03   2.54e-02 6.43e+00
        pdb=" C   TYR A  61 "   -0.044 2.00e-02 2.50e+03
        pdb=" O   TYR A  61 "    0.016 2.00e-02 2.50e+03
        pdb=" N   SER A  62 "    0.015 2.00e-02 2.50e+03
  ... (remaining 525 not shown)

  Histogram of nonbonded interaction distances:
        2.32 -     2.83: 1027
        2.83 -     3.35: 3005
        3.35 -     3.87: 5221
        3.87 -     4.38: 5967
        4.38 -     4.90: 10133
  Nonbonded interactions: 25353
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 151 "
            pdb=" OE2 GLU A 320 "
     model   vdw
     2.318 3.040
  nonbonded pdb=" O   GLN A 418 "
            pdb=" OG1 THR A 422 "
     model   vdw
     2.371 3.040
  nonbonded pdb=" OE2 GLU A  54 "
            pdb=" NE2 GLN A 428 "
     model   vdw
     2.382 3.120
  nonbonded pdb=" NE2 GLN A 294 "
            pdb=" OG1 THR A 422 "
     model   vdw
     2.386 3.120
  nonbonded pdb=" ND2 ASN A  53 "
            pdb=" O   LEU A 433 "
     model   vdw
     2.414 3.120
  ... (remaining 25348 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== 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:             1.330
  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:          0.050
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     5.320
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.000
  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:1.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.060
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7224
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.214   3225  Z= 0.408
  Angle     :  0.986  12.443   4406  Z= 0.506
  Chirality :  0.056   0.202    502
  Planarity :  0.008   0.053    528
  Dihedral  :  9.841  73.672   1085
  Min Nonbonded Distance : 2.318

Molprobity Statistics.
  All-atom Clashscore : 2.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.21 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  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 aren not related in a simple way.
  whole: -3.54 (0.33), residues: 384
  helix: -1.92 (0.23), residues: 282
  sheet:  None (None), residues: 0
  loop : -3.09 (0.54), residues: 102

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  29 
 TYR   0.057   0.004   TYR A  63 
 PHE   0.028   0.003   PHE A 439 
 TRP   0.040   0.003   TRP A 284 
 HIS   0.003   0.001   HIS A 200 

Details of bonding type rmsd
  covalent geometry    : bond        0.00850 ( 3225)
  covalent geometry    : angle       0.98591 ( 4406)
  hydrogen bonds       : bond        0.14356 (  225)
  hydrogen bonds       : angle       6.77629 (  675)

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

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

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 122
  time to evaluate  : 0.090 
Fit side-chains
   revert: symmetry clash
REVERT: A   34 PHE cc_start: 0.7993 (m-80) cc_final: 0.7793 (m-10)
REVERT: A   61 TYR cc_start: 0.7845 (m-10) cc_final: 0.7555 (m-80)
REVERT: A   73 LEU cc_start: 0.7463 (tp) cc_final: 0.7263 (tp)
REVERT: A   91 ILE cc_start: 0.8298 (mt) cc_final: 0.8070 (mm)
REVERT: A   98 LEU cc_start: 0.8166 (mt) cc_final: 0.7797 (mm)
REVERT: A  105 THR cc_start: 0.7228 (p) cc_final: 0.6995 (p)
REVERT: A  113 TYR cc_start: 0.7811 (t80) cc_final: 0.7598 (t80)
REVERT: A  159 GLN cc_start: 0.6641 (tm-30) cc_final: 0.6208 (tm-30)
REVERT: A  160 LEU cc_start: 0.7459 (mt) cc_final: 0.7219 (tp)
REVERT: A  161 LEU cc_start: 0.7954 (mt) cc_final: 0.7639 (tp)
REVERT: A  167 MET cc_start: 0.6672 (ttm) cc_final: 0.6041 (ttm)
REVERT: A  175 ILE cc_start: 0.8539 (mt) cc_final: 0.8178 (mp)
REVERT: A  176 SER cc_start: 0.8290 (m) cc_final: 0.7665 (p)
REVERT: A  198 PHE cc_start: 0.8204 (m-80) cc_final: 0.7754 (m-80)
REVERT: A  283 LEU cc_start: 0.7909 (tp) cc_final: 0.7682 (tp)
REVERT: A  300 GLN cc_start: 0.8328 (mt0) cc_final: 0.8091 (mt0)
REVERT: A  325 PHE cc_start: 0.8449 (t80) cc_final: 0.8103 (t80)
REVERT: A  361 PHE cc_start: 0.7886 (m-10) cc_final: 0.7586 (m-80)
REVERT: A  363 MET cc_start: 0.6951 (mtm) cc_final: 0.6643 (mtm)
REVERT: A  384 MET cc_start: 0.7864 (tpp) cc_final: 0.7482 (tpt)
REVERT: A  387 ILE cc_start: 0.8227 (tp) cc_final: 0.7806 (tp)
REVERT: A  403 TYR cc_start: 0.7903 (t80) cc_final: 0.7683 (t80)
REVERT: A  406 VAL cc_start: 0.7813 (t) cc_final: 0.6833 (p)
REVERT: A  410 ASN cc_start: 0.7593 (m-40) cc_final: 0.7231 (m-40)
REVERT: A  418 GLN cc_start: 0.8140 (tt0) cc_final: 0.7904 (tt0)
REVERT: A  425 VAL cc_start: 0.8383 (t) cc_final: 0.8162 (p)
REVERT: A  432 ASN cc_start: 0.7278 (t0) cc_final: 0.7034 (t0)
REVERT: A  438 GLN cc_start: 0.7665 (mt0) cc_final: 0.7374 (mt0)
  outliers start: 0
  outliers final: 0
  residues processed: 122
  average time/residue: 0.0421
  time to fit residues: 6.7876
Evaluate side-chains
  104 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.128 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 24 optimal weight:    0.9990
   chunk 26 optimal weight:    2.9990
   chunk 2 optimal weight:    0.8980
   chunk 16 optimal weight:    0.5980
   chunk 32 optimal weight:    2.9990
   chunk 31 optimal weight:    0.5980
   chunk 25 optimal weight:    1.9990
   chunk 19 optimal weight:    0.6980
   chunk 30 optimal weight:    0.9980
   chunk 22 optimal weight:    0.5980
   chunk 37 optimal weight:    0.9980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A  86 GLN
A 200 HIS
** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 397 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.113568 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.099234 restraints weight = 5725.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.102594 restraints weight = 2804.527|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.104761 restraints weight = 1667.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.106046 restraints weight = 1133.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.107024 restraints weight = 870.382|
|-----------------------------------------------------------------------------|
r_work (final): 0.3373
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7236
moved from start:          0.1983

