Starting phenix.real_space_refine
on Tue Feb 11 08:19:02 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6ukj_20806/02_2025/6ukj_20806_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6ukj_20806/02_2025/6ukj_20806.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6ukj_20806/02_2025/6ukj_20806.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6ukj_20806/02_2025/6ukj_20806.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6ukj_20806/02_2025/6ukj_20806_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6ukj_20806/02_2025/6ukj_20806_neut.cif"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   1.000
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      28      5.16       5
     C    3037      2.51       5
     N     723      2.21       5
     O     837      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 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: 4625
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 2810
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 350, 2810
          Classifications: {'peptide': 350}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 7, 'TRANS': 342}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 41
          Unresolved non-hydrogen angles: 48
          Unresolved non-hydrogen dihedrals: 36
          Planarities with less than four sites: {'ARG:plan': 4, 'HIS:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 28
    Chain: "H"
      Number of atoms: 986
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 127, 986
          Classifications: {'peptide': 127}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 123}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
    Chain: "L"
      Number of atoms: 794
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 105, 794
          Classifications: {'peptide': 105}
          Link IDs: {'PTRANS': 6, 'TRANS': 98}
    Chain: "A"
      Number of atoms: 35
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 35
          Unusual residues: {'Y01': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 3.53, per 1000 atoms: 0.76
  Number of scatterers: 4625
  At special positions: 0
  Unit cell: (63.135, 84.87, 99.36, 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      28     16.00
     O     837      8.00
     N     723      7.00
     C    3037      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 289 " - pdb=" SG  CYS A 312 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 301 " - pdb=" SG  CYS A 309 " distance=2.04
    Simple disulfide: pdb=" SG  CYS H  25 " - pdb=" SG  CYS H  99 " distance=2.04
    Simple disulfide: pdb=" SG  CYS L  24 " - pdb=" SG  CYS L  89 " 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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.25
  Conformation dependent library (CDL) restraints added in 503.4 milliseconds
  

  1148 Ramachandran restraints generated.
    574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1092

  Finding SS restraints...
    Secondary structure from input PDB file:
      16 helices and 7 sheets defined
      48.6% alpha, 19.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.44
  Creating SS restraints...
    Processing helix  chain 'A' and resid 49 through 58
      removed outlier: 4.232A  pdb=" N   LYS A  53 " --> pdb=" O   LYS A  49 " (cutoff:3.500A)
      removed outlier: 3.967A  pdb=" N   ASN A  58 " --> pdb=" O   GLU A  54 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 59 through 83
      removed outlier: 3.858A  pdb=" N   MET A  74 " --> pdb=" O   SER A  70 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 89 through 112
    Processing helix  chain 'A' and resid 126 through 148
    Processing helix  chain 'A' and resid 152 through 174
      removed outlier: 3.949A  pdb=" N   SER A 157 " --> pdb=" O   GLY A 153 " (cutoff:3.500A)
      Proline residue:  A 165  - end of helix
    Processing helix  chain 'A' and resid 180 through 205
      removed outlier: 3.915A  pdb=" N   GLU A 204 " --> pdb=" O   LYS A 200 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 210 through 237
      Proline residue:  A 223  - end of helix
    Processing helix  chain 'A' and resid 241 through 259
    Processing helix  chain 'A' and resid 260 through 264
      removed outlier: 3.598A  pdb=" N   TYR A 264 " --> pdb=" O   LEU A 261 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 279 through 291
    Processing helix  chain 'A' and resid 314 through 340
      removed outlier: 4.388A  pdb=" N   THR A 318 " --> pdb=" O   GLY A 314 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 343 through 351
      removed outlier: 3.753A  pdb=" N   ILE A 347 " --> pdb=" O   MET A 343 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 351 through 360
      removed outlier: 3.622A  pdb=" N   ALA A 357 " --> pdb=" O   GLY A 353 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 374 through 404
      removed outlier: 3.692A  pdb=" N   PHE A 378 " --> pdb=" O   ARG A 374 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 31 through 35
      removed outlier: 3.502A  pdb=" N   TYR H  34 " --> pdb=" O   ASN H  31 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   SER H  35 " --> pdb=" O   VAL H  32 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 31 through 35'
    Processing helix  chain 'H' and resid 90 through 94
      removed outlier: 3.804A  pdb=" N   ASP H  93 " --> pdb=" O   ARG H  90 " (cutoff:3.500A)
      removed outlier: 3.989A  pdb=" N   THR H  94 " --> pdb=" O   ALA H  91 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 90 through 94'
    Processing sheet with id=AA1, first strand: chain 'H' and resid 6 through 8
      removed outlier: 3.622A  pdb=" N   GLN H   6 " --> pdb=" O   SER H  28 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   THR H  81 " --> pdb=" O   ASP H  76 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   ASP H  76 " --> pdb=" O   THR H  81 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'H' and resid 48 through 50
      removed outlier: 6.904A  pdb=" N   CYS H  99 " --> pdb=" O   TRP H 122 " (cutoff:3.500A)
      removed outlier: 4.889A  pdb=" N   TRP H 122 " --> pdb=" O   CYS H  99 " (cutoff:3.500A)
      removed outlier: 6.984A  pdb=" N   ARG H 101 " --> pdb=" O   ASP H 120 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'H' and resid 48 through 50
    Processing sheet with id=AA4, first strand: chain 'H' and resid 52 through 55
    Processing sheet with id=AA5, first strand: chain 'L' and resid 5 through 7
      removed outlier: 3.535A  pdb=" N   VAL L  20 " --> pdb=" O   ILE L  76 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'L' and resid 11 through 12
    Processing sheet with id=AA7, first strand: chain 'L' and resid 54 through 55
      removed outlier: 6.550A  pdb=" N   TRP L  36 " --> pdb=" O   LEU L  48 " (cutoff:3.500A)
      removed outlier: 4.920A  pdb=" N   TYR L  50 " --> pdb=" O   VAL L  34 " (cutoff:3.500A)
      removed outlier: 6.543A  pdb=" N   VAL L  34 " --> pdb=" O   TYR L  50 " (cutoff:3.500A)

