Starting phenix.real_space_refine
on Tue Feb  3 17:42:34 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9irc_60809/02_2026/9irc_60809.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9irc_60809/02_2026/9irc_60809.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.82
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9irc_60809/02_2026/9irc_60809.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9irc_60809/02_2026/9irc_60809.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9irc_60809/02_2026/9irc_60809.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9irc_60809/02_2026/9irc_60809.map"
  }
  resolution = 2.82
  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=   0.043
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      32      5.16       5
     C    3646      2.51       5
     N     912      2.21       5
     O     999      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5589
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3675
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 479, 3675
          Classifications: {'peptide': 479}
          Link IDs: {'PTRANS': 21, 'TRANS': 457}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 164
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 19, 164
          Classifications: {'peptide': 19}
          Link IDs: {'TRANS': 18}
    Chain: "H"
      Number of atoms: 935
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 120, 935
          Classifications: {'peptide': 120}
          Link IDs: {'PTRANS': 3, 'TRANS': 116}
    Chain: "L"
      Number of atoms: 815
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 815
          Classifications: {'peptide': 108}
          Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 102}
  Time building chain proxies: 1.40, per 1000 atoms: 0.25
  Number of scatterers: 5589
  At special positions: 0
  Unit cell: (70, 70, 116, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      32     16.00
     O     999      8.00
     N     912      7.00
     C    3646      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 133 " - pdb=" SG  CYS A 153 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  89 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.39
  Conformation dependent library (CDL) restraints added in 346.4 milliseconds
  

  1428 Ramachandran restraints generated.
    714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1324

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 6 sheets defined
      57.7% alpha, 15.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.19
  Creating SS restraints...
    Processing helix  chain 'A' and resid 33 through 63
      removed outlier: 3.912A  pdb=" N   ASN A  57 " --> pdb=" O   GLY A  53 " (cutoff:3.500A)
      removed outlier: 5.171A  pdb=" N   VAL A  59 " --> pdb=" O   THR A  55 " (cutoff:3.500A)
      removed outlier: 5.664A  pdb=" N   LEU A  60 " --> pdb=" O   SER A  56 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 70 through 99
      removed outlier: 4.261A  pdb=" N   SER A  89 " --> pdb=" O   THR A  85 " (cutoff:3.500A)
      Proline residue:  A  90  - end of helix
      removed outlier: 3.564A  pdb=" N   ARG A  99 " --> pdb=" O   LEU A  95 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 102 through 118
    Processing helix  chain 'A' and resid 118 through 125
      removed outlier: 3.646A  pdb=" N   LEU A 122 " --> pdb=" O   LEU A 118 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 125 through 133
      removed outlier: 3.772A  pdb=" N   ALA A 130 " --> pdb=" O   PRO A 126 " (cutoff:3.500A)
      removed outlier: 4.226A  pdb=" N   ALA A 131 " --> pdb=" O   ALA A 127 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 153 through 184
      removed outlier: 3.630A  pdb=" N   THR A 157 " --> pdb=" O   CYS A 153 " (cutoff:3.500A)
      removed outlier: 4.569A  pdb=" N   THR A 176 " --> pdb=" O   LYS A 172 " (cutoff:3.500A)
      Proline residue:  A 177  - end of helix
    Processing helix  chain 'A' and resid 187 through 219
      removed outlier: 4.181A  pdb=" N   ALA A 214 " --> pdb=" O   LEU A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 221 through 244
      Proline residue:  A 229  - end of helix
    Processing helix  chain 'A' and resid 255 through 265
      removed outlier: 4.063A  pdb=" N   ASP A 259 " --> pdb=" O   SER A 255 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 308 through 348
      Proline residue:  A 323  - end of helix
      Proline residue:  A 330  - end of helix
      removed outlier: 3.969A  pdb=" N   MET A 338 " --> pdb=" O   VAL A 334 " (cutoff:3.500A)
      removed outlier: 4.722A  pdb=" N   GLN A 339 " --> pdb=" O   TYR A 335 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   THR A 340 " --> pdb=" O   PHE A 336 " (cutoff:3.500A)
      removed outlier: 4.365A  pdb=" N   TYR A 342 " --> pdb=" O   MET A 338 " (cutoff:3.500A)
      removed outlier: 4.762A  pdb=" N   VAL A 343 " --> pdb=" O   GLN A 339 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   LEU A 344 " --> pdb=" O   THR A 340 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   HIS A 348 " --> pdb=" O   LEU A 344 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 367 through 387
      Proline residue:  A 382  - end of helix
    Processing helix  chain 'A' and resid 387 through 396
    Processing helix  chain 'A' and resid 400 through 431
    Processing helix  chain 'A' and resid 450 through 453
    Processing helix  chain 'A' and resid 454 through 468
      removed outlier: 3.626A  pdb=" N   TYR A 458 " --> pdb=" O   GLN A 454 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 468 through 479
    Processing helix  chain 'A' and resid 481 through 485
    Processing helix  chain 'A' and resid 487 through 511
    Processing helix  chain 'A' and resid 526 through 530
      removed outlier: 3.808A  pdb=" N   GLY A 529 " --> pdb=" O   ASN A 526 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 531 through 558
      removed outlier: 3.502A  pdb=" N   TYR A 535 " --> pdb=" O   TYR A 531 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 3 through 9
      removed outlier: 3.728A  pdb=" N   GLY B   9 " --> pdb=" O   GLY B   5 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 9 through 14
      removed outlier: 3.935A  pdb=" N   TRP B  13 " --> pdb=" O   GLY B   9 " (cutoff:3.500A)
      removed outlier: 4.416A  pdb=" N   ASN B  14 " --> pdb=" O   LEU B  10 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 9 through 14'
    Processing helix  chain 'H' and resid 87 through 91
    Processing helix  chain 'L' and resid 30 through 32
      No H-bonds generated for 'chain 'L' and resid 30 through 32'
    Processing helix  chain 'L' and resid 80 through 84
    Processing sheet with id=AA1, first strand: chain 'A' and resid 435 through 437
    Processing sheet with id=AA2, first strand: chain 'H' and resid 3 through 7
    Processing sheet with id=AA3, first strand: chain 'H' and resid 11 through 12
      removed outlier: 6.882A  pdb=" N   MET H  34 " --> pdb=" O   TYR H  50 " (cutoff:3.500A)
      removed outlier: 4.591A  pdb=" N   TYR H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 6.572A  pdb=" N   TRP H  36 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'H' and resid 11 through 12
      removed outlier: 4.037A  pdb=" N   TYR H 109 " --> pdb=" O   ARG H  98 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'L' and resid 4 through 7
      removed outlier: 6.155A  pdb=" N   THR L  70 " --> pdb=" O   ALA L  25 " (cutoff:3.500A)
      removed outlier: 10.436A  pdb=" N   SER L  27 " --> pdb=" O   SER L  68 " (cutoff:3.500A)
      removed outlier: 9.917A  pdb=" N   SER L  68 " --> pdb=" O   SER L  27 " (cutoff:3.500A)
      removed outlier: 11.635A  pdb=" N   VAL L  29 " --> pdb=" O   SER L  66 " (cutoff:3.500A)
      removed outlier: 11.849A  pdb=" N   SER L  66 " --> pdb=" O   VAL L  29 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'L' and resid 10 through 13
      removed outlier: 7.023A  pdb=" N   LEU L  34 " --> pdb=" O   TYR L  50 " (cutoff:3.500A)
      removed outlier: 5.118A  pdb=" N   TYR L  50 " --> pdb=" O   LEU L  34 " (cutoff:3.500A)
      removed outlier: 6.442A  pdb=" N   TRP L  36 " --> pdb=" O   TRP L  48 " (cutoff:3.500A)

