Starting phenix.real_space_refine
on Tue Feb 11 07:44:44 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ttf_41606/02_2025/8ttf_41606.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ttf_41606/02_2025/8ttf_41606.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.61
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ttf_41606/02_2025/8ttf_41606.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ttf_41606/02_2025/8ttf_41606.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ttf_41606/02_2025/8ttf_41606.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ttf_41606/02_2025/8ttf_41606.cif"
  }
  resolution = 3.61
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.055
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      27      5.16       5
     C    3121      2.51       5
     N     755      2.21       5
     O     860      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 4763
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 2987
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 388, 2987
          Classifications: {'peptide': 388}
          Link IDs: {'PTRANS': 14, 'TRANS': 373}
    Chain: "C"
      Number of atoms: 990
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 990
          Classifications: {'peptide': 128}
          Link IDs: {'PTRANS': 3, 'TRANS': 124}
    Chain: "D"
      Number of atoms: 786
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 105, 786
          Classifications: {'peptide': 105}
          Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 99}
  Time building chain proxies: 3.36, per 1000 atoms: 0.71
  Number of scatterers: 4763
  At special positions: 0
  Unit cell: (59.924, 74.272, 104.656, 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      27     16.00
     O     860      8.00
     N     755      7.00
     C    3121      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS C  48 " - pdb=" SG  CYS C 122 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  47 " - pdb=" SG  CYS D 112 " distance=2.04

  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: 1.25
  Conformation dependent library (CDL) restraints added in 622.6 milliseconds
  

  1230 Ramachandran restraints generated.
    615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1126

  Finding SS restraints...
    Secondary structure from input PDB file:
      18 helices and 6 sheets defined
      56.2% alpha, 15.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.49
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2 through 18
      removed outlier: 3.552A  pdb=" N   ILE A  12 " --> pdb=" O   LEU A   8 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   ILE A  15 " --> pdb=" O   ASN A  11 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 22 through 24
      No H-bonds generated for 'chain 'A' and resid 22 through 24'
    Processing helix  chain 'A' and resid 25 through 33
      removed outlier: 3.579A  pdb=" N   TYR A  29 " --> pdb=" O   VAL A  25 " (cutoff:3.500A)
      removed outlier: 5.337A  pdb=" N   LYS A  31 " --> pdb=" O   PRO A  27 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   LEU A  33 " --> pdb=" O   TYR A  29 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 36 through 65
      removed outlier: 3.590A  pdb=" N   LEU A  40 " --> pdb=" O   THR A  36 " (cutoff:3.500A)
      removed outlier: 4.570A  pdb=" N   PHE A  47 " --> pdb=" O   LEU A  43 " (cutoff:3.500A)
      removed outlier: 4.271A  pdb=" N   ALA A  48 " --> pdb=" O   VAL A  44 " (cutoff:3.500A)
      Proline residue:  A  56  - end of helix
    Processing helix  chain 'A' and resid 67 through 88
    Processing helix  chain 'A' and resid 90 through 120
      Proline residue:  A 110  - end of helix
    Processing helix  chain 'A' and resid 121 through 125
      removed outlier: 3.609A  pdb=" N   GLN A 124 " --> pdb=" O   PRO A 121 " (cutoff:3.500A)
      removed outlier: 3.939A  pdb=" N   LYS A 125 " --> pdb=" O   SER A 122 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 121 through 125'
    Processing helix  chain 'A' and resid 126 through 152
      Proline residue:  A 144  - end of helix
    Processing helix  chain 'A' and resid 156 through 177
    Processing helix  chain 'A' and resid 201 through 203
      No H-bonds generated for 'chain 'A' and resid 201 through 203'
    Processing helix  chain 'A' and resid 204 through 233
      removed outlier: 3.886A  pdb=" N   GLN A 222 " --> pdb=" O   LEU A 218 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   THR A 223 " --> pdb=" O   SER A 219 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 236 through 264
      removed outlier: 3.728A  pdb=" N   TYR A 257 " --> pdb=" O   LEU A 253 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   PHE A 259 " --> pdb=" O   GLN A 255 " (cutoff:3.500A)
      removed outlier: 6.865A  pdb=" N   ASP A 260 " --> pdb=" O   ILE A 256 " (cutoff:3.500A)
      removed outlier: 4.666A  pdb=" N   LYS A 261 " --> pdb=" O   TYR A 257 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 267 through 288
      removed outlier: 3.679A  pdb=" N   VAL A 287 " --> pdb=" O   LEU A 283 " (cutoff:3.500A)
      removed outlier: 4.204A  pdb=" N   PHE A 288 " --> pdb=" O   ILE A 284 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 291 through 308
      removed outlier: 4.059A  pdb=" N   ILE A 295 " --> pdb=" O   ASP A 291 " (cutoff:3.500A)
      removed outlier: 4.070A  pdb=" N   SER A 299 " --> pdb=" O   ILE A 295 " (cutoff:3.500A)
      removed outlier: 3.908A  pdb=" N   PHE A 300 " --> pdb=" O   MET A 296 " (cutoff:3.500A)
      removed outlier: 4.173A  pdb=" N   ILE A 304 " --> pdb=" O   PHE A 300 " (cutoff:3.500A)
      removed outlier: 4.232A  pdb=" N   GLY A 305 " --> pdb=" O   VAL A 301 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   PHE A 306 " --> pdb=" O   VAL A 302 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 309 through 322
      removed outlier: 3.551A  pdb=" N   ALA A 321 " --> pdb=" O   PHE A 317 " (cutoff:3.500A)
      removed outlier: 3.946A  pdb=" N   GLY A 322 " --> pdb=" O   SER A 318 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 324 through 354
      Proline residue:  A 344  - end of helix
      removed outlier: 3.862A  pdb=" N   PHE A 351 " --> pdb=" O   ALA A 347 " (cutoff:3.500A)
      removed outlier: 3.957A  pdb=" N   ASP A 352 " --> pdb=" O   GLY A 348 " (cutoff:3.500A)
      removed outlier: 4.164A  pdb=" N   VAL A 353 " --> pdb=" O   ALA A 349 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 356 through 386
      removed outlier: 3.820A  pdb=" N   GLN A 378 " --> pdb=" O   LEU A 374 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   HIS A 379 " --> pdb=" O   ILE A 375 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 103 through 107
    Processing sheet with id=AA1, first strand: chain 'C' and resid 31 through 33
    Processing sheet with id=AA2, first strand: chain 'C' and resid 84 through 86
      removed outlier: 5.628A  pdb=" N   TRP C  73 " --> pdb=" O   ARG C  64 " (cutoff:3.500A)
      removed outlier: 6.266A  pdb=" N   ARG C  64 " --> pdb=" O   TRP C  73 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 129 through 132
    Processing sheet with id=AA4, first strand: chain 'D' and resid 28 through 31
    Processing sheet with id=AA5, first strand: chain 'D' and resid 34 through 36
      removed outlier: 7.110A  pdb=" N   LEU D  35 " --> pdb=" O   GLU D 129 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   THR D 126 " --> pdb=" O   TYR D 110 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   TYR D 110 " --> pdb=" O   THR D 126 " (cutoff:3.500A)
      removed outlier: 6.625A  pdb=" N   TRP D  59 " --> pdb=" O   LEU D  71 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 34 through 36
      removed outlier: 7.110A  pdb=" N   LEU D  35 " --> pdb=" O   GLU D 129 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   THR D 126 " --> pdb=" O   TYR D 110 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   TYR D 110 " --> pdb=" O   THR D 126 " (cutoff:3.500A)