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   3225  Z= 0.206
  Angle     :  0.644   6.803   4406  Z= 0.345
  Chirality :  0.045   0.150    502
  Planarity :  0.005   0.045    528
  Dihedral  :  6.943  67.571    428
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 9.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 12.31 %
    Favored  : 85.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.69 (0.40), residues: 384
  helix:  0.21 (0.28), residues: 288
  sheet:  None (None), residues: 0
  loop : -2.33 (0.60), residues: 96

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  78 
 TYR   0.023   0.002   TYR A  63 
 PHE   0.017   0.002   PHE A 439 
 TRP   0.026   0.002   TRP A 284 
 HIS   0.005   0.002   HIS A 364 

Details of bonding type rmsd
  covalent geometry    : bond        0.00423 ( 3225)
  covalent geometry    : angle       0.64423 ( 4406)
  hydrogen bonds       : bond        0.05092 (  225)
  hydrogen bonds       : angle       4.54619 (  675)

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

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

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 113
  time to evaluate  : 0.113 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 PHE cc_start: 0.7971 (m-80) cc_final: 0.7683 (m-10)
REVERT: A   52 THR cc_start: 0.8094 (m) cc_final: 0.7687 (p)
REVERT: A   73 LEU cc_start: 0.7832 (tp) cc_final: 0.7347 (tp)
REVERT: A   86 GLN cc_start: 0.8198 (tt0) cc_final: 0.7742 (tt0)
REVERT: A   89 SER cc_start: 0.8118 (m) cc_final: 0.7810 (p)
REVERT: A   90 PHE cc_start: 0.7445 (m-80) cc_final: 0.7221 (m-80)
REVERT: A   98 LEU cc_start: 0.8294 (mt) cc_final: 0.7912 (mm)
REVERT: A  156 VAL cc_start: 0.8205 (OUTLIER) cc_final: 0.7987 (m)
REVERT: A  161 LEU cc_start: 0.8150 (mt) cc_final: 0.7806 (tp)
REVERT: A  167 MET cc_start: 0.6790 (ttm) cc_final: 0.6038 (ttm)
REVERT: A  283 LEU cc_start: 0.7919 (tp) cc_final: 0.7699 (tp)
REVERT: A  300 GLN cc_start: 0.8321 (mt0) cc_final: 0.8112 (mt0)
REVERT: A  325 PHE cc_start: 0.8469 (t80) cc_final: 0.8264 (t80)
REVERT: A  361 PHE cc_start: 0.7882 (m-10) cc_final: 0.7607 (m-80)
REVERT: A  384 MET cc_start: 0.7959 (tpp) cc_final: 0.7721 (mmm)
REVERT: A  387 ILE cc_start: 0.8080 (tp) cc_final: 0.7779 (tp)
REVERT: A  406 VAL cc_start: 0.7804 (t) cc_final: 0.6869 (p)
REVERT: A  410 ASN cc_start: 0.7633 (m-40) cc_final: 0.7273 (m-40)
REVERT: A  431 LEU cc_start: 0.7587 (mt) cc_final: 0.7368 (mt)
REVERT: A  432 ASN cc_start: 0.7501 (t0) cc_final: 0.7174 (t0)
REVERT: A  433 LEU cc_start: 0.8203 (mt) cc_final: 0.7824 (mt)
  outliers start: 8
  outliers final: 4
  residues processed: 116
  average time/residue: 0.0429
  time to fit residues: 6.4942
Evaluate side-chains
  119 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 114
  time to evaluate  : 0.100 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 ILE
Chi-restraints excluded: chain A residue   88 ILE
Chi-restraints excluded: chain A residue  156 VAL
Chi-restraints excluded: chain A residue  420 ILE
Chi-restraints excluded: chain A residue  449 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 18 optimal weight:    0.1980
   chunk 9 optimal weight:    1.9990
   chunk 32 optimal weight:    3.9990
   chunk 8 optimal weight:    0.9980
   chunk 7 optimal weight:    0.7980
   chunk 21 optimal weight:    0.6980
   chunk 0 optimal weight:    0.9990
   chunk 20 optimal weight:    0.7980
   chunk 37 optimal weight:    0.6980
   chunk 4 optimal weight:    0.0970
   chunk 5 optimal weight:    0.5980
   overall best weight:    0.4578

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

Flipped N/Q/H residues before XYZ refinement:
A 418 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.114110 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.099620 restraints weight = 5652.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.102966 restraints weight = 2779.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.105102 restraints weight = 1660.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.106493 restraints weight = 1139.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.107376 restraints weight = 861.385|
|-----------------------------------------------------------------------------|
r_work (final): 0.3378
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7220
moved from start:          0.2692

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3225  Z= 0.157
  Angle     :  0.588   7.142   4406  Z= 0.310
  Chirality :  0.043   0.134    502
  Planarity :  0.004   0.044    528
  Dihedral  :  6.655  65.064    428
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 9.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 15.32 %
    Favored  : 81.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.59 (0.42), residues: 384
  helix:  1.20 (0.29), residues: 286
  sheet:  None (None), residues: 0
  loop : -2.03 (0.60), residues: 98

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  78 
 TYR   0.018   0.002   TYR A  63 
 PHE   0.016   0.002   PHE A  99 
 TRP   0.022   0.001   TRP A 284 
 HIS   0.005   0.001   HIS A 364 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 3225)
  covalent geometry    : angle       0.58789 ( 4406)
  hydrogen bonds       : bond        0.04638 (  225)
  hydrogen bonds       : angle       4.16578 (  675)