    353 hydrogen bonds defined for protein.
    993 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.09

  Time building geometry restraints manager: 0.54 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 852
        1.31 -     1.43: 1671
        1.43 -     1.56: 3160
        1.56 -     1.69: 0
        1.69 -     1.81: 50
  Bond restraints: 5733
  Sorted by residual:
  bond pdb=" C   PRO L  45 "
       pdb=" O   PRO L  45 "
    ideal  model  delta    sigma   weight residual
    1.232  1.183  0.050 1.27e-02 6.20e+03 1.55e+01
  bond pdb=" C   ILE L  49 "
       pdb=" O   ILE L  49 "
    ideal  model  delta    sigma   weight residual
    1.237  1.202  0.035 1.09e-02 8.42e+03 1.05e+01
  bond pdb=" N   GLU B  11 "
       pdb=" CA  GLU B  11 "
    ideal  model  delta    sigma   weight residual
    1.455  1.489 -0.034 1.25e-02 6.40e+03 7.32e+00
  bond pdb=" C   SER L  44 "
       pdb=" N   PRO L  45 "
    ideal  model  delta    sigma   weight residual
    1.330  1.362 -0.032 1.25e-02 6.40e+03 6.59e+00
  bond pdb=" N   LEU L  47 "
       pdb=" CA  LEU L  47 "
    ideal  model  delta    sigma   weight residual
    1.456  1.486 -0.030 1.23e-02 6.61e+03 6.06e+00
  ... (remaining 5728 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.69: 7596
        1.69 -     3.37: 154
        3.37 -     5.06: 29
        5.06 -     6.74: 9
        6.74 -     8.43: 3
  Bond angle restraints: 7791
  Sorted by residual:
  angle pdb=" CA  ARG L  46 "
        pdb=" C   ARG L  46 "
        pdb=" N   LEU L  47 "
      ideal   model   delta    sigma   weight residual
     116.29  122.21   -5.92 1.45e+00 4.76e-01 1.67e+01
  angle pdb=" CA  ILE L  49 "
        pdb=" C   ILE L  49 "
        pdb=" O   ILE L  49 "
      ideal   model   delta    sigma   weight residual
     120.27  116.92    3.35 1.01e+00 9.80e-01 1.10e+01
  angle pdb=" CA  LEU L  47 "
        pdb=" C   LEU L  47 "
        pdb=" O   LEU L  47 "
      ideal   model   delta    sigma   weight residual
     121.19  117.65    3.54 1.10e+00 8.26e-01 1.04e+01
  angle pdb=" C   SER L  51 "
        pdb=" N   THR L  52 "
        pdb=" CA  THR L  52 "
      ideal   model   delta    sigma   weight residual
     121.54  127.58   -6.04 1.91e+00 2.74e-01 1.00e+01
  angle pdb=" N   TRP L  48 "
        pdb=" CA  TRP L  48 "
        pdb=" C   TRP L  48 "
      ideal   model   delta    sigma   weight residual
     112.13  107.81    4.32 1.37e+00 5.33e-01 9.96e+00
  ... (remaining 7786 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.07: 3020
       17.07 -    34.14: 236
       34.14 -    51.21: 45
       51.21 -    68.29: 10
       68.29 -    85.36: 5
  Dihedral angle restraints: 3316
    sinusoidal: 1240
      harmonic: 2076
  Sorted by residual:
  dihedral pdb=" CD  ARG L  46 "
           pdb=" NE  ARG L  46 "
           pdb=" CZ  ARG L  46 "
           pdb=" NH1 ARG L  46 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   85.36  -85.36     1      1.00e+01 1.00e-02 8.82e+01
  dihedral pdb=" CB  CYS A 133 "
           pdb=" SG  CYS A 133 "
           pdb=" SG  CYS A 153 "
           pdb=" CB  CYS A 153 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -11.32  -74.68     1      1.00e+01 1.00e-02 7.06e+01
  dihedral pdb=" CA  ARG A  99 "
           pdb=" C   ARG A  99 "
           pdb=" N   LEU A 100 "
           pdb=" CA  LEU A 100 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.89   20.11     0      5.00e+00 4.00e-02 1.62e+01
  ... (remaining 3313 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 640
       0.040 -    0.080: 170
       0.080 -    0.120: 65
       0.120 -    0.160: 7
       0.160 -    0.200: 2
  Chirality restraints: 884
  Sorted by residual:
  chirality pdb=" CA  ILE L  49 "
            pdb=" N   ILE L  49 "
            pdb=" C   ILE L  49 "
            pdb=" CB  ILE L  49 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.63   -0.20 2.00e-01 2.50e+01 9.98e-01
  chirality pdb=" CA  LEU L  47 "
            pdb=" N   LEU L  47 "
            pdb=" C   LEU L  47 "
            pdb=" CB  LEU L  47 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.69   -0.18 2.00e-01 2.50e+01 7.72e-01
  chirality pdb=" CA  ARG L  46 "
            pdb=" N   ARG L  46 "
            pdb=" C   ARG L  46 "
            pdb=" CB  ARG L  46 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.66   -0.15 2.00e-01 2.50e+01 5.91e-01
  ... (remaining 881 not shown)