    303 hydrogen bonds defined for protein.
    867 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: 1.30

  Time building geometry restraints manager: 1.45 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: 1443
        1.34 -     1.46: 1277
        1.46 -     1.58: 2110
        1.58 -     1.70: 1
        1.70 -     1.82: 49
  Bond restraints: 4880
  Sorted by residual:
  bond pdb=" CB  PRO C 140 "
       pdb=" CG  PRO C 140 "
    ideal  model  delta    sigma   weight residual
    1.492  1.595 -0.103 5.00e-02 4.00e+02 4.23e+00
  bond pdb=" CA  GLU A 192 "
       pdb=" CB  GLU A 192 "
    ideal  model  delta    sigma   weight residual
    1.522  1.531 -0.009 7.00e-03 2.04e+04 1.58e+00
  bond pdb=" CG1 ILE A  15 "
       pdb=" CD1 ILE A  15 "
    ideal  model  delta    sigma   weight residual
    1.513  1.476  0.037 3.90e-02 6.57e+02 8.76e-01
  bond pdb=" C   PHE C 134 "
       pdb=" N   TYR C 135 "
    ideal  model  delta    sigma   weight residual
    1.330  1.341 -0.011 1.23e-02 6.61e+03 7.87e-01
  bond pdb=" CG  PRO C 140 "
       pdb=" CD  PRO C 140 "
    ideal  model  delta    sigma   weight residual
    1.503  1.475  0.028 3.40e-02 8.65e+02 6.70e-01
  ... (remaining 4875 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.74: 6488
        1.74 -     3.49: 95
        3.49 -     5.23: 24
        5.23 -     6.98: 6
        6.98 -     8.72: 1
  Bond angle restraints: 6614
  Sorted by residual:
  angle pdb=" CA  PRO C 140 "
        pdb=" N   PRO C 140 "
        pdb=" CD  PRO C 140 "
      ideal   model   delta    sigma   weight residual
     112.00  105.31    6.69 1.40e+00 5.10e-01 2.28e+01
  angle pdb=" C   TYR C 133 "
        pdb=" N   PHE C 134 "
        pdb=" CA  PHE C 134 "
      ideal   model   delta    sigma   weight residual
     123.05  129.10   -6.05 1.57e+00 4.06e-01 1.48e+01
  angle pdb=" C   LEU A 191 "
        pdb=" N   GLU A 192 "
        pdb=" CA  GLU A 192 "
      ideal   model   delta    sigma   weight residual
     122.83  126.38   -3.55 1.08e+00 8.57e-01 1.08e+01
  angle pdb=" CB  MET A  95 "
        pdb=" CG  MET A  95 "
        pdb=" SD  MET A  95 "
      ideal   model   delta    sigma   weight residual
     112.70  121.42   -8.72 3.00e+00 1.11e-01 8.46e+00
  angle pdb=" N   PRO C 140 "
        pdb=" CD  PRO C 140 "
        pdb=" CG  PRO C 140 "
      ideal   model   delta    sigma   weight residual
     103.20   98.96    4.24 1.50e+00 4.44e-01 8.00e+00
  ... (remaining 6609 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.70: 2537
       16.70 -    33.40: 244
       33.40 -    50.10: 43
       50.10 -    66.80: 4
       66.80 -    83.50: 6
  Dihedral angle restraints: 2834
    sinusoidal: 1062
      harmonic: 1772
  Sorted by residual:
  dihedral pdb=" CA  TRP C 131 "
           pdb=" C   TRP C 131 "
           pdb=" N   TYR C 132 "
           pdb=" CA  TYR C 132 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.75   22.25     0      5.00e+00 4.00e-02 1.98e+01
  dihedral pdb=" CA  GLU A 192 "
           pdb=" C   GLU A 192 "
           pdb=" N   PRO A 193 "
           pdb=" CA  PRO A 193 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.11   18.89     0      5.00e+00 4.00e-02 1.43e+01
  dihedral pdb=" CA  TYR A 235 "
           pdb=" C   TYR A 235 "
           pdb=" N   SER A 236 "
           pdb=" CA  SER A 236 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.96   18.04     0      5.00e+00 4.00e-02 1.30e+01
  ... (remaining 2831 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 588
       0.046 -    0.092: 136
       0.092 -    0.139: 29
       0.139 -    0.185: 1
       0.185 -    0.231: 1
  Chirality restraints: 755
  Sorted by residual:
  chirality pdb=" CA  PHE C 134 "
            pdb=" N   PHE C 134 "
            pdb=" C   PHE C 134 "
            pdb=" CB  PHE C 134 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.34e+00
  chirality pdb=" CA  LEU A  26 "
            pdb=" N   LEU A  26 "
            pdb=" C   LEU A  26 "
            pdb=" CB  LEU A  26 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.09e-01
  chirality pdb=" CA  ASN A 234 "
            pdb=" N   ASN A 234 "
            pdb=" C   ASN A 234 "
            pdb=" CB  ASN A 234 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 3.93e-01
  ... (remaining 752 not shown)