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

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

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 116
  time to evaluate  : 0.071 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 PHE cc_start: 0.8081 (m-80) cc_final: 0.7757 (m-10)
REVERT: A   52 THR cc_start: 0.7967 (m) cc_final: 0.7573 (p)
REVERT: A   73 LEU cc_start: 0.7836 (tp) cc_final: 0.7622 (tp)
REVERT: A   86 GLN cc_start: 0.8180 (tt0) cc_final: 0.7703 (tt0)
REVERT: A   89 SER cc_start: 0.8103 (m) cc_final: 0.7794 (p)
REVERT: A  161 LEU cc_start: 0.8189 (mt) cc_final: 0.7740 (tp)
REVERT: A  167 MET cc_start: 0.6827 (ttm) cc_final: 0.6086 (ttm)
REVERT: A  283 LEU cc_start: 0.7910 (tp) cc_final: 0.7664 (tp)
REVERT: A  325 PHE cc_start: 0.8433 (t80) cc_final: 0.8185 (t80)
REVERT: A  361 PHE cc_start: 0.7873 (m-10) cc_final: 0.7625 (m-80)
REVERT: A  385 LEU cc_start: 0.8127 (tt) cc_final: 0.7820 (tp)
REVERT: A  387 ILE cc_start: 0.8028 (tp) cc_final: 0.7692 (tp)
REVERT: A  406 VAL cc_start: 0.7814 (t) cc_final: 0.6803 (p)
REVERT: A  407 PHE cc_start: 0.7830 (OUTLIER) cc_final: 0.7544 (m-80)
REVERT: A  410 ASN cc_start: 0.7658 (m-40) cc_final: 0.7239 (m-40)
REVERT: A  431 LEU cc_start: 0.7600 (mt) cc_final: 0.7342 (mt)
REVERT: A  432 ASN cc_start: 0.7610 (t0) cc_final: 0.7258 (t0)
REVERT: A  433 LEU cc_start: 0.8165 (mt) cc_final: 0.7782 (mt)
  outliers start: 9
  outliers final: 3
  residues processed: 119
  average time/residue: 0.0408
  time to fit residues: 6.3820
Evaluate side-chains
  117 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 113
  time to evaluate  : 0.112 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 ASP
Chi-restraints excluded: chain A residue  188 LEU
Chi-restraints excluded: chain A residue  401 GLU
Chi-restraints excluded: chain A residue  407 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 3 optimal weight:    0.8980
   chunk 26 optimal weight:    1.9990
   chunk 19 optimal weight:    0.0370
   chunk 28 optimal weight:    2.9990
   chunk 21 optimal weight:    0.6980
   chunk 1 optimal weight:    0.9980
   chunk 35 optimal weight:    0.9990
   chunk 24 optimal weight:    0.7980
   chunk 6 optimal weight:    0.0270
   chunk 17 optimal weight:    0.5980
   chunk 2 optimal weight:    0.6980
   overall best weight:    0.4116

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

Flipped N/Q/H residues before XYZ refinement:
A 300 GLN
** A 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.113824 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.099227 restraints weight = 5625.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.102553 restraints weight = 2792.545|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.104716 restraints weight = 1670.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.106005 restraints weight = 1143.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.106997 restraints weight = 881.339|
|-----------------------------------------------------------------------------|
r_work (final): 0.3371
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7214
moved from start:          0.3056

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3225  Z= 0.149
  Angle     :  0.582   6.394   4406  Z= 0.310
  Chirality :  0.042   0.138    502
  Planarity :  0.004   0.043    528
  Dihedral  :  6.379  62.654    428
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 9.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 20.12 %
    Favored  : 78.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.18 (0.42), residues: 384
  helix:  1.61 (0.30), residues: 288
  sheet:  None (None), residues: 0
  loop : -1.81 (0.60), residues: 96

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  78 
 TYR   0.016   0.002   TYR A 383 
 PHE   0.019   0.001   PHE A  99 
 TRP   0.020   0.001   TRP A 284 
 HIS   0.005   0.001   HIS A 364 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 3225)
  covalent geometry    : angle       0.58227 ( 4406)
  hydrogen bonds       : bond        0.04546 (  225)
  hydrogen bonds       : angle       4.06345 (  675)

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

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

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 110
  time to evaluate  : 0.092 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 THR cc_start: 0.7966 (m) cc_final: 0.7612 (p)
REVERT: A   73 LEU cc_start: 0.7968 (tp) cc_final: 0.7666 (tp)
REVERT: A   89 SER cc_start: 0.8046 (m) cc_final: 0.7778 (p)
REVERT: A  161 LEU cc_start: 0.8186 (mt) cc_final: 0.7710 (tp)
REVERT: A  167 MET cc_start: 0.6808 (ttm) cc_final: 0.5992 (ttm)
REVERT: A  283 LEU cc_start: 0.7881 (tp) cc_final: 0.7667 (tp)
REVERT: A  325 PHE cc_start: 0.8431 (t80) cc_final: 0.8184 (t80)
REVERT: A  361 PHE cc_start: 0.7858 (m-10) cc_final: 0.7631 (m-80)
REVERT: A  376 TYR cc_start: 0.8683 (t80) cc_final: 0.8356 (t80)
REVERT: A  380 LYS cc_start: 0.8422 (tttt) cc_final: 0.8165 (ttmm)
REVERT: A  385 LEU cc_start: 0.8042 (tt) cc_final: 0.7788 (tp)
REVERT: A  387 ILE cc_start: 0.8020 (tp) cc_final: 0.7678 (tp)
REVERT: A  406 VAL cc_start: 0.7818 (t) cc_final: 0.6804 (p)
REVERT: A  407 PHE cc_start: 0.7853 (OUTLIER) cc_final: 0.7546 (m-80)
REVERT: A  410 ASN cc_start: 0.7580 (m-40) cc_final: 0.7178 (m-40)
REVERT: A  418 GLN cc_start: 0.7878 (tt0) cc_final: 0.7586 (tt0)
REVERT: A  419 THR cc_start: 0.8290 (OUTLIER) cc_final: 0.7863 (p)
REVERT: A  431 LEU cc_start: 0.7539 (mt) cc_final: 0.7292 (mt)
REVERT: A  432 ASN cc_start: 0.7641 (t0) cc_final: 0.7313 (t0)
REVERT: A  433 LEU cc_start: 0.8145 (mt) cc_final: 0.7751 (mt)
  outliers start: 5
  outliers final: 3
  residues processed: 111
  average time/residue: 0.0466
  time to fit residues: 6.7130
Evaluate side-chains
  115 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 110
  time to evaluate  : 0.111 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 ASP
Chi-restraints excluded: chain A residue  160 LEU
Chi-restraints excluded: chain A residue  300 GLN
Chi-restraints excluded: chain A residue  407 PHE
Chi-restraints excluded: chain A residue  419 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 20 optimal weight:    0.0570
   chunk 30 optimal weight:    0.3980
   chunk 3 optimal weight:    0.0670
   chunk 31 optimal weight:    0.6980
   chunk 8 optimal weight:    0.8980
   chunk 22 optimal weight:    0.9980
   chunk 29 optimal weight:    0.5980
   chunk 5 optimal weight:    0.5980
   chunk 12 optimal weight:    5.9990
   chunk 37 optimal weight:    0.5980
   chunk 0 optimal weight:    0.9990
   overall best weight:    0.3436