  Planarity restraints: 964
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG L  46 "   -1.092 9.50e-02 1.11e+02   4.89e-01 1.44e+02
        pdb=" NE  ARG L  46 "    0.066 2.00e-02 2.50e+03
        pdb=" CZ  ARG L  46 "    0.011 2.00e-02 2.50e+03
        pdb=" NH1 ARG L  46 "   -0.012 2.00e-02 2.50e+03
        pdb=" NH2 ARG L  46 "   -0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 360 "    0.035 5.00e-02 4.00e+02   5.43e-02 4.71e+00
        pdb=" N   PRO A 361 "   -0.094 5.00e-02 4.00e+02
        pdb=" CA  PRO A 361 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A 361 "    0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG L  46 "   -0.009 2.00e-02 2.50e+03   1.83e-02 3.36e+00
        pdb=" C   ARG L  46 "    0.032 2.00e-02 2.50e+03
        pdb=" O   ARG L  46 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   LEU L  47 "   -0.011 2.00e-02 2.50e+03
  ... (remaining 961 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.69: 130
        2.69 -     3.24: 5846
        3.24 -     3.80: 9630
        3.80 -     4.35: 12590
        4.35 -     4.90: 20934
  Nonbonded interactions: 49130
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A  47 "
            pdb=" NH1 ARG A  48 "
     model   vdw
     2.141 3.120
  nonbonded pdb=" OG  SER A 346 "
            pdb=" OE1 GLN A 454 "
     model   vdw
     2.163 3.040
  nonbonded pdb=" ND2 ASN A 526 "
            pdb=" OG  SER H  56 "
     model   vdw
     2.205 3.120
  nonbonded pdb=" OG1 THR H 100 "
            pdb=" O   ARG H 104 "
     model   vdw
     2.217 3.040
  nonbonded pdb=" O   VAL L  29 "
            pdb=" OH  TYR L  72 "
     model   vdw
     2.228 3.040
  ... (remaining 49125 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.030
  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:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     7.390
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:10.800
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.350
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7925
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      :  0.003   0.050   5736  Z= 0.169
  Angle     :  0.630   8.426   7797  Z= 0.341
  Chirality :  0.042   0.200    884
  Planarity :  0.016   0.489    964
  Dihedral  : 12.911  85.357   1983
  Min Nonbonded Distance : 2.141

Molprobity Statistics.
  All-atom Clashscore : 11.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.04 %
    Favored  : 94.96 %
  Rotamer:
    Outliers :  0.17 %
    Allowed  :  0.34 %
    Favored  : 99.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.82 (0.33), residues: 714
  helix:  1.69 (0.27), residues: 368
  sheet: -0.93 (0.52), residues: 93
  loop : -0.51 (0.43), residues: 253

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  48 
 TYR   0.019   0.001   TYR L  92 
 PHE   0.021   0.001   PHE L  63 
 TRP   0.011   0.001   TRP A 332 
 HIS   0.005   0.001   HIS A 303 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 5733)
  covalent geometry    : angle       0.62953 ( 7791)
  SS BOND              : bond        0.00193 (    3)
  SS BOND              : angle       1.38755 (    6)
  hydrogen bonds       : bond        0.12208 (  348)
  hydrogen bonds       : angle       5.64577 (  993)

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

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

  1428 Ramachandran restraints generated.
    714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1428 Ramachandran restraints generated.
    714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 108
  time to evaluate  : 0.130 
Fit side-chains
REVERT: A  185 ASP cc_start: 0.8901 (m-30) cc_final: 0.8626 (m-30)
REVERT: A  203 ASN cc_start: 0.8289 (m110) cc_final: 0.7957 (m-40)
REVERT: A  353 GLU cc_start: 0.8866 (mt-10) cc_final: 0.8659 (tm-30)
REVERT: B   17 HIS cc_start: 0.6221 (t-90) cc_final: 0.5501 (t-170)
REVERT: H    3 GLN cc_start: 0.7477 (pp30) cc_final: 0.7057 (pp30)
REVERT: H   46 GLU cc_start: 0.8863 (tt0) cc_final: 0.8554 (tt0)
REVERT: H   87 ARG cc_start: 0.8487 (ptp90) cc_final: 0.8231 (ptt-90)
REVERT: L   50 TYR cc_start: 0.8938 (p90) cc_final: 0.8633 (p90)
REVERT: L   83 ASP cc_start: 0.8534 (m-30) cc_final: 0.7955 (m-30)
  outliers start: 1
  outliers final: 1
  residues processed: 109
  average time/residue: 0.4438
  time to fit residues: 50.5427
Evaluate side-chains
  86 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 85
  time to evaluate  : 0.130 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  266 TYR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 49 optimal weight:    0.2980
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    0.0870
   chunk 62 optimal weight:    0.0670
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    0.8980
   chunk 61 optimal weight:    0.1980
   chunk 45 optimal weight:    0.9990
   chunk 27 optimal weight:    3.9990
   overall best weight:    0.3096

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

Flipped N/Q/H residues before XYZ refinement:
A 526 ASN
H  77 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.085637 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2890 r_free = 0.2890 target = 0.070316 restraints weight = 10586.472|
|-----------------------------------------------------------------------------|
r_work (start): 0.2897 rms_B_bonded: 2.41
r_work: 0.2780 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.2657 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.2657
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8024
moved from start:          0.1171

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5736  Z= 0.138
  Angle     :  0.592   8.207   7797  Z= 0.302
  Chirality :  0.042   0.194    884
  Planarity :  0.004   0.045    964
  Dihedral  :  4.465  33.427    781
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 9.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 10.15 %
    Favored  : 87.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.15 (0.33), residues: 714
  helix:  2.11 (0.26), residues: 375
  sheet: -0.93 (0.52), residues: 93
  loop : -0.62 (0.44), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG L  46 
 TYR   0.018   0.001   TYR A 113 
 PHE   0.012   0.001   PHE A 495 
 TRP   0.008   0.001   TRP A 368 
 HIS   0.005   0.001   HIS A 445 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 5733)
  covalent geometry    : angle       0.59166 ( 7791)
  SS BOND              : bond        0.00163 (    3)
  SS BOND              : angle       1.15397 (    6)
  hydrogen bonds       : bond        0.03958 (  348)
  hydrogen bonds       : angle       4.40063 (  993)