  Planarity restraints: 816
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER C 139 "    0.053 5.00e-02 4.00e+02   7.72e-02 9.54e+00
        pdb=" N   PRO C 140 "   -0.133 5.00e-02 4.00e+02
        pdb=" CA  PRO C 140 "    0.038 5.00e-02 4.00e+02
        pdb=" CD  PRO C 140 "    0.043 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A  26 "    0.030 5.00e-02 4.00e+02   4.47e-02 3.20e+00
        pdb=" N   PRO A  27 "   -0.077 5.00e-02 4.00e+02
        pdb=" CA  PRO A  27 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO A  27 "    0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR C 133 "    0.008 2.00e-02 2.50e+03   1.62e-02 2.64e+00
        pdb=" C   TYR C 133 "   -0.028 2.00e-02 2.50e+03
        pdb=" O   TYR C 133 "    0.011 2.00e-02 2.50e+03
        pdb=" N   PHE C 134 "    0.009 2.00e-02 2.50e+03
  ... (remaining 813 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.69: 78
        2.69 -     3.25: 4748
        3.25 -     3.80: 7620
        3.80 -     4.35: 9371
        4.35 -     4.90: 15937
  Nonbonded interactions: 37754
  Sorted by model distance:
  nonbonded pdb=" OG  SER C  76 "
            pdb=" OG  SER C  85 "
     model   vdw
     2.144 3.040
  nonbonded pdb=" OG  SER C  57 "
            pdb=" OE1 GLU C 128 "
     model   vdw
     2.270 3.040
  nonbonded pdb=" OE1 GLN D  30 "
            pdb=" OG1 THR D 126 "
     model   vdw
     2.312 3.040
  nonbonded pdb=" O   SER A  81 "
            pdb=" OG  SER A  97 "
     model   vdw
     2.328 3.040
  nonbonded pdb=" NZ  LYS A  68 "
            pdb=" O   ILE A 177 "
     model   vdw
     2.335 3.120
  ... (remaining 37749 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.840
  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:          0.220
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     15.400
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.580
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.200
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7458
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   0.103   4880  Z= 0.174
  Angle     :  0.599   8.724   6614  Z= 0.319
  Chirality :  0.041   0.231    755
  Planarity :  0.005   0.077    816
  Dihedral  : 13.410  83.495   1702
  Min Nonbonded Distance : 2.144

Molprobity Statistics.
  All-atom Clashscore : 9.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.19 %
    Favored  : 99.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.37 (0.36), residues: 615
  helix:  1.69 (0.31), residues: 331
  sheet:  0.62 (0.51), residues: 122
  loop : -0.41 (0.49), residues: 162

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C  73 
 HIS   0.004   0.001   HIS C  61 
 PHE   0.012   0.001   PHE A  10 
 TYR   0.024   0.002   TYR A 235 
 ARG   0.002   0.000   ARG A 324 

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

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

  1230 Ramachandran restraints generated.
    615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1230 Ramachandran restraints generated.
    615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 0.477 
Fit side-chains
REVERT: A  231 ASP cc_start: 0.8218 (t70) cc_final: 0.7974 (t0)
REVERT: A  308 MET cc_start: 0.6697 (mmt) cc_final: 0.6378 (tpp)
REVERT: A  346 ILE cc_start: 0.8752 (mm) cc_final: 0.8513 (mm)
REVERT: A  385 GLU cc_start: 0.5275 (mp0) cc_final: 0.5061 (mp0)
REVERT: C  125 MET cc_start: 0.8044 (mtm) cc_final: 0.7776 (mtm)
  outliers start: 0
  outliers final: 0
  residues processed: 110
  average time/residue: 0.1858
  time to fit residues: 25.5831
Evaluate side-chains
  97 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.533 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 50 optimal weight:    2.9990
   chunk 45 optimal weight:    0.9990
   chunk 25 optimal weight:    0.8980
   chunk 15 optimal weight:    0.0670
   chunk 30 optimal weight:    0.9990
   chunk 24 optimal weight:    2.9990
   chunk 47 optimal weight:    0.9980
   chunk 18 optimal weight:    4.9990
   chunk 28 optimal weight:    1.9990
   chunk 35 optimal weight:    2.9990
   chunk 54 optimal weight:    7.9990
   overall best weight:    0.7922