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

Flipped N/Q/H residues before XYZ refinement:
A 173 ASN
A 294 GLN
A 300 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.114836 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.100275 restraints weight = 5679.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.103631 restraints weight = 2807.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.105772 restraints weight = 1678.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.107156 restraints weight = 1150.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.107944 restraints weight = 875.675|
|-----------------------------------------------------------------------------|
r_work (final): 0.3387
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7206
moved from start:          0.3272

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   3225  Z= 0.138
  Angle     :  0.575   7.063   4406  Z= 0.304
  Chirality :  0.041   0.129    502
  Planarity :  0.004   0.042    528
  Dihedral  :  6.113  58.288    428
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 9.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 18.62 %
    Favored  : 78.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.44 (0.43), residues: 384
  helix:  1.70 (0.30), residues: 293
  sheet:  None (None), residues: 0
  loop : -1.54 (0.63), residues: 91

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  78 
 TYR   0.015   0.002   TYR A 383 
 PHE   0.020   0.001   PHE A  99 
 TRP   0.018   0.001   TRP A 284 
 HIS   0.005   0.001   HIS A 364 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 3225)
  covalent geometry    : angle       0.57536 ( 4406)
  hydrogen bonds       : bond        0.04515 (  225)
  hydrogen bonds       : angle       3.95142 (  675)

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

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

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 108
  time to evaluate  : 0.139 
Fit side-chains
   revert: symmetry clash
REVERT: A   33 PRO cc_start: 0.8306 (Cg_exo) cc_final: 0.8078 (Cg_endo)
REVERT: A   52 THR cc_start: 0.7965 (m) cc_final: 0.7636 (p)
REVERT: A   59 TRP cc_start: 0.8381 (t60) cc_final: 0.7495 (t60)
REVERT: A   73 LEU cc_start: 0.8018 (tp) cc_final: 0.7779 (tp)
REVERT: A   81 PRO cc_start: 0.8208 (Cg_exo) cc_final: 0.7985 (Cg_endo)
REVERT: A   89 SER cc_start: 0.8045 (m) cc_final: 0.7800 (p)
REVERT: A  161 LEU cc_start: 0.8204 (mt) cc_final: 0.7747 (tp)
REVERT: A  167 MET cc_start: 0.6730 (ttm) cc_final: 0.5933 (ttm)
REVERT: A  283 LEU cc_start: 0.7881 (tp) cc_final: 0.7677 (tp)
REVERT: A  325 PHE cc_start: 0.8378 (t80) cc_final: 0.8164 (t80)
REVERT: A  361 PHE cc_start: 0.7864 (m-10) cc_final: 0.7628 (m-80)
REVERT: A  363 MET cc_start: 0.7206 (mtm) cc_final: 0.6905 (mtm)
REVERT: A  380 LYS cc_start: 0.8403 (tttt) cc_final: 0.8153 (ttmm)
REVERT: A  387 ILE cc_start: 0.8022 (tp) cc_final: 0.7665 (tp)
REVERT: A  406 VAL cc_start: 0.7828 (t) cc_final: 0.6811 (p)
REVERT: A  407 PHE cc_start: 0.7846 (OUTLIER) cc_final: 0.7536 (m-80)
REVERT: A  410 ASN cc_start: 0.7597 (m-40) cc_final: 0.7177 (m-40)
REVERT: A  418 GLN cc_start: 0.7763 (tt0) cc_final: 0.7520 (tt0)
REVERT: A  419 THR cc_start: 0.8264 (OUTLIER) cc_final: 0.7859 (p)
REVERT: A  431 LEU cc_start: 0.7506 (mt) cc_final: 0.7257 (mt)
REVERT: A  432 ASN cc_start: 0.7612 (t0) cc_final: 0.7295 (t0)
REVERT: A  433 LEU cc_start: 0.8190 (mt) cc_final: 0.7874 (mt)
  outliers start: 10
  outliers final: 6
  residues processed: 111
  average time/residue: 0.0421
  time to fit residues: 6.1312
Evaluate side-chains
  116 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 108
  time to evaluate  : 0.099 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 ASP
Chi-restraints excluded: chain A residue  160 LEU
Chi-restraints excluded: chain A residue  173 ASN
Chi-restraints excluded: chain A residue  188 LEU
Chi-restraints excluded: chain A residue  300 GLN
Chi-restraints excluded: chain A residue  407 PHE
Chi-restraints excluded: chain A residue  419 THR
Chi-restraints excluded: chain A residue  458 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 35 optimal weight:    0.0010
   chunk 17 optimal weight:    0.9980
   chunk 37 optimal weight:    0.9980
   chunk 28 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   chunk 25 optimal weight:    0.6980
   chunk 30 optimal weight:    0.5980
   chunk 7 optimal weight:    0.4980
   chunk 26 optimal weight:    0.3980
   chunk 4 optimal weight:    0.3980
   overall best weight:    0.3786