    271 hydrogen bonds defined for protein.
    786 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: 1.23

  Time building geometry restraints manager: 1.40 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 711
        1.32 -     1.44: 1397
        1.44 -     1.57: 2590
        1.57 -     1.69: 1
        1.69 -     1.81: 41
  Bond restraints: 4740
  Sorted by residual:
  bond pdb=" C   PRO L   9 "
       pdb=" O   PRO L   9 "
    ideal  model  delta    sigma   weight residual
    1.235  1.196  0.039 1.30e-02 5.92e+03 8.98e+00
  bond pdb=" CA  SER L  10 "
       pdb=" CB  SER L  10 "
    ideal  model  delta    sigma   weight residual
    1.529  1.489  0.040 1.55e-02 4.16e+03 6.64e+00
  bond pdb=" N   GLN L   7 "
       pdb=" CA  GLN L   7 "
    ideal  model  delta    sigma   weight residual
    1.456  1.488 -0.032 1.29e-02 6.01e+03 6.21e+00
  bond pdb=" N   SER L   8 "
       pdb=" CA  SER L   8 "
    ideal  model  delta    sigma   weight residual
    1.457  1.492 -0.035 1.41e-02 5.03e+03 6.07e+00
  bond pdb=" CA  SER L  11 "
       pdb=" CB  SER L  11 "
    ideal  model  delta    sigma   weight residual
    1.534  1.492  0.042 1.72e-02 3.38e+03 5.85e+00
  ... (remaining 4735 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.92: 6170
        1.92 -     3.85: 222
        3.85 -     5.77: 33
        5.77 -     7.70: 11
        7.70 -     9.62: 4
  Bond angle restraints: 6440
  Sorted by residual:
  angle pdb=" N   PRO L   9 "
        pdb=" CA  PRO L   9 "
        pdb=" C   PRO L   9 "
      ideal   model   delta    sigma   weight residual
     112.47  104.55    7.92 2.06e+00 2.36e-01 1.48e+01
  angle pdb=" C   GLN L   7 "
        pdb=" N   SER L   8 "
        pdb=" CA  SER L   8 "
      ideal   model   delta    sigma   weight residual
     121.80  130.34   -8.54 2.44e+00 1.68e-01 1.22e+01
  angle pdb=" O   GLN L   7 "
        pdb=" C   GLN L   7 "
        pdb=" N   SER L   8 "
      ideal   model   delta    sigma   weight residual
     123.22  126.77   -3.55 1.14e+00 7.69e-01 9.70e+00
  angle pdb=" CB  GLN L   7 "
        pdb=" CG  GLN L   7 "
        pdb=" CD  GLN L   7 "
      ideal   model   delta    sigma   weight residual
     112.60  107.55    5.05 1.70e+00 3.46e-01 8.84e+00
  angle pdb=" C   ILE A 260 "
        pdb=" CA  ILE A 260 "
        pdb=" CB  ILE A 260 "
      ideal   model   delta    sigma   weight residual
     112.26  107.55    4.71 1.62e+00 3.81e-01 8.45e+00
  ... (remaining 6435 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.66: 2502
       16.66 -    33.33: 244
       33.33 -    49.99: 56
       49.99 -    66.65: 8
       66.65 -    83.31: 2
  Dihedral angle restraints: 2812
    sinusoidal: 1106
      harmonic: 1706
  Sorted by residual:
  dihedral pdb=" CB  CYS A 301 "
           pdb=" SG  CYS A 301 "
           pdb=" SG  CYS A 309 "
           pdb=" CB  CYS A 309 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -154.46   68.46     1      1.00e+01 1.00e-02 6.07e+01
  dihedral pdb=" CB  CYS H  25 "
           pdb=" SG  CYS H  25 "
           pdb=" SG  CYS H  99 "
           pdb=" CB  CYS H  99 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   44.16   48.84     1      1.00e+01 1.00e-02 3.28e+01
  dihedral pdb=" CA  LEU A 175 "
           pdb=" C   LEU A 175 "
           pdb=" N   ARG A 176 "
           pdb=" CA  ARG A 176 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.05   23.95     0      5.00e+00 4.00e-02 2.29e+01
  ... (remaining 2809 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.076: 654
       0.076 -    0.152: 78
       0.152 -    0.228: 4
       0.228 -    0.305: 2
       0.305 -    0.381: 1
  Chirality restraints: 739
  Sorted by residual:
  chirality pdb=" CBG Y01 A 501 "
            pdb=" CAQ Y01 A 501 "
            pdb=" CBD Y01 A 501 "
            pdb=" CBI Y01 A 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.33   -2.71    0.38 2.00e-01 2.50e+01 3.62e+00
  chirality pdb=" CBF Y01 A 501 "
            pdb=" CAS Y01 A 501 "
            pdb=" CBD Y01 A 501 "
            pdb=" CBH Y01 A 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.45   -2.71    0.26 2.00e-01 2.50e+01 1.74e+00
  chirality pdb=" CA  PRO L   9 "
            pdb=" N   PRO L   9 "
            pdb=" C   PRO L   9 "
            pdb=" CB  PRO L   9 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.97   -0.25 2.00e-01 2.50e+01 1.62e+00
  ... (remaining 736 not shown)