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

Flipped N/Q/H residues before XYZ refinement:
** C  29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4109 r_free = 0.4109 target = 0.187162 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.149974 restraints weight = 5568.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.155734 restraints weight = 3318.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.159591 restraints weight = 2395.157|
|-----------------------------------------------------------------------------|
r_work (final): 0.3772
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7469
moved from start:          0.0958

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   4880  Z= 0.188
  Angle     :  0.608  11.595   6614  Z= 0.300
  Chirality :  0.043   0.202    755
  Planarity :  0.004   0.037    816
  Dihedral  :  4.262  22.203    660
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 7.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  1.16 %
    Allowed  : 11.41 %
    Favored  : 87.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.54 (0.36), residues: 615
  helix:  1.94 (0.31), residues: 327
  sheet:  0.65 (0.51), residues: 122
  loop : -0.48 (0.48), residues: 166

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C  73 
 HIS   0.003   0.001   HIS A 155 
 PHE   0.025   0.001   PHE C 134 
 TYR   0.022   0.002   TYR A 235 
 ARG   0.002   0.000   ARG C  93 

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

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

  1230 Ramachandran restraints generated.
    615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1230 Ramachandran restraints generated.
    615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 103
  time to evaluate  : 0.528 
Fit side-chains
REVERT: A  231 ASP cc_start: 0.8334 (t70) cc_final: 0.8042 (t0)
REVERT: A  308 MET cc_start: 0.6876 (mmt) cc_final: 0.6519 (tpp)
REVERT: A  341 PHE cc_start: 0.7721 (t80) cc_final: 0.7200 (t80)
REVERT: D  127 LYS cc_start: 0.8411 (ttpp) cc_final: 0.8049 (tmmt)
  outliers start: 6
  outliers final: 2
  residues processed: 105
  average time/residue: 0.1735
  time to fit residues: 23.0773
Evaluate side-chains
  97 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 95
  time to evaluate  : 0.489 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 SER
Chi-restraints excluded: chain A residue  379 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 5 optimal weight:    0.5980
   chunk 26 optimal weight:    3.9990
   chunk 38 optimal weight:    7.9990
   chunk 33 optimal weight:    1.9990
   chunk 13 optimal weight:    3.9990
   chunk 27 optimal weight:    1.9990
   chunk 3 optimal weight:    0.0470
   chunk 4 optimal weight:    0.6980
   chunk 12 optimal weight:    2.9990
   chunk 47 optimal weight:    1.9990
   chunk 35 optimal weight:    0.0270
   overall best weight:    0.6738

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

Flipped N/Q/H residues before XYZ refinement:
C  29 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4049 r_free = 0.4049 target = 0.180590 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.143380 restraints weight = 5696.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.149235 restraints weight = 3254.085|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.153228 restraints weight = 2287.253|
|-----------------------------------------------------------------------------|
r_work (final): 0.3767
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7470
moved from start:          0.1176

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   4880  Z= 0.168
  Angle     :  0.581   8.337   6614  Z= 0.286
  Chirality :  0.042   0.198    755
  Planarity :  0.004   0.032    816
  Dihedral  :  4.111  22.139    660
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 7.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 14.70 %
    Favored  : 82.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.63 (0.36), residues: 615
  helix:  2.01 (0.31), residues: 327
  sheet:  0.66 (0.50), residues: 122
  loop : -0.40 (0.49), residues: 166

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 136 
 HIS   0.003   0.001   HIS C  61 
 PHE   0.017   0.001   PHE A 341 
 TYR   0.019   0.001   TYR A 235 
 ARG   0.002   0.000   ARG C  93 

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

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

  1230 Ramachandran restraints generated.
    615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1230 Ramachandran restraints generated.
    615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 97
  time to evaluate  : 0.505 
Fit side-chains
REVERT: A  308 MET cc_start: 0.6909 (mmt) cc_final: 0.6562 (tpp)
REVERT: A  341 PHE cc_start: 0.7799 (t80) cc_final: 0.7545 (t80)
REVERT: D  127 LYS cc_start: 0.8418 (ttpp) cc_final: 0.8005 (tmmt)
  outliers start: 14
  outliers final: 6
  residues processed: 102
  average time/residue: 0.1696
  time to fit residues: 22.0805
Evaluate side-chains
  102 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 96
  time to evaluate  : 0.544 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 SER
Chi-restraints excluded: chain A residue  209 ILE
Chi-restraints excluded: chain A residue  285 LEU
Chi-restraints excluded: chain A residue  379 HIS
Chi-restraints excluded: chain C residue  117 THR
Chi-restraints excluded: chain D residue   98 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 9 optimal weight:    0.6980
   chunk 13 optimal weight:    2.9990
   chunk 40 optimal weight:    3.9990
   chunk 25 optimal weight:    2.9990
   chunk 59 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9980
   chunk 36 optimal weight:    0.9990
   chunk 47 optimal weight:    2.9990
   chunk 18 optimal weight:   10.0000
   chunk 56 optimal weight:   10.0000
   chunk 14 optimal weight:    4.9990
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:
A 234 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.173850 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.136605 restraints weight = 5805.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.142024 restraints weight = 3377.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.145644 restraints weight = 2405.217|
|-----------------------------------------------------------------------------|
r_work (final): 0.3686
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7604
moved from start:          0.1636