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

Flipped N/Q/H residues before XYZ refinement:
** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 173 ASN
A 294 GLN
A 300 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.115183 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.100367 restraints weight = 5617.558|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.103720 restraints weight = 2810.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.105740 restraints weight = 1700.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.107147 restraints weight = 1190.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.108078 restraints weight = 914.798|
|-----------------------------------------------------------------------------|
r_work (final): 0.3395
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7211
moved from start:          0.3441

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3225  Z= 0.146
  Angle     :  0.630  12.314   4406  Z= 0.319
  Chirality :  0.043   0.165    502
  Planarity :  0.004   0.043    528
  Dihedral  :  6.038  56.825    428
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 10.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 19.82 %
    Favored  : 77.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.58 (0.43), residues: 384
  helix:  1.83 (0.29), residues: 291
  sheet:  None (None), residues: 0
  loop : -1.51 (0.64), residues: 93

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  78 
 TYR   0.018   0.002   TYR A 136 
 PHE   0.024   0.001   PHE A  99 
 TRP   0.018   0.001   TRP A 284 
 HIS   0.004   0.001   HIS A 364 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 3225)
  covalent geometry    : angle       0.62985 ( 4406)
  hydrogen bonds       : bond        0.04514 (  225)
  hydrogen bonds       : angle       3.97358 (  675)

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

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

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 108
  time to evaluate  : 0.115 
Fit side-chains
REVERT: A   52 THR cc_start: 0.7996 (m) cc_final: 0.7558 (p)
REVERT: A   59 TRP cc_start: 0.8392 (t60) cc_final: 0.7613 (t60)
REVERT: A   67 LEU cc_start: 0.8391 (tp) cc_final: 0.8102 (tt)
REVERT: A   89 SER cc_start: 0.8114 (m) cc_final: 0.7880 (p)
REVERT: A  161 LEU cc_start: 0.8231 (mt) cc_final: 0.7759 (tp)
REVERT: A  167 MET cc_start: 0.6674 (ttm) cc_final: 0.5896 (ttm)
REVERT: A  171 TYR cc_start: 0.8046 (m-10) cc_final: 0.7820 (m-10)
REVERT: A  320 GLU cc_start: 0.7227 (tp30) cc_final: 0.7012 (tp30)
REVERT: A  325 PHE cc_start: 0.8395 (t80) cc_final: 0.8169 (t80)
REVERT: A  361 PHE cc_start: 0.7855 (m-10) cc_final: 0.7617 (m-80)
REVERT: A  363 MET cc_start: 0.7190 (mtm) cc_final: 0.6905 (mtm)
REVERT: A  376 TYR cc_start: 0.8582 (t80) cc_final: 0.8019 (t80)
REVERT: A  380 LYS cc_start: 0.8437 (tttt) cc_final: 0.8180 (ttmm)
REVERT: A  387 ILE cc_start: 0.8015 (tp) cc_final: 0.7690 (tp)
REVERT: A  406 VAL cc_start: 0.7846 (t) cc_final: 0.6804 (p)
REVERT: A  407 PHE cc_start: 0.7827 (OUTLIER) cc_final: 0.7534 (m-80)
REVERT: A  410 ASN cc_start: 0.7583 (m-40) cc_final: 0.7166 (m-40)
REVERT: A  418 GLN cc_start: 0.7730 (tt0) cc_final: 0.7480 (tt0)
REVERT: A  419 THR cc_start: 0.8232 (OUTLIER) cc_final: 0.7830 (p)
REVERT: A  431 LEU cc_start: 0.7499 (mt) cc_final: 0.7271 (mt)
REVERT: A  432 ASN cc_start: 0.7596 (t0) cc_final: 0.7299 (t0)
REVERT: A  433 LEU cc_start: 0.8177 (mt) cc_final: 0.7883 (mt)
REVERT: A  438 GLN cc_start: 0.6940 (mt0) cc_final: 0.6555 (mt0)
  outliers start: 9
  outliers final: 5
  residues processed: 111
  average time/residue: 0.0476
  time to fit residues: 6.9389
Evaluate side-chains
  113 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 106
  time to evaluate  : 0.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 ASP
Chi-restraints excluded: chain A residue  160 LEU
Chi-restraints excluded: chain A residue  188 LEU
Chi-restraints excluded: chain A residue  300 GLN
Chi-restraints excluded: chain A residue  407 PHE
Chi-restraints excluded: chain A residue  419 THR
Chi-restraints excluded: chain A residue  458 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 32 optimal weight:    0.0770
   chunk 4 optimal weight:    0.0980
   chunk 25 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9980
   chunk 2 optimal weight:    0.5980
   chunk 17 optimal weight:    0.9980
   chunk 33 optimal weight:    0.7980
   chunk 6 optimal weight:    0.7980
   chunk 14 optimal weight:    0.8980
   chunk 28 optimal weight:    1.9990
   overall best weight:    0.4738

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

Flipped N/Q/H residues before XYZ refinement:
A 173 ASN
A 294 GLN
A 300 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.114479 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.099813 restraints weight = 5753.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.103124 restraints weight = 2842.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.105258 restraints weight = 1714.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.106649 restraints weight = 1185.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.107582 restraints weight = 904.799|
|-----------------------------------------------------------------------------|
r_work (final): 0.3387
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7223
moved from start:          0.3555

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3225  Z= 0.161
  Angle     :  0.632  10.185   4406  Z= 0.322
  Chirality :  0.043   0.146    502
  Planarity :  0.004   0.043    528
  Dihedral  :  5.925  56.406    428
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 10.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 20.72 %
    Favored  : 76.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.65 (0.43), residues: 384
  helix:  1.87 (0.29), residues: 291
  sheet:  None (None), residues: 0
  loop : -1.43 (0.65), residues: 93