  Planarity restraints: 788
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER L   8 "   -0.012 2.00e-02 2.50e+03   2.36e-02 5.59e+00
        pdb=" C   SER L   8 "    0.041 2.00e-02 2.50e+03
        pdb=" O   SER L   8 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   PRO L   9 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TRP L  95 "    0.031 5.00e-02 4.00e+02   4.65e-02 3.47e+00
        pdb=" N   PRO L  96 "   -0.080 5.00e-02 4.00e+02
        pdb=" CA  PRO L  96 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO L  96 "    0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER L  11 "    0.008 2.00e-02 2.50e+03   1.73e-02 2.99e+00
        pdb=" C   SER L  11 "   -0.030 2.00e-02 2.50e+03
        pdb=" O   SER L  11 "    0.011 2.00e-02 2.50e+03
        pdb=" N   LEU L  12 "    0.010 2.00e-02 2.50e+03
  ... (remaining 785 not shown)

  Histogram of nonbonded interaction distances:
        2.11 -     2.67: 86
        2.67 -     3.23: 4571
        3.23 -     3.79: 7169
        3.79 -     4.34: 9760
        4.34 -     4.90: 16423
  Nonbonded interactions: 38009
  Sorted by model distance:
  nonbonded pdb=" O   ILE A 347 "
            pdb=" OH  TYR A 384 "
     model   vdw
     2.114 3.040
  nonbonded pdb=" OG  SER A  72 "
            pdb=" OE1 GLN A 352 "
     model   vdw
     2.216 3.040
  nonbonded pdb=" OG  SER A 157 "
            pdb=" OE2 GLU A 198 "
     model   vdw
     2.260 3.040
  nonbonded pdb=" OG  SER L   8 "
            pdb=" CD  PRO L   9 "
     model   vdw
     2.262 3.440
  nonbonded pdb=" OE2 GLU A 208 "
            pdb=" NZ  LYS A 270 "
     model   vdw
     2.284 3.120
  ... (remaining 38004 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:             1.370
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     14.950
  Find NCS groups from input model:        0.040
  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:             0.010
  Load rotamer database and sin/cos tables:3.010
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.660
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7861
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      :  0.007   0.058   4740  Z= 0.456
  Angle     :  0.907   9.621   6440  Z= 0.477
  Chirality :  0.052   0.381    739
  Planarity :  0.005   0.047    788
  Dihedral  : 13.739  83.312   1708
  Min Nonbonded Distance : 2.114