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.059   4880  Z= 0.310
  Angle     :  0.662   9.179   6614  Z= 0.334
  Chirality :  0.045   0.208    755
  Planarity :  0.004   0.033    816
  Dihedral  :  4.311  22.526    660
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 8.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 17.21 %
    Favored  : 79.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.25 (0.36), residues: 615
  helix:  1.61 (0.30), residues: 329
  sheet:  0.64 (0.50), residues: 122
  loop : -0.52 (0.49), residues: 164

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP C 136 
 HIS   0.005   0.001   HIS A 155 
 PHE   0.019   0.002   PHE C 134 
 TYR   0.020   0.002   TYR A 235 
 ARG   0.003   0.000   ARG C  93 

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

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

  1230 Ramachandran restraints generated.
    615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1230 Ramachandran restraints generated.
    615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 109
  time to evaluate  : 0.565 
Fit side-chains
REVERT: A  125 LYS cc_start: 0.6751 (mttt) cc_final: 0.6429 (mmtm)
REVERT: A  308 MET cc_start: 0.7073 (mmt) cc_final: 0.6740 (tpp)
REVERT: D  106 ASP cc_start: 0.7759 (m-30) cc_final: 0.7506 (m-30)
REVERT: D  127 LYS cc_start: 0.8448 (ttpp) cc_final: 0.8007 (tmmt)
  outliers start: 18
  outliers final: 13
  residues processed: 118
  average time/residue: 0.1876
  time to fit residues: 27.6855
Evaluate side-chains
  114 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 101
  time to evaluate  : 0.491 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue   79 SER
Chi-restraints excluded: chain A residue  116 ILE
Chi-restraints excluded: chain A residue  133 SER
Chi-restraints excluded: chain A residue  177 ILE
Chi-restraints excluded: chain A residue  205 ILE
Chi-restraints excluded: chain A residue  209 ILE
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  379 HIS
Chi-restraints excluded: chain C residue  117 THR
Chi-restraints excluded: chain C residue  151 LEU
Chi-restraints excluded: chain D residue   98 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 55 optimal weight:    0.9990
   chunk 33 optimal weight:    2.9990
   chunk 20 optimal weight:    3.9990
   chunk 59 optimal weight:    0.9990
   chunk 30 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9990
   chunk 31 optimal weight:    0.5980
   chunk 47 optimal weight:    0.8980
   chunk 52 optimal weight:    0.7980
   chunk 49 optimal weight:    2.9990
   chunk 9 optimal weight:    1.9990
   overall best weight:    0.8584

-------------------------------------------------------------------------------
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 = 0.4068 r_free = 0.4068 target = 0.182058 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.144539 restraints weight = 5617.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.150479 restraints weight = 3236.710|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.154553 restraints weight = 2269.597|
|-----------------------------------------------------------------------------|
r_work (final): 0.3732
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7498
moved from start:          0.1669

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   4880  Z= 0.196
  Angle     :  0.606   8.745   6614  Z= 0.301
  Chirality :  0.043   0.204    755
  Planarity :  0.004   0.033    816
  Dihedral  :  4.223  23.002    660
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 7.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 19.73 %
    Favored  : 77.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.51 (0.36), residues: 615
  helix:  1.88 (0.31), residues: 327
  sheet:  0.68 (0.50), residues: 122
  loop : -0.48 (0.49), residues: 166

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP C 136 
 HIS   0.004   0.001   HIS A 155 
 PHE   0.019   0.001   PHE C 134 
 TYR   0.023   0.002   TYR A 235 
 ARG   0.003   0.000   ARG C  93 

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

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

  1230 Ramachandran restraints generated.
    615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1230 Ramachandran restraints generated.
    615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 101
  time to evaluate  : 0.528 
Fit side-chains
REVERT: A  125 LYS cc_start: 0.6749 (mttt) cc_final: 0.6382 (mmtm)
REVERT: A  308 MET cc_start: 0.6983 (mmt) cc_final: 0.6689 (tpp)
REVERT: D  106 ASP cc_start: 0.7747 (m-30) cc_final: 0.7341 (m-30)
REVERT: D  127 LYS cc_start: 0.8377 (ttpp) cc_final: 0.7920 (tmmt)
  outliers start: 13
  outliers final: 13
  residues processed: 107
  average time/residue: 0.1741
  time to fit residues: 23.5578
Evaluate side-chains
  110 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 97
  time to evaluate  : 0.476 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue   26 LEU
Chi-restraints excluded: chain A residue   79 SER
Chi-restraints excluded: chain A residue  209 ILE
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  379 HIS
Chi-restraints excluded: chain C residue   63 VAL
Chi-restraints excluded: chain C residue  100 THR
Chi-restraints excluded: chain C residue  117 THR
Chi-restraints excluded: chain C residue  125 MET
Chi-restraints excluded: chain D residue   98 THR
Chi-restraints excluded: chain D residue  126 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 57 optimal weight:    3.9990
   chunk 16 optimal weight:    0.9990
   chunk 27 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9990
   chunk 9 optimal weight:    0.9990
   chunk 59 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9990
   chunk 35 optimal weight:    0.9980
   chunk 45 optimal weight:    1.9990
   chunk 55 optimal weight:    5.9990
   overall best weight:    0.9986

-------------------------------------------------------------------------------
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 = 0.4060 r_free = 0.4060 target = 0.181281 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.143555 restraints weight = 5581.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.149451 restraints weight = 3244.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.153427 restraints weight = 2286.852|
|-----------------------------------------------------------------------------|
r_work (final): 0.3708
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7519
moved from start:          0.1826