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

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

  1428 Ramachandran restraints generated.
    714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1428 Ramachandran restraints generated.
    714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 95
  time to evaluate  : 0.126 
Fit side-chains
REVERT: A   44 GLU cc_start: 0.8631 (tp30) cc_final: 0.8339 (tp30)
REVERT: A  203 ASN cc_start: 0.8384 (m110) cc_final: 0.8116 (m-40)
REVERT: B   17 HIS cc_start: 0.6233 (t-90) cc_final: 0.5511 (t-170)
REVERT: H    3 GLN cc_start: 0.7429 (pp30) cc_final: 0.7228 (pp30)
REVERT: H    4 LEU cc_start: 0.8607 (mt) cc_final: 0.8387 (mt)
REVERT: H   46 GLU cc_start: 0.9126 (tt0) cc_final: 0.8840 (tt0)
REVERT: H   87 ARG cc_start: 0.8413 (ptp90) cc_final: 0.8169 (ptt-90)
REVERT: L   46 ARG cc_start: 0.8710 (mtm-85) cc_final: 0.8384 (mtm180)
REVERT: L   83 ASP cc_start: 0.8752 (m-30) cc_final: 0.8411 (m-30)
  outliers start: 12
  outliers final: 4
  residues processed: 97
  average time/residue: 0.4466
  time to fit residues: 45.2283
Evaluate side-chains
  84 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 80
  time to evaluate  : 0.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain H residue   11 LEU
Chi-restraints excluded: chain H residue   65 LYS
Chi-restraints excluded: chain H residue  101 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 37 optimal weight:    1.9990
   chunk 51 optimal weight:    3.9990
   chunk 66 optimal weight:    3.9990
   chunk 6 optimal weight:    0.6980
   chunk 58 optimal weight:    0.6980
   chunk 31 optimal weight:    0.2980
   chunk 50 optimal weight:    0.7980
   chunk 33 optimal weight:    0.9990
   chunk 39 optimal weight:    0.8980
   chunk 15 optimal weight:    0.9980
   chunk 40 optimal weight:    1.9990
   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 337 GLN
H  77 ASN
H 112 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.083324 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2847 r_free = 0.2847 target = 0.067905 restraints weight = 10501.339|
|-----------------------------------------------------------------------------|
r_work (start): 0.2861 rms_B_bonded: 2.37
r_work: 0.2740 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.2616 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.2616
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8050
moved from start:          0.1438

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   5736  Z= 0.169
  Angle     :  0.597   8.532   7797  Z= 0.303
  Chirality :  0.042   0.166    884
  Planarity :  0.004   0.035    964
  Dihedral  :  4.275  19.889    779
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 9.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 12.52 %
    Favored  : 83.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.19 (0.33), residues: 714
  helix:  2.20 (0.26), residues: 375
  sheet: -1.04 (0.50), residues: 92
  loop : -0.66 (0.44), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  48 
 TYR   0.026   0.002   TYR L  50 
 PHE   0.012   0.001   PHE A 495 
 TRP   0.007   0.001   TRP A 332 
 HIS   0.007   0.001   HIS A 303 

Details of bonding type rmsd
  covalent geometry    : bond        0.00378 ( 5733)
  covalent geometry    : angle       0.59613 ( 7791)
  SS BOND              : bond        0.00163 (    3)
  SS BOND              : angle       1.21772 (    6)
  hydrogen bonds       : bond        0.03836 (  348)
  hydrogen bonds       : angle       4.23954 (  993)

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

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

  1428 Ramachandran restraints generated.
    714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1428 Ramachandran restraints generated.
    714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 84
  time to evaluate  : 0.131 
Fit side-chains
REVERT: A   44 GLU cc_start: 0.8685 (tp30) cc_final: 0.8415 (tp30)
REVERT: A  203 ASN cc_start: 0.8372 (m110) cc_final: 0.8091 (m-40)
REVERT: B   17 HIS cc_start: 0.6391 (t-90) cc_final: 0.5683 (t-170)
REVERT: H    3 GLN cc_start: 0.7517 (pp30) cc_final: 0.7087 (pp30)
REVERT: H    4 LEU cc_start: 0.8681 (mt) cc_final: 0.8199 (mt)
REVERT: H   87 ARG cc_start: 0.8365 (ptp90) cc_final: 0.7986 (ptt-90)
REVERT: H  103 ILE cc_start: 0.8784 (pt) cc_final: 0.8376 (mp)
REVERT: L   83 ASP cc_start: 0.8900 (m-30) cc_final: 0.8582 (m-30)
  outliers start: 21
  outliers final: 6
  residues processed: 90
  average time/residue: 0.4220
  time to fit residues: 39.8640
Evaluate side-chains
  82 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 76
  time to evaluate  : 0.206 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  379 LEU
Chi-restraints excluded: chain H residue   11 LEU
Chi-restraints excluded: chain H residue   19 LYS
Chi-restraints excluded: chain H residue  101 THR
Chi-restraints excluded: chain L residue   10 ILE
Chi-restraints excluded: chain L residue   15 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 31 optimal weight:    1.9990
   chunk 30 optimal weight:    0.5980
   chunk 0 optimal weight:    6.9990
   chunk 9 optimal weight:    0.9980
   chunk 12 optimal weight:    0.9980
   chunk 27 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9990
   chunk 56 optimal weight:    0.9980
   chunk 47 optimal weight:    0.4980
   chunk 68 optimal weight:    0.9990
   chunk 43 optimal weight:    3.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 339 GLN
B  19 ASN
H  77 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.081872 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2820 r_free = 0.2820 target = 0.066319 restraints weight = 10633.730|
|-----------------------------------------------------------------------------|
r_work (start): 0.2836 rms_B_bonded: 2.39
r_work: 0.2716 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.2592 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.2592
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8073
moved from start:          0.1626

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   5736  Z= 0.189
  Angle     :  0.600  10.879   7797  Z= 0.304
  Chirality :  0.042   0.165    884
  Planarity :  0.004   0.033    964
  Dihedral  :  4.268  19.235    779
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 8.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 15.06 %
    Favored  : 81.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.21 (0.32), residues: 714
  helix:  2.25 (0.26), residues: 375
  sheet: -1.07 (0.50), residues: 92
  loop : -0.70 (0.43), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG L  46 
 TYR   0.019   0.002   TYR A 113 
 PHE   0.012   0.001   PHE A 495 
 TRP   0.007   0.001   TRP A 332 
 HIS   0.006   0.001   HIS A 303 

Details of bonding type rmsd
  covalent geometry    : bond        0.00425 ( 5733)
  covalent geometry    : angle       0.59879 ( 7791)
  SS BOND              : bond        0.00179 (    3)
  SS BOND              : angle       1.26913 (    6)
  hydrogen bonds       : bond        0.03802 (  348)
  hydrogen bonds       : angle       4.19652 (  993)