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  78 
 TYR   0.015   0.002   TYR A 383 
 PHE   0.024   0.001   PHE A  99 
 TRP   0.018   0.001   TRP A 284 
 HIS   0.004   0.001   HIS A 364 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 3225)
  covalent geometry    : angle       0.63186 ( 4406)
  hydrogen bonds       : bond        0.04622 (  225)
  hydrogen bonds       : angle       4.03381 (  675)

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

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

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 113
  time to evaluate  : 0.124 
Fit side-chains
   revert: symmetry clash
REVERT: A   52 THR cc_start: 0.8005 (m) cc_final: 0.7569 (p)
REVERT: A   59 TRP cc_start: 0.8373 (t60) cc_final: 0.7575 (t60)
REVERT: A   67 LEU cc_start: 0.8469 (tp) cc_final: 0.8175 (tt)
REVERT: A   89 SER cc_start: 0.8115 (m) cc_final: 0.7906 (p)
REVERT: A  161 LEU cc_start: 0.8254 (mt) cc_final: 0.7773 (tp)
REVERT: A  167 MET cc_start: 0.6755 (ttm) cc_final: 0.5995 (ttm)
REVERT: A  298 TYR cc_start: 0.8205 (m-80) cc_final: 0.7992 (m-80)
REVERT: A  325 PHE cc_start: 0.8391 (t80) cc_final: 0.8175 (t80)
REVERT: A  361 PHE cc_start: 0.7866 (m-10) cc_final: 0.7630 (m-80)
REVERT: A  363 MET cc_start: 0.7206 (mtm) cc_final: 0.6929 (mtm)
REVERT: A  376 TYR cc_start: 0.8599 (t80) cc_final: 0.8124 (t80)
REVERT: A  387 ILE cc_start: 0.8054 (tp) cc_final: 0.7717 (tp)
REVERT: A  406 VAL cc_start: 0.7869 (t) cc_final: 0.6975 (p)
REVERT: A  407 PHE cc_start: 0.7839 (OUTLIER) cc_final: 0.7604 (m-80)
REVERT: A  410 ASN cc_start: 0.7564 (m-40) cc_final: 0.7226 (m-40)
REVERT: A  419 THR cc_start: 0.8218 (OUTLIER) cc_final: 0.7810 (p)
REVERT: A  431 LEU cc_start: 0.7507 (mt) cc_final: 0.7287 (mt)
REVERT: A  432 ASN cc_start: 0.7601 (t0) cc_final: 0.7299 (t0)
REVERT: A  433 LEU cc_start: 0.8213 (mt) cc_final: 0.7884 (mt)
REVERT: A  438 GLN cc_start: 0.7012 (mt0) cc_final: 0.6613 (mt0)
  outliers start: 8
  outliers final: 6
  residues processed: 116
  average time/residue: 0.0460
  time to fit residues: 7.0236
Evaluate side-chains
  120 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 112
  time to evaluate  : 0.114 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 ASP
Chi-restraints excluded: chain A residue  160 LEU
Chi-restraints excluded: chain A residue  188 LEU
Chi-restraints excluded: chain A residue  300 GLN
Chi-restraints excluded: chain A residue  401 GLU
Chi-restraints excluded: chain A residue  407 PHE
Chi-restraints excluded: chain A residue  419 THR
Chi-restraints excluded: chain A residue  458 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 9 optimal weight:    0.8980
   chunk 21 optimal weight:    0.5980
   chunk 14 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9980
   chunk 19 optimal weight:    0.4980
   chunk 3 optimal weight:    0.0370
   chunk 12 optimal weight:    1.9990
   chunk 17 optimal weight:    0.4980
   chunk 26 optimal weight:    0.8980
   chunk 16 optimal weight:    0.5980
   overall best weight:    0.4458

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

Flipped N/Q/H residues before XYZ refinement:
A 300 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.114290 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.099421 restraints weight = 5897.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.102848 restraints weight = 2902.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.105052 restraints weight = 1728.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.106481 restraints weight = 1181.839|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.107295 restraints weight = 896.802|
|-----------------------------------------------------------------------------|
r_work (final): 0.3384
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7227
moved from start:          0.3675

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3225  Z= 0.155
  Angle     :  0.626   9.838   4406  Z= 0.320
  Chirality :  0.043   0.141    502
  Planarity :  0.004   0.043    528
  Dihedral  :  5.833  55.606    428
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 10.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 23.42 %
    Favored  : 74.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.60 (0.42), residues: 384
  helix:  1.89 (0.29), residues: 297
  sheet:  None (None), residues: 0
  loop : -1.97 (0.62), residues: 87

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  78 
 TYR   0.016   0.002   TYR A 383 
 PHE   0.027   0.001   PHE A  99 
 TRP   0.018   0.001   TRP A 284 
 HIS   0.004   0.001   HIS A 364 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 3225)
  covalent geometry    : angle       0.62570 ( 4406)
  hydrogen bonds       : bond        0.04593 (  225)
  hydrogen bonds       : angle       4.04332 (  675)