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   4880  Z= 0.218
  Angle     :  0.621   8.680   6614  Z= 0.308
  Chirality :  0.043   0.204    755
  Planarity :  0.004   0.032    816
  Dihedral  :  4.170  22.991    660
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 7.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  4.26 %
    Allowed  : 19.34 %
    Favored  : 76.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.49 (0.36), residues: 615
  helix:  1.85 (0.30), residues: 329
  sheet:  0.71 (0.50), residues: 122
  loop : -0.51 (0.49), residues: 164

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C 136 
 HIS   0.002   0.001   HIS A 155 
 PHE   0.020   0.001   PHE C 134 
 TYR   0.023   0.002   TYR A 235 
 ARG   0.002   0.000   ARG C  93 

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

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

  1230 Ramachandran restraints generated.
    615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1230 Ramachandran restraints generated.
    615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 101
  time to evaluate  : 0.524 
Fit side-chains
REVERT: A  125 LYS cc_start: 0.6795 (mttt) cc_final: 0.6394 (mmtm)
REVERT: A  308 MET cc_start: 0.7027 (mmt) cc_final: 0.6742 (tpp)
REVERT: D  106 ASP cc_start: 0.7625 (m-30) cc_final: 0.7286 (m-30)
REVERT: D  127 LYS cc_start: 0.8366 (ttpp) cc_final: 0.7870 (tmmt)
  outliers start: 22
  outliers final: 16
  residues processed: 115
  average time/residue: 0.1751
  time to fit residues: 25.7442
Evaluate side-chains
  115 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 99
  time to evaluate  : 0.530 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue   26 LEU
Chi-restraints excluded: chain A residue   79 SER
Chi-restraints excluded: chain A residue  116 ILE
Chi-restraints excluded: chain A residue  177 ILE
Chi-restraints excluded: chain A residue  209 ILE
Chi-restraints excluded: chain A residue  213 VAL
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  379 HIS
Chi-restraints excluded: chain C residue   63 VAL
Chi-restraints excluded: chain C residue  100 THR
Chi-restraints excluded: chain C residue  117 THR
Chi-restraints excluded: chain C residue  125 MET
Chi-restraints excluded: chain D residue   98 THR
Chi-restraints excluded: chain D residue  126 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 20 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9990
   chunk 18 optimal weight:    4.9990
   chunk 11 optimal weight:    0.9990
   chunk 53 optimal weight:    3.9990
   chunk 13 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 39 optimal weight:    8.9990
   chunk 2 optimal weight:    0.0060
   chunk 58 optimal weight:    2.9990
   chunk 56 optimal weight:    3.9990
   overall best weight:    1.0004

-------------------------------------------------------------------------------
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 = 0.4065 r_free = 0.4065 target = 0.181734 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.143533 restraints weight = 5676.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.149391 restraints weight = 3324.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.153349 restraints weight = 2375.447|
|-----------------------------------------------------------------------------|
r_work (final): 0.3728
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7550
moved from start:          0.1864

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   4880  Z= 0.221
  Angle     :  0.610   8.272   6614  Z= 0.307
  Chirality :  0.043   0.203    755
  Planarity :  0.004   0.033    816
  Dihedral  :  4.157  23.068    660
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 7.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  4.06 %
    Allowed  : 20.70 %
    Favored  : 75.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.54 (0.36), residues: 615
  helix:  1.88 (0.31), residues: 329
  sheet:  0.77 (0.50), residues: 122
  loop : -0.49 (0.49), residues: 164

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C 136 
 HIS   0.002   0.001   HIS A 155 
 PHE   0.021   0.002   PHE A   6 
 TYR   0.022   0.002   TYR A 235 
 ARG   0.002   0.000   ARG C  93 

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

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

  1230 Ramachandran restraints generated.
    615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1230 Ramachandran restraints generated.
    615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 95
  time to evaluate  : 0.570 
Fit side-chains
REVERT: A  125 LYS cc_start: 0.6739 (mttt) cc_final: 0.6318 (mmtm)
REVERT: A  176 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8192 (mp)
REVERT: A  308 MET cc_start: 0.7024 (mmt) cc_final: 0.6733 (tpp)
REVERT: D  106 ASP cc_start: 0.7688 (m-30) cc_final: 0.7346 (m-30)
REVERT: D  127 LYS cc_start: 0.8295 (ttpp) cc_final: 0.7828 (tmmt)
  outliers start: 21
  outliers final: 18
  residues processed: 108
  average time/residue: 0.1660
  time to fit residues: 23.3638
Evaluate side-chains
  114 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 95
  time to evaluate  : 0.642 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue   79 SER
Chi-restraints excluded: chain A residue  116 ILE
Chi-restraints excluded: chain A residue  174 ILE
Chi-restraints excluded: chain A residue  176 LEU
Chi-restraints excluded: chain A residue  177 ILE
Chi-restraints excluded: chain A residue  209 ILE
Chi-restraints excluded: chain A residue  213 VAL
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  379 HIS
Chi-restraints excluded: chain C residue   63 VAL
Chi-restraints excluded: chain C residue  100 THR
Chi-restraints excluded: chain C residue  117 THR
Chi-restraints excluded: chain C residue  125 MET
Chi-restraints excluded: chain C residue  135 TYR
Chi-restraints excluded: chain C residue  151 LEU
Chi-restraints excluded: chain D residue   98 THR
Chi-restraints excluded: chain D residue  126 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 46 optimal weight:    9.9990
   chunk 48 optimal weight:    0.7980
   chunk 41 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9980
   chunk 30 optimal weight:    0.7980
   chunk 33 optimal weight:    0.9990
   chunk 37 optimal weight:    0.9980
   chunk 2 optimal weight:    0.4980
   chunk 45 optimal weight:    1.9990
   chunk 53 optimal weight:    2.9990
   chunk 11 optimal weight:    0.0980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.4033 r_free = 0.4033 target = 0.178958 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.141261 restraints weight = 5747.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.147071 restraints weight = 3301.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.150921 restraints weight = 2328.567|
|-----------------------------------------------------------------------------|
r_work (final): 0.3737
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7505
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      :  0.003   0.039   4880  Z= 0.184
  Angle     :  0.592   8.840   6614  Z= 0.296
  Chirality :  0.042   0.197    755
  Planarity :  0.004   0.042    816
  Dihedral  :  4.098  23.265    660
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 6.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 21.08 %
    Favored  : 75.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.68 (0.37), residues: 615
  helix:  2.06 (0.31), residues: 329
  sheet:  0.75 (0.51), residues: 122
  loop : -0.51 (0.50), residues: 164