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

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

  1428 Ramachandran restraints generated.
    714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1428 Ramachandran restraints generated.
    714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 82
  time to evaluate  : 0.157 
Fit side-chains
REVERT: A   44 GLU cc_start: 0.8644 (tp30) cc_final: 0.8433 (tp30)
REVERT: A  203 ASN cc_start: 0.8394 (m110) cc_final: 0.8075 (m-40)
REVERT: A  526 ASN cc_start: 0.8476 (t0) cc_final: 0.8120 (t0)
REVERT: B   17 HIS cc_start: 0.6481 (t-90) cc_final: 0.5780 (t-170)
REVERT: H    3 GLN cc_start: 0.7657 (pp30) cc_final: 0.7143 (pp30)
REVERT: H   87 ARG cc_start: 0.8391 (ptp90) cc_final: 0.7725 (ptp-170)
REVERT: H   89 GLU cc_start: 0.8948 (pm20) cc_final: 0.8636 (pm20)
REVERT: H  103 ILE cc_start: 0.8820 (pt) cc_final: 0.8296 (mp)
REVERT: L   83 ASP cc_start: 0.8964 (m-30) cc_final: 0.8709 (m-30)
  outliers start: 18
  outliers final: 9
  residues processed: 92
  average time/residue: 0.4047
  time to fit residues: 39.1832
Evaluate side-chains
  84 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 75
  time to evaluate  : 0.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 PHE
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain A residue  319 VAL
Chi-restraints excluded: chain A residue  379 LEU
Chi-restraints excluded: chain A residue  461 ILE
Chi-restraints excluded: chain H residue   19 LYS
Chi-restraints excluded: chain H residue  101 THR
Chi-restraints excluded: chain L residue   10 ILE
Chi-restraints excluded: chain L residue   15 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 26 optimal weight:    0.9980
   chunk 55 optimal weight:    0.5980
   chunk 33 optimal weight:    0.7980
   chunk 21 optimal weight:    0.9990
   chunk 59 optimal weight:    0.7980
   chunk 31 optimal weight:    0.7980
   chunk 40 optimal weight:    0.8980
   chunk 53 optimal weight:    0.7980
   chunk 6 optimal weight:    0.9980
   chunk 0 optimal weight:    6.9990
   chunk 29 optimal weight:    0.7980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
B  19 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.081323 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2810 r_free = 0.2810 target = 0.066040 restraints weight = 10789.855|
|-----------------------------------------------------------------------------|
r_work (start): 0.2819 rms_B_bonded: 2.33
r_work: 0.2696 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.2570 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.2570
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8076
moved from start:          0.1731

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   5736  Z= 0.179
  Angle     :  0.594  10.586   7797  Z= 0.299
  Chirality :  0.041   0.158    884
  Planarity :  0.004   0.033    964
  Dihedral  :  4.236  18.794    779
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 8.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 15.40 %
    Favored  : 81.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.23 (0.32), residues: 714
  helix:  2.27 (0.26), residues: 375
  sheet: -1.07 (0.51), residues: 92
  loop : -0.70 (0.43), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG L  46 
 TYR   0.017   0.002   TYR L  50 
 PHE   0.012   0.001   PHE A 495 
 TRP   0.007   0.001   TRP A 332 
 HIS   0.007   0.001   HIS A 303 

Details of bonding type rmsd
  covalent geometry    : bond        0.00402 ( 5733)
  covalent geometry    : angle       0.59329 ( 7791)
  SS BOND              : bond        0.00198 (    3)
  SS BOND              : angle       1.27257 (    6)
  hydrogen bonds       : bond        0.03782 (  348)
  hydrogen bonds       : angle       4.16352 (  993)

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

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

  1428 Ramachandran restraints generated.
    714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1428 Ramachandran restraints generated.
    714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 77
  time to evaluate  : 0.131 
Fit side-chains
REVERT: A  203 ASN cc_start: 0.8387 (m110) cc_final: 0.8087 (m110)
REVERT: A  379 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8555 (mt)
REVERT: A  526 ASN cc_start: 0.8519 (OUTLIER) cc_final: 0.8099 (t0)
REVERT: B   13 TRP cc_start: 0.8164 (OUTLIER) cc_final: 0.6532 (p90)
REVERT: B   17 HIS cc_start: 0.6517 (t-90) cc_final: 0.5821 (t-170)
REVERT: H    3 GLN cc_start: 0.7789 (pp30) cc_final: 0.7392 (pp30)
REVERT: H  103 ILE cc_start: 0.8901 (pt) cc_final: 0.8663 (mp)
REVERT: H  104 ARG cc_start: 0.8177 (mtp85) cc_final: 0.7971 (mtp85)
REVERT: L   79 MET cc_start: 0.9216 (OUTLIER) cc_final: 0.7796 (ttt)
REVERT: L   83 ASP cc_start: 0.9012 (m-30) cc_final: 0.8748 (m-30)
  outliers start: 21
  outliers final: 12
  residues processed: 85
  average time/residue: 0.4446
  time to fit residues: 39.6195
Evaluate side-chains
  91 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 75
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 PHE
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain A residue  379 LEU
Chi-restraints excluded: chain A residue  412 VAL
Chi-restraints excluded: chain A residue  461 ILE
Chi-restraints excluded: chain A residue  526 ASN
Chi-restraints excluded: chain B residue   13 TRP
Chi-restraints excluded: chain B residue   19 ASN
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   11 LEU
Chi-restraints excluded: chain H residue   19 LYS
Chi-restraints excluded: chain H residue  101 THR
Chi-restraints excluded: chain L residue   10 ILE
Chi-restraints excluded: chain L residue   15 LEU
Chi-restraints excluded: chain L residue   34 LEU
Chi-restraints excluded: chain L residue   79 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 29 optimal weight:    1.9990
   chunk 64 optimal weight:    0.8980
   chunk 32 optimal weight:    2.9990
   chunk 21 optimal weight:    0.3980
   chunk 28 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9990
   chunk 58 optimal weight:    0.4980
   chunk 61 optimal weight:    1.9990
   chunk 69 optimal weight:    0.9980
   chunk 10 optimal weight:    2.9990
   chunk 41 optimal weight:    0.8980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
B  19 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.081189 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2808 r_free = 0.2808 target = 0.065849 restraints weight = 10660.526|
|-----------------------------------------------------------------------------|
r_work (start): 0.2814 rms_B_bonded: 2.35
r_work: 0.2691 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.2565 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.2565
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8074
moved from start:          0.1822

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   5736  Z= 0.178
  Angle     :  0.598  11.247   7797  Z= 0.301
  Chirality :  0.041   0.152    884
  Planarity :  0.004   0.031    964
  Dihedral  :  4.211  18.478    779
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 9.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 16.07 %
    Favored  : 80.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.23 (0.32), residues: 714
  helix:  2.27 (0.26), residues: 375
  sheet: -1.07 (0.51), residues: 92
  loop : -0.70 (0.43), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG L  46 
 TYR   0.016   0.002   TYR L  50 
 PHE   0.012   0.001   PHE A 495 
 TRP   0.008   0.001   TRP A 332 
 HIS   0.007   0.001   HIS A 303 