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

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

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 112
  time to evaluate  : 0.114 
Fit side-chains
REVERT: A   52 THR cc_start: 0.8000 (m) cc_final: 0.7591 (p)
REVERT: A   59 TRP cc_start: 0.8377 (t60) cc_final: 0.7675 (t60)
REVERT: A   67 LEU cc_start: 0.8480 (tp) cc_final: 0.8216 (tt)
REVERT: A   89 SER cc_start: 0.8119 (m) cc_final: 0.7893 (p)
REVERT: A  161 LEU cc_start: 0.8244 (mt) cc_final: 0.7789 (tp)
REVERT: A  167 MET cc_start: 0.6710 (ttm) cc_final: 0.5965 (ttm)
REVERT: A  361 PHE cc_start: 0.7863 (m-10) cc_final: 0.7633 (m-80)
REVERT: A  363 MET cc_start: 0.7207 (mtm) cc_final: 0.6924 (mtm)
REVERT: A  376 TYR cc_start: 0.8613 (t80) cc_final: 0.8142 (t80)
REVERT: A  380 LYS cc_start: 0.8462 (tttt) cc_final: 0.8200 (ttmm)
REVERT: A  387 ILE cc_start: 0.8006 (tp) cc_final: 0.7676 (tp)
REVERT: A  406 VAL cc_start: 0.7865 (t) cc_final: 0.6980 (p)
REVERT: A  407 PHE cc_start: 0.7834 (OUTLIER) cc_final: 0.7580 (m-80)
REVERT: A  410 ASN cc_start: 0.7583 (m-40) cc_final: 0.7239 (m-40)
REVERT: A  419 THR cc_start: 0.8221 (OUTLIER) cc_final: 0.7827 (p)
REVERT: A  431 LEU cc_start: 0.7510 (mt) cc_final: 0.7278 (mt)
REVERT: A  432 ASN cc_start: 0.7603 (t0) cc_final: 0.7294 (t0)
REVERT: A  433 LEU cc_start: 0.8234 (mt) cc_final: 0.7876 (mt)
REVERT: A  438 GLN cc_start: 0.6982 (mt0) cc_final: 0.6605 (mt0)
  outliers start: 6
  outliers final: 4
  residues processed: 114
  average time/residue: 0.0485
  time to fit residues: 7.1916
Evaluate side-chains
  111 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 105
  time to evaluate  : 0.120 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 ASP
Chi-restraints excluded: chain A residue  188 LEU
Chi-restraints excluded: chain A residue  300 GLN
Chi-restraints excluded: chain A residue  407 PHE
Chi-restraints excluded: chain A residue  419 THR
Chi-restraints excluded: chain A residue  458 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 32 optimal weight:    0.9980
   chunk 2 optimal weight:    0.5980
   chunk 17 optimal weight:    0.6980
   chunk 26 optimal weight:    0.1980
   chunk 0 optimal weight:    0.9980
   chunk 13 optimal weight:    0.5980
   chunk 9 optimal weight:    0.8980
   chunk 22 optimal weight:    0.6980
   chunk 18 optimal weight:    0.5980
   chunk 36 optimal weight:    0.2980
   chunk 14 optimal weight:    0.9980
   overall best weight:    0.4580

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

Flipped N/Q/H residues before XYZ refinement:
A 300 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.114448 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.100004 restraints weight = 5759.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.103348 restraints weight = 2835.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.105518 restraints weight = 1690.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.106882 restraints weight = 1158.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.107824 restraints weight = 884.469|
|-----------------------------------------------------------------------------|
r_work (final): 0.3394
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7221
moved from start:          0.3764

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3225  Z= 0.161
  Angle     :  0.621   9.445   4406  Z= 0.325
  Chirality :  0.043   0.139    502
  Planarity :  0.004   0.043    528
  Dihedral  :  5.811  54.366    428
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 10.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 23.72 %
    Favored  : 74.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.62 (0.43), residues: 384
  helix:  1.90 (0.29), residues: 297
  sheet:  None (None), residues: 0
  loop : -1.92 (0.63), residues: 87

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  78 
 TYR   0.015   0.002   TYR A 383 
 PHE   0.030   0.001   PHE A  99 
 TRP   0.019   0.001   TRP A 284 
 HIS   0.004   0.001   HIS A 364 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 3225)
  covalent geometry    : angle       0.62133 ( 4406)
  hydrogen bonds       : bond        0.04665 (  225)
  hydrogen bonds       : angle       4.05989 (  675)

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

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

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 110
  time to evaluate  : 0.115 
Fit side-chains
REVERT: A   52 THR cc_start: 0.7982 (m) cc_final: 0.7608 (p)
REVERT: A   59 TRP cc_start: 0.8355 (t60) cc_final: 0.7669 (t60)
REVERT: A   67 LEU cc_start: 0.8506 (tp) cc_final: 0.8247 (tt)
REVERT: A   89 SER cc_start: 0.8114 (m) cc_final: 0.7885 (p)
REVERT: A  361 PHE cc_start: 0.7864 (m-10) cc_final: 0.7637 (m-80)
REVERT: A  363 MET cc_start: 0.7207 (mtm) cc_final: 0.6931 (mtm)
REVERT: A  380 LYS cc_start: 0.8469 (tttt) cc_final: 0.8183 (ttmm)
REVERT: A  387 ILE cc_start: 0.8028 (tp) cc_final: 0.7689 (tp)
REVERT: A  406 VAL cc_start: 0.7861 (t) cc_final: 0.6954 (p)
REVERT: A  407 PHE cc_start: 0.7831 (OUTLIER) cc_final: 0.7565 (m-80)
REVERT: A  410 ASN cc_start: 0.7565 (m-40) cc_final: 0.7219 (m-40)
REVERT: A  419 THR cc_start: 0.8214 (OUTLIER) cc_final: 0.7833 (p)
REVERT: A  431 LEU cc_start: 0.7500 (mt) cc_final: 0.7282 (mt)
REVERT: A  432 ASN cc_start: 0.7612 (t0) cc_final: 0.7257 (t0)
REVERT: A  433 LEU cc_start: 0.8232 (mt) cc_final: 0.7878 (mt)
REVERT: A  438 GLN cc_start: 0.7022 (mt0) cc_final: 0.6688 (mt0)
  outliers start: 7
  outliers final: 5
  residues processed: 113
  average time/residue: 0.0461
  time to fit residues: 6.8678
Evaluate side-chains
  113 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 106
  time to evaluate  : 0.137 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 ASP
Chi-restraints excluded: chain A residue  160 LEU
Chi-restraints excluded: chain A residue  188 LEU
Chi-restraints excluded: chain A residue  300 GLN
Chi-restraints excluded: chain A residue  407 PHE
Chi-restraints excluded: chain A residue  419 THR
Chi-restraints excluded: chain A residue  458 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 29 optimal weight:    0.5980
   chunk 1 optimal weight:    0.9980
   chunk 4 optimal weight:    0.1980
   chunk 11 optimal weight:    0.9990
   chunk 2 optimal weight:    0.3980
   chunk 10 optimal weight:    0.5980
   chunk 8 optimal weight:    0.9990
   chunk 16 optimal weight:    0.5980
   chunk 25 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9980
   chunk 23 optimal weight:    0.8980
   overall best weight:    0.4780