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP C 136 
 HIS   0.002   0.000   HIS A 155 
 PHE   0.021   0.001   PHE C 134 
 TYR   0.023   0.002   TYR A 235 
 ARG   0.001   0.000   ARG C  93 

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

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

  1230 Ramachandran restraints generated.
    615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1230 Ramachandran restraints generated.
    615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 100
  time to evaluate  : 0.527 
Fit side-chains
REVERT: A  125 LYS cc_start: 0.6819 (mttt) cc_final: 0.6347 (mmtm)
REVERT: A  176 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8196 (mp)
REVERT: A  308 MET cc_start: 0.6966 (mmt) cc_final: 0.6682 (tpp)
REVERT: D  106 ASP cc_start: 0.7648 (m-30) cc_final: 0.7267 (m-30)
REVERT: D  127 LYS cc_start: 0.8242 (ttpp) cc_final: 0.7760 (tmmt)
  outliers start: 18
  outliers final: 15
  residues processed: 111
  average time/residue: 0.1803
  time to fit residues: 25.5090
Evaluate side-chains
  115 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 99
  time to evaluate  : 0.525 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue   79 SER
Chi-restraints excluded: chain A residue  133 SER
Chi-restraints excluded: chain A residue  174 ILE
Chi-restraints excluded: chain A residue  176 LEU
Chi-restraints excluded: chain A residue  177 ILE
Chi-restraints excluded: chain A residue  209 ILE
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain C residue   63 VAL
Chi-restraints excluded: chain C residue  100 THR
Chi-restraints excluded: chain C residue  117 THR
Chi-restraints excluded: chain C residue  135 TYR
Chi-restraints excluded: chain D residue   76 SER
Chi-restraints excluded: chain D residue   98 THR
Chi-restraints excluded: chain D residue  126 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 3 optimal weight:    2.9990
   chunk 49 optimal weight:    5.9990
   chunk 31 optimal weight:    0.6980
   chunk 19 optimal weight:    0.0270
   chunk 0 optimal weight:    3.9990
   chunk 27 optimal weight:    3.9990
   chunk 9 optimal weight:    4.9990
   chunk 25 optimal weight:    1.9990
   chunk 59 optimal weight:    4.9990
   chunk 21 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   overall best weight:    1.5444

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

Flipped N/Q/H residues before XYZ refinement:
A   4 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.174476 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.136310 restraints weight = 5730.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.141769 restraints weight = 3370.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.145486 restraints weight = 2429.074|
|-----------------------------------------------------------------------------|
r_work (final): 0.3676
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7600
moved from start:          0.2105

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056   4880  Z= 0.297
  Angle     :  0.654   9.299   6614  Z= 0.329
  Chirality :  0.044   0.205    755
  Planarity :  0.004   0.050    816
  Dihedral  :  4.233  22.790    660
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 7.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  4.06 %
    Allowed  : 21.08 %
    Favored  : 74.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.41 (0.36), residues: 615
  helix:  1.76 (0.30), residues: 329
  sheet:  0.66 (0.51), residues: 122
  loop : -0.47 (0.51), residues: 164

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 136 
 HIS   0.003   0.001   HIS A 155 
 PHE   0.023   0.002   PHE C 134 
 TYR   0.023   0.002   TYR A 235 
 ARG   0.002   0.000   ARG C  93 