Details of bonding type rmsd
  covalent geometry    : bond        0.00400 ( 5733)
  covalent geometry    : angle       0.59736 ( 7791)
  SS BOND              : bond        0.00192 (    3)
  SS BOND              : angle       1.24750 (    6)
  hydrogen bonds       : bond        0.03766 (  348)
  hydrogen bonds       : angle       4.14938 (  993)

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

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

  1428 Ramachandran restraints generated.
    714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1428 Ramachandran restraints generated.
    714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 77
  time to evaluate  : 0.238 
Fit side-chains
REVERT: A  203 ASN cc_start: 0.8387 (m110) cc_final: 0.8092 (m110)
REVERT: A  526 ASN cc_start: 0.8548 (OUTLIER) cc_final: 0.8113 (t0)
REVERT: B   13 TRP cc_start: 0.8209 (OUTLIER) cc_final: 0.6616 (p90)
REVERT: B   17 HIS cc_start: 0.6555 (t-90) cc_final: 0.5843 (t-170)
REVERT: H    3 GLN cc_start: 0.7787 (pp30) cc_final: 0.7461 (pp30)
REVERT: H  103 ILE cc_start: 0.8939 (pt) cc_final: 0.8505 (mp)
REVERT: L   79 MET cc_start: 0.9223 (OUTLIER) cc_final: 0.7828 (ttt)
REVERT: L   82 GLU cc_start: 0.9119 (pm20) cc_final: 0.8742 (pm20)
REVERT: L   83 ASP cc_start: 0.9016 (m-30) cc_final: 0.8756 (m-30)
  outliers start: 21
  outliers final: 11
  residues processed: 86
  average time/residue: 0.4189
  time to fit residues: 37.7979
Evaluate side-chains
  88 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 74
  time to evaluate  : 0.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 PHE
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain A residue  319 VAL
Chi-restraints excluded: chain A residue  412 VAL
Chi-restraints excluded: chain A residue  461 ILE
Chi-restraints excluded: chain A residue  526 ASN
Chi-restraints excluded: chain B residue   13 TRP
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   19 LYS
Chi-restraints excluded: chain H residue  101 THR
Chi-restraints excluded: chain L residue   10 ILE
Chi-restraints excluded: chain L residue   15 LEU
Chi-restraints excluded: chain L residue   34 LEU
Chi-restraints excluded: chain L residue   79 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 39 optimal weight:    0.7980
   chunk 4 optimal weight:    0.9980
   chunk 25 optimal weight:    0.0980
   chunk 53 optimal weight:    0.9980
   chunk 7 optimal weight:    1.9990
   chunk 66 optimal weight:    0.9990
   chunk 59 optimal weight:    2.9990
   chunk 50 optimal weight:    3.9990
   chunk 45 optimal weight:    0.3980
   chunk 35 optimal weight:    0.8980
   chunk 23 optimal weight:    2.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
B  19 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.081378 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2811 r_free = 0.2811 target = 0.066034 restraints weight = 10824.851|
|-----------------------------------------------------------------------------|
r_work (start): 0.2845 rms_B_bonded: 2.37
r_work: 0.2725 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.2605 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.2605
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8116
moved from start:          0.1898

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   5736  Z= 0.164
  Angle     :  0.601  12.320   7797  Z= 0.301
  Chirality :  0.041   0.151    884
  Planarity :  0.004   0.038    964
  Dihedral  :  4.226  18.267    779
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 9.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 16.75 %
    Favored  : 79.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.28 (0.32), residues: 714
  helix:  2.31 (0.26), residues: 375
  sheet: -1.01 (0.51), residues: 92
  loop : -0.67 (0.43), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG L  46 
 TYR   0.015   0.001   TYR L  50 
 PHE   0.012   0.001   PHE A 495 
 TRP   0.008   0.001   TRP A 332 
 HIS   0.007   0.001   HIS A 303 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 ( 5733)
  covalent geometry    : angle       0.59977 ( 7791)
  SS BOND              : bond        0.00180 (    3)
  SS BOND              : angle       1.23046 (    6)
  hydrogen bonds       : bond        0.03691 (  348)
  hydrogen bonds       : angle       4.11829 (  993)

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

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

  1428 Ramachandran restraints generated.
    714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1428 Ramachandran restraints generated.
    714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 79
  time to evaluate  : 0.197 
Fit side-chains
REVERT: A  203 ASN cc_start: 0.8457 (m110) cc_final: 0.8152 (m110)
REVERT: A  526 ASN cc_start: 0.8557 (OUTLIER) cc_final: 0.8113 (t0)
REVERT: B   13 TRP cc_start: 0.8271 (OUTLIER) cc_final: 0.6764 (p90)
REVERT: B   17 HIS cc_start: 0.6605 (t-90) cc_final: 0.5910 (t-170)
REVERT: H    3 GLN cc_start: 0.7887 (pp30) cc_final: 0.7485 (pp30)
REVERT: H   87 ARG cc_start: 0.8044 (OUTLIER) cc_final: 0.7033 (ptp90)
REVERT: H  103 ILE cc_start: 0.8975 (pt) cc_final: 0.8703 (mp)
REVERT: L   79 MET cc_start: 0.9233 (OUTLIER) cc_final: 0.7984 (ttt)
REVERT: L   82 GLU cc_start: 0.9113 (pm20) cc_final: 0.8742 (pm20)
REVERT: L   83 ASP cc_start: 0.9028 (m-30) cc_final: 0.8789 (m-30)
  outliers start: 22
  outliers final: 10
  residues processed: 88
  average time/residue: 0.3931
  time to fit residues: 36.4157
Evaluate side-chains
  89 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 75
  time to evaluate  : 0.128 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 PHE
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain A residue  319 VAL
Chi-restraints excluded: chain A residue  412 VAL
Chi-restraints excluded: chain A residue  461 ILE
Chi-restraints excluded: chain A residue  526 ASN
Chi-restraints excluded: chain B residue   13 TRP
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   19 LYS
Chi-restraints excluded: chain H residue   87 ARG
Chi-restraints excluded: chain H residue  101 THR
Chi-restraints excluded: chain L residue   10 ILE
Chi-restraints excluded: chain L residue   15 LEU
Chi-restraints excluded: chain L residue   79 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 67 optimal weight:    2.9990
   chunk 22 optimal weight:    0.8980
   chunk 58 optimal weight:    0.9990
   chunk 39 optimal weight:    0.7980
   chunk 69 optimal weight:    0.9980
   chunk 68 optimal weight:    0.9980
   chunk 57 optimal weight:    3.9990
   chunk 36 optimal weight:    0.9980
   chunk 4 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9980
   chunk 59 optimal weight:    0.5980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
H 112 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.081213 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2805 r_free = 0.2805 target = 0.065937 restraints weight = 10659.056|
|-----------------------------------------------------------------------------|
r_work (start): 0.2821 rms_B_bonded: 2.37
r_work: 0.2702 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.2580 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.2580
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8083
moved from start:          0.1941