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

Flipped N/Q/H residues before XYZ refinement:
A 101 GLN
A 173 ASN
A 300 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.113953 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.099227 restraints weight = 5624.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.102641 restraints weight = 2773.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.104842 restraints weight = 1655.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.106281 restraints weight = 1131.286|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.107243 restraints weight = 856.302|
|-----------------------------------------------------------------------------|
r_work (final): 0.3392
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7223
moved from start:          0.3838

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   3225  Z= 0.166
  Angle     :  0.653   9.540   4406  Z= 0.339
  Chirality :  0.043   0.137    502
  Planarity :  0.004   0.043    528
  Dihedral  :  5.798  53.372    428
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 10.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 24.02 %
    Favored  : 73.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.67 (0.43), residues: 384
  helix:  1.91 (0.29), residues: 298
  sheet:  None (None), residues: 0
  loop : -1.85 (0.65), residues: 86

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  78 
 TYR   0.015   0.002   TYR A 383 
 PHE   0.028   0.001   PHE A  99 
 TRP   0.019   0.001   TRP A 284 
 HIS   0.004   0.001   HIS A 364 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 ( 3225)
  covalent geometry    : angle       0.65347 ( 4406)
  hydrogen bonds       : bond        0.04693 (  225)
  hydrogen bonds       : angle       4.09534 (  675)

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

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

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 110
  time to evaluate  : 0.112 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 THR cc_start: 0.7989 (m) cc_final: 0.7696 (p)
REVERT: A   67 LEU cc_start: 0.8485 (tp) cc_final: 0.8229 (tt)
REVERT: A   89 SER cc_start: 0.8119 (m) cc_final: 0.7904 (p)
REVERT: A  161 LEU cc_start: 0.8051 (mt) cc_final: 0.7702 (tp)
REVERT: A  197 MET cc_start: 0.7949 (tpp) cc_final: 0.7667 (tpp)
REVERT: A  314 ILE cc_start: 0.8124 (pt) cc_final: 0.7880 (pt)
REVERT: A  361 PHE cc_start: 0.7862 (m-10) cc_final: 0.7622 (m-80)
REVERT: A  363 MET cc_start: 0.7208 (mtm) cc_final: 0.6927 (mtm)
REVERT: A  380 LYS cc_start: 0.8481 (tttt) cc_final: 0.8199 (ttmm)
REVERT: A  387 ILE cc_start: 0.8052 (tp) cc_final: 0.7724 (tp)
REVERT: A  406 VAL cc_start: 0.7866 (t) cc_final: 0.6975 (p)
REVERT: A  407 PHE cc_start: 0.7826 (OUTLIER) cc_final: 0.7574 (m-80)
REVERT: A  410 ASN cc_start: 0.7546 (m-40) cc_final: 0.7215 (m-40)
REVERT: A  419 THR cc_start: 0.8209 (OUTLIER) cc_final: 0.7849 (p)
REVERT: A  431 LEU cc_start: 0.7503 (mt) cc_final: 0.7277 (mt)
REVERT: A  432 ASN cc_start: 0.7616 (t0) cc_final: 0.7265 (t0)
REVERT: A  433 LEU cc_start: 0.8250 (mt) cc_final: 0.7900 (mt)
  outliers start: 8
  outliers final: 4
  residues processed: 112
  average time/residue: 0.0441
  time to fit residues: 6.5163
Evaluate side-chains
  116 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 110
  time to evaluate  : 0.110 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 ASP
Chi-restraints excluded: chain A residue  188 LEU
Chi-restraints excluded: chain A residue  300 GLN
Chi-restraints excluded: chain A residue  407 PHE
Chi-restraints excluded: chain A residue  419 THR
Chi-restraints excluded: chain A residue  458 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 26 optimal weight:    0.8980
   chunk 33 optimal weight:    1.9990
   chunk 12 optimal weight:    3.9990
   chunk 21 optimal weight:    0.5980
   chunk 27 optimal weight:    0.6980
   chunk 16 optimal weight:    0.8980
   chunk 36 optimal weight:    1.9990
   chunk 20 optimal weight:    0.6980
   chunk 25 optimal weight:    0.5980
   chunk 0 optimal weight:    0.6980
   chunk 35 optimal weight:    0.9980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 101 GLN
A 173 ASN
** A 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.113437 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.098885 restraints weight = 5771.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.102221 restraints weight = 2841.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.104399 restraints weight = 1695.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.105844 restraints weight = 1161.085|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.106653 restraints weight = 878.597|
|-----------------------------------------------------------------------------|
r_work (final): 0.3366
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7243
moved from start:          0.3856

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   3225  Z= 0.201
  Angle     :  0.661   9.205   4406  Z= 0.349
  Chirality :  0.045   0.160    502
  Planarity :  0.004   0.045    528
  Dihedral  :  5.835  53.499    428
  Min Nonbonded Distance : 2.400

Molprobity Statistics.
  All-atom Clashscore : 10.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 24.62 %
    Favored  : 73.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.52 (0.42), residues: 384
  helix:  1.79 (0.29), residues: 297
  sheet:  None (None), residues: 0
  loop : -1.82 (0.64), residues: 87

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  78 
 TYR   0.014   0.002   TYR A 298 
 PHE   0.030   0.002   PHE A  99 
 TRP   0.020   0.001   TRP A 284 
 HIS   0.003   0.001   HIS A 364 

Details of bonding type rmsd
  covalent geometry    : bond        0.00430 ( 3225)
  covalent geometry    : angle       0.66070 ( 4406)
  hydrogen bonds       : bond        0.04968 (  225)
  hydrogen bonds       : angle       4.23689 (  675)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 772.20 seconds
wall clock time: 14 minutes 4.11 seconds (844.11 seconds total)