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

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

  1230 Ramachandran restraints generated.
    615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1230 Ramachandran restraints generated.
    615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 101
  time to evaluate  : 0.504 
Fit side-chains
REVERT: A  109 MET cc_start: 0.8296 (tpp) cc_final: 0.8043 (mmm)
REVERT: A  125 LYS cc_start: 0.6987 (mttt) cc_final: 0.6418 (mmtm)
REVERT: A  176 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8250 (mp)
REVERT: A  308 MET cc_start: 0.7029 (mmt) cc_final: 0.6741 (tpp)
REVERT: D  106 ASP cc_start: 0.7655 (m-30) cc_final: 0.7309 (m-30)
REVERT: D  127 LYS cc_start: 0.8202 (ttpp) cc_final: 0.7714 (tmmt)
  outliers start: 21
  outliers final: 17
  residues processed: 115
  average time/residue: 0.1614
  time to fit residues: 23.9362
Evaluate side-chains
  118 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 100
  time to evaluate  : 0.484 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue   79 SER
Chi-restraints excluded: chain A residue  116 ILE
Chi-restraints excluded: chain A residue  133 SER
Chi-restraints excluded: chain A residue  174 ILE
Chi-restraints excluded: chain A residue  176 LEU
Chi-restraints excluded: chain A residue  177 ILE
Chi-restraints excluded: chain A residue  209 ILE
Chi-restraints excluded: chain A residue  213 VAL
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  379 HIS
Chi-restraints excluded: chain C residue   63 VAL
Chi-restraints excluded: chain C residue  100 THR
Chi-restraints excluded: chain C residue  117 THR
Chi-restraints excluded: chain D residue   76 SER
Chi-restraints excluded: chain D residue   98 THR
Chi-restraints excluded: chain D residue  126 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 27 optimal weight:    0.5980
   chunk 43 optimal weight:    0.0980
   chunk 48 optimal weight:    0.7980
   chunk 2 optimal weight:    0.4980
   chunk 24 optimal weight:    2.9990
   chunk 1 optimal weight:    0.7980
   chunk 32 optimal weight:    0.9980
   chunk 38 optimal weight:    0.7980
   chunk 46 optimal weight:    9.9990
   chunk 34 optimal weight:    0.7980
   chunk 9 optimal weight:    3.9990
   overall best weight:    0.5580

-------------------------------------------------------------------------------
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 = 0.4022 r_free = 0.4022 target = 0.178047 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.140462 restraints weight = 5641.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.146194 restraints weight = 3263.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.150044 restraints weight = 2314.876|
|-----------------------------------------------------------------------------|
r_work (final): 0.3725
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7517
moved from start:          0.2078

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4880  Z= 0.188
  Angle     :  0.623   8.746   6614  Z= 0.305
  Chirality :  0.042   0.201    755
  Planarity :  0.004   0.049    816
  Dihedral  :  4.146  23.411    660
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 7.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 21.86 %
    Favored  : 75.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.63 (0.37), residues: 615
  helix:  2.04 (0.31), residues: 329
  sheet:  0.57 (0.51), residues: 124
  loop : -0.46 (0.51), residues: 162

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP C 136 
 HIS   0.002   0.001   HIS A 155 
 PHE   0.021   0.001   PHE C 134 
 TYR   0.025   0.002   TYR A 235 
 ARG   0.001   0.000   ARG C  93 

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

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

  1230 Ramachandran restraints generated.
    615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1230 Ramachandran restraints generated.
    615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 96
  time to evaluate  : 0.512 
Fit side-chains
REVERT: A  125 LYS cc_start: 0.6982 (mttt) cc_final: 0.6472 (mmtm)
REVERT: A  176 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8211 (mp)
REVERT: A  308 MET cc_start: 0.6906 (mmt) cc_final: 0.6627 (tpp)
REVERT: D  106 ASP cc_start: 0.7707 (m-30) cc_final: 0.7266 (m-30)
REVERT: D  127 LYS cc_start: 0.8180 (ttpp) cc_final: 0.7698 (tmmt)
  outliers start: 16
  outliers final: 13
  residues processed: 107
  average time/residue: 0.1754
  time to fit residues: 23.9821
Evaluate side-chains
  109 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 95
  time to evaluate  : 0.493 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue   79 SER
Chi-restraints excluded: chain A residue  116 ILE
Chi-restraints excluded: chain A residue  133 SER
Chi-restraints excluded: chain A residue  174 ILE
Chi-restraints excluded: chain A residue  176 LEU
Chi-restraints excluded: chain A residue  177 ILE
Chi-restraints excluded: chain A residue  209 ILE
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain C residue   63 VAL
Chi-restraints excluded: chain C residue  100 THR
Chi-restraints excluded: chain C residue  117 THR
Chi-restraints excluded: chain D residue   98 THR
Chi-restraints excluded: chain D residue  126 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 25 optimal weight:    3.9990
   chunk 31 optimal weight:    2.9990
   chunk 7 optimal weight:    2.9990
   chunk 44 optimal weight:    5.9990
   chunk 0 optimal weight:    3.9990
   chunk 33 optimal weight:    3.9990
   chunk 57 optimal weight:    0.9980
   chunk 18 optimal weight:    3.9990
   chunk 32 optimal weight:    0.6980
   chunk 39 optimal weight:    0.8980
   chunk 6 optimal weight:    2.9990
   overall best weight:    1.7184

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

Flipped N/Q/H residues before XYZ refinement:
C 129 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.173217 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.135237 restraints weight = 5767.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.140602 restraints weight = 3380.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.144240 restraints weight = 2445.950|
|-----------------------------------------------------------------------------|
r_work (final): 0.3657
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7626
moved from start:          0.2251

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   4880  Z= 0.326
  Angle     :  0.683   8.981   6614  Z= 0.347
  Chirality :  0.045   0.210    755
  Planarity :  0.004   0.052    816
  Dihedral  :  4.348  22.652    660
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 8.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 22.05 %
    Favored  : 74.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.22 (0.36), residues: 615
  helix:  1.62 (0.30), residues: 329
  sheet:  0.43 (0.50), residues: 124
  loop : -0.46 (0.52), residues: 162

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP C 136 
 HIS   0.002   0.001   HIS A  89 
 PHE   0.024   0.002   PHE C 134 
 TYR   0.026   0.002   TYR A 235 
 ARG   0.002   0.000   ARG C  93 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1709.88 seconds
wall clock time: 31 minutes 19.54 seconds (1879.54 seconds total)