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   5736  Z= 0.197
  Angle     :  0.636  13.499   7797  Z= 0.318
  Chirality :  0.043   0.197    884
  Planarity :  0.004   0.051    964
  Dihedral  :  4.293  18.492    779
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 8.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 17.94 %
    Favored  : 79.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.26 (0.32), residues: 714
  helix:  2.27 (0.26), residues: 375
  sheet: -0.98 (0.52), residues: 92
  loop : -0.67 (0.43), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG L  46 
 TYR   0.018   0.002   TYR L  50 
 PHE   0.012   0.001   PHE A 495 
 TRP   0.007   0.001   TRP A 332 
 HIS   0.007   0.001   HIS A 303 

Details of bonding type rmsd
  covalent geometry    : bond        0.00448 ( 5733)
  covalent geometry    : angle       0.63508 ( 7791)
  SS BOND              : bond        0.00194 (    3)
  SS BOND              : angle       1.30957 (    6)
  hydrogen bonds       : bond        0.03824 (  348)
  hydrogen bonds       : angle       4.17786 (  993)

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

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

  1428 Ramachandran restraints generated.
    714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1428 Ramachandran restraints generated.
    714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 75
  time to evaluate  : 0.182 
Fit side-chains
REVERT: A  203 ASN cc_start: 0.8445 (m110) cc_final: 0.8140 (m110)
REVERT: A  526 ASN cc_start: 0.8639 (OUTLIER) cc_final: 0.8216 (t0)
REVERT: B   13 TRP cc_start: 0.8325 (OUTLIER) cc_final: 0.6999 (p90)
REVERT: B   17 HIS cc_start: 0.6615 (t-90) cc_final: 0.5927 (t-170)
REVERT: H    3 GLN cc_start: 0.7914 (pp30) cc_final: 0.7508 (pp30)
REVERT: H    4 LEU cc_start: 0.8762 (mt) cc_final: 0.8367 (mt)
REVERT: H   87 ARG cc_start: 0.8271 (OUTLIER) cc_final: 0.7318 (ptp90)
REVERT: H  103 ILE cc_start: 0.9020 (pt) cc_final: 0.8744 (mp)
REVERT: L   79 MET cc_start: 0.9247 (OUTLIER) cc_final: 0.7974 (ttt)
REVERT: L   82 GLU cc_start: 0.9111 (pm20) cc_final: 0.8744 (pm20)
REVERT: L   83 ASP cc_start: 0.9028 (m-30) cc_final: 0.8775 (m-30)
  outliers start: 18
  outliers final: 11
  residues processed: 82
  average time/residue: 0.3798
  time to fit residues: 32.8047
Evaluate side-chains
  89 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 74
  time to evaluate  : 0.172 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 PHE
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain A residue  319 VAL
Chi-restraints excluded: chain A residue  412 VAL
Chi-restraints excluded: chain A residue  461 ILE
Chi-restraints excluded: chain A residue  515 ILE
Chi-restraints excluded: chain A residue  526 ASN
Chi-restraints excluded: chain B residue   13 TRP
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   19 LYS
Chi-restraints excluded: chain H residue   87 ARG
Chi-restraints excluded: chain H residue  101 THR
Chi-restraints excluded: chain L residue   10 ILE
Chi-restraints excluded: chain L residue   15 LEU
Chi-restraints excluded: chain L residue   79 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 9 optimal weight:    0.7980
   chunk 16 optimal weight:    0.5980
   chunk 35 optimal weight:    0.8980
   chunk 19 optimal weight:    0.9980
   chunk 37 optimal weight:    0.0170
   chunk 45 optimal weight:    0.6980
   chunk 63 optimal weight:    0.6980
   chunk 40 optimal weight:    0.4980
   chunk 5 optimal weight:    0.9990
   chunk 20 optimal weight:    0.0970
   chunk 46 optimal weight:    0.5980
   overall best weight:    0.3616

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

Flipped N/Q/H residues before XYZ refinement:
H  77 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.083470 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2848 r_free = 0.2848 target = 0.068253 restraints weight = 10587.204|
|-----------------------------------------------------------------------------|
r_work (start): 0.2864 rms_B_bonded: 2.39
r_work: 0.2745 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.2622 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.2622
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8053
moved from start:          0.1954

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   5736  Z= 0.138
  Angle     :  0.624  14.599   7797  Z= 0.312
  Chirality :  0.042   0.192    884
  Planarity :  0.004   0.056    964
  Dihedral  :  4.270  17.812    779
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 9.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 17.77 %
    Favored  : 79.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.33 (0.33), residues: 714
  helix:  2.35 (0.26), residues: 375
  sheet: -0.98 (0.51), residues: 92
  loop : -0.65 (0.43), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG L  46 
 TYR   0.018   0.001   TYR L  50 
 PHE   0.012   0.001   PHE A 495 
 TRP   0.009   0.001   TRP A 332 
 HIS   0.006   0.001   HIS A 303 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 5733)
  covalent geometry    : angle       0.62382 ( 7791)
  SS BOND              : bond        0.00169 (    3)
  SS BOND              : angle       1.14513 (    6)
  hydrogen bonds       : bond        0.03551 (  348)
  hydrogen bonds       : angle       4.05786 (  993)

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

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

  1428 Ramachandran restraints generated.
    714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1428 Ramachandran restraints generated.
    714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 86
  time to evaluate  : 0.131 
Fit side-chains
REVERT: A  115 LEU cc_start: 0.9164 (tp) cc_final: 0.8947 (tm)
REVERT: A  203 ASN cc_start: 0.8415 (m110) cc_final: 0.8080 (m110)
REVERT: A  526 ASN cc_start: 0.8475 (OUTLIER) cc_final: 0.7998 (t0)
REVERT: B   13 TRP cc_start: 0.8314 (OUTLIER) cc_final: 0.6867 (p90)
REVERT: B   17 HIS cc_start: 0.6567 (t-90) cc_final: 0.5909 (t-170)
REVERT: H    3 GLN cc_start: 0.7867 (pp30) cc_final: 0.7447 (pp30)
REVERT: H   87 ARG cc_start: 0.8317 (OUTLIER) cc_final: 0.7786 (ptt-90)
REVERT: H   89 GLU cc_start: 0.9170 (pm20) cc_final: 0.8847 (pm20)
REVERT: H  103 ILE cc_start: 0.8983 (pt) cc_final: 0.8687 (mp)
REVERT: L   82 GLU cc_start: 0.9090 (pm20) cc_final: 0.8704 (pm20)
REVERT: L   83 ASP cc_start: 0.8980 (m-30) cc_final: 0.8753 (m-30)
  outliers start: 18
  outliers final: 8
  residues processed: 96
  average time/residue: 0.3800
  time to fit residues: 38.2339
Evaluate side-chains
  90 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 79
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 PHE
Chi-restraints excluded: chain A residue  412 VAL
Chi-restraints excluded: chain A residue  461 ILE
Chi-restraints excluded: chain A residue  515 ILE
Chi-restraints excluded: chain A residue  526 ASN
Chi-restraints excluded: chain B residue   13 TRP
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   87 ARG
Chi-restraints excluded: chain H residue  101 THR
Chi-restraints excluded: chain L residue   10 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 21 optimal weight:    0.7980
   chunk 14 optimal weight:    0.7980
   chunk 42 optimal weight:    0.5980
   chunk 32 optimal weight:    0.6980
   chunk 26 optimal weight:    0.8980
   chunk 3 optimal weight:    0.9980
   chunk 22 optimal weight:    1.9990
   chunk 50 optimal weight:    0.4980
   chunk 30 optimal weight:    0.7980
   chunk 1 optimal weight:    0.9980
   chunk 24 optimal weight:    0.0980
   overall best weight:    0.5380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.082450 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2836 r_free = 0.2836 target = 0.067210 restraints weight = 10764.706|
|-----------------------------------------------------------------------------|
r_work (start): 0.2851 rms_B_bonded: 2.39
r_work: 0.2733 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.2609 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.2609
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8060
moved from start:          0.2015

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   5736  Z= 0.155
  Angle     :  0.641  15.182   7797  Z= 0.319
  Chirality :  0.042   0.185    884
  Planarity :  0.004   0.059    964
  Dihedral  :  4.288  19.526    779
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 9.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.06 %
    Favored  : 95.94 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 19.80 %
    Favored  : 78.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.31 (0.33), residues: 714
  helix:  2.32 (0.26), residues: 375
  sheet: -1.05 (0.51), residues: 92
  loop : -0.63 (0.43), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG L  46 
 TYR   0.018   0.001   TYR L  50 
 PHE   0.015   0.001   PHE H  80 
 TRP   0.008   0.001   TRP A 332 
 HIS   0.006   0.001   HIS A 303 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 ( 5733)
  covalent geometry    : angle       0.64070 ( 7791)
  SS BOND              : bond        0.00174 (    3)
  SS BOND              : angle       1.15201 (    6)
  hydrogen bonds       : bond        0.03613 (  348)
  hydrogen bonds       : angle       4.08554 (  993)

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

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

  1428 Ramachandran restraints generated.
    714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1428 Ramachandran restraints generated.
    714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 84
  time to evaluate  : 0.135 
Fit side-chains
REVERT: A  115 LEU cc_start: 0.9158 (tp) cc_final: 0.8946 (tm)
REVERT: A  203 ASN cc_start: 0.8406 (m110) cc_final: 0.8073 (m110)
REVERT: A  526 ASN cc_start: 0.8433 (OUTLIER) cc_final: 0.8009 (t0)
REVERT: B   13 TRP cc_start: 0.8337 (OUTLIER) cc_final: 0.7090 (p90)
REVERT: B   17 HIS cc_start: 0.6586 (t-90) cc_final: 0.5949 (t-170)
REVERT: H    3 GLN cc_start: 0.7940 (pp30) cc_final: 0.7514 (pp30)
REVERT: H   87 ARG cc_start: 0.8399 (ptt-90) cc_final: 0.8039 (ptt-90)
REVERT: H   89 GLU cc_start: 0.9162 (pm20) cc_final: 0.8843 (pm20)
REVERT: H  103 ILE cc_start: 0.8993 (pt) cc_final: 0.8690 (mp)
REVERT: L   82 GLU cc_start: 0.9072 (pm20) cc_final: 0.8681 (pm20)
REVERT: L   83 ASP cc_start: 0.9001 (m-30) cc_final: 0.8695 (m-30)
  outliers start: 12
  outliers final: 9
  residues processed: 90
  average time/residue: 0.3662
  time to fit residues: 34.8631
Evaluate side-chains
  91 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 80
  time to evaluate  : 0.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 PHE
Chi-restraints excluded: chain A residue  412 VAL
Chi-restraints excluded: chain A residue  461 ILE
Chi-restraints excluded: chain A residue  515 ILE
Chi-restraints excluded: chain A residue  526 ASN
Chi-restraints excluded: chain B residue   13 TRP
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue  101 THR
Chi-restraints excluded: chain L residue   10 ILE
Chi-restraints excluded: chain L residue   15 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 3 optimal weight:    1.9990
   chunk 20 optimal weight:    3.9990
   chunk 29 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9980
   chunk 34 optimal weight:    0.6980
   chunk 32 optimal weight:    0.7980
   chunk 31 optimal weight:    0.0670
   chunk 43 optimal weight:    0.0030
   chunk 49 optimal weight:    0.3980
   chunk 65 optimal weight:    0.1980
   chunk 48 optimal weight:    0.9980
   overall best weight:    0.2728

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.084819 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2878 r_free = 0.2878 target = 0.069770 restraints weight = 10567.032|
|-----------------------------------------------------------------------------|
r_work (start): 0.2889 rms_B_bonded: 2.36
r_work: 0.2775 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.2653 rms_B_bonded: 4.62 restraints_weight: 0.2500
r_work (final): 0.2653
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8021
moved from start:          0.2057

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   5736  Z= 0.128
  Angle     :  0.630  14.630   7797  Z= 0.313
  Chirality :  0.041   0.181    884
  Planarity :  0.004   0.061    964
  Dihedral  :  4.249  21.595    779
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 10.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 19.80 %
    Favored  : 78.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.36 (0.33), residues: 714
  helix:  2.39 (0.26), residues: 375
  sheet: -0.95 (0.51), residues: 91
  loop : -0.69 (0.43), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG L  46 
 TYR   0.018   0.001   TYR L  50 
 PHE   0.013   0.001   PHE H  80 
 TRP   0.009   0.001   TRP A 332 
 HIS   0.006   0.001   HIS A 303 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 5733)
  covalent geometry    : angle       0.62915 ( 7791)
  SS BOND              : bond        0.00180 (    3)
  SS BOND              : angle       1.02945 (    6)
  hydrogen bonds       : bond        0.03400 (  348)
  hydrogen bonds       : angle       4.00861 (  993)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1589.75 seconds
wall clock time: 27 minutes 58.35 seconds (1678.35 seconds total)