Molprobity Statistics.
  All-atom Clashscore : 6.29
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  4.53 %
    Favored  : 95.12 %
  Rotamer:
    Outliers :  0.79 %
    Allowed  :  5.95 %
    Favored  : 93.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.21 (0.28), residues: 574
  helix: -1.69 (0.25), residues: 263
  sheet: -1.94 (0.47), residues: 93
  loop : -2.58 (0.34), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP L  95 
 HIS   0.006   0.001   HIS H  38 
 PHE   0.018   0.002   PHE A 251 
 TYR   0.019   0.002   TYR H 102 
 ARG   0.013   0.001   ARG A 231 

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

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

  1148 Ramachandran restraints generated.
    574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1148 Ramachandran restraints generated.
    574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 125
  time to evaluate  : 0.512 
Fit side-chains
   revert: symmetry clash
REVERT: A   80 LYS cc_start: 0.8349 (ptmt) cc_final: 0.8051 (ptpt)
REVERT: A  218 ILE cc_start: 0.8468 (OUTLIER) cc_final: 0.8237 (mp)
REVERT: A  307 LYS cc_start: 0.8745 (mptt) cc_final: 0.8526 (mmtt)
REVERT: A  347 ILE cc_start: 0.8027 (mm) cc_final: 0.7775 (mt)
REVERT: A  384 TYR cc_start: 0.8336 (t80) cc_final: 0.7693 (t80)
REVERT: A  397 ILE cc_start: 0.7268 (OUTLIER) cc_final: 0.6664 (mp)
REVERT: H   68 LYS cc_start: 0.8338 (tttt) cc_final: 0.7973 (ttpp)
REVERT: H   80 ASN cc_start: 0.8448 (t0) cc_final: 0.8204 (t0)
REVERT: L   56 TYR cc_start: 0.8449 (t80) cc_final: 0.8003 (t80)
  outliers start: 4
  outliers final: 2
  residues processed: 129
  average time/residue: 0.2189
  time to fit residues: 33.8851
Evaluate side-chains
  103 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 99
  time to evaluate  : 0.474 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  218 ILE
Chi-restraints excluded: chain A residue  289 CYS
Chi-restraints excluded: chain A residue  397 ILE
Chi-restraints excluded: chain L residue   10 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 48 optimal weight:    3.9990
   chunk 43 optimal weight:    1.9990
   chunk 23 optimal weight:    0.6980
   chunk 14 optimal weight:    0.9980
   chunk 29 optimal weight:    0.5980
   chunk 44 optimal weight:    0.8980
   chunk 17 optimal weight:    0.6980
   chunk 27 optimal weight:    0.9980
   chunk 33 optimal weight:    0.6980
   chunk 51 optimal weight:    0.8980
   chunk 28 optimal weight:    0.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 352 GLN
H  38 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.121616 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.113108 restraints weight = 7599.493|
|-----------------------------------------------------------------------------|
r_work (start): 0.3365 rms_B_bonded: 1.94
r_work: 0.3274 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.3166 rms_B_bonded: 4.20 restraints_weight: 0.2500
r_work (final): 0.3166
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8153
moved from start:          0.1905

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   4740  Z= 0.206
  Angle     :  0.597   7.221   6440  Z= 0.315
  Chirality :  0.042   0.169    739
  Planarity :  0.004   0.043    788
  Dihedral  :  7.837  57.512    710
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 5.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.53 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 11.71 %
    Favored  : 85.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.62 (0.32), residues: 574
  helix: -0.12 (0.30), residues: 266
  sheet: -1.17 (0.51), residues: 91
  loop : -2.16 (0.37), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP L  95 
 HIS   0.003   0.001   HIS A  97 
 PHE   0.015   0.001   PHE A 268 
 TYR   0.014   0.001   TYR A 345 
 ARG   0.007   0.001   ARG H  41 

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

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

  1148 Ramachandran restraints generated.
    574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1148 Ramachandran restraints generated.
    574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 126
  time to evaluate  : 0.524 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  106 PHE cc_start: 0.7861 (t80) cc_final: 0.6938 (m-10)
REVERT: A  310 ASP cc_start: 0.8748 (p0) cc_final: 0.8460 (p0)
REVERT: A  333 THR cc_start: 0.8952 (m) cc_final: 0.8710 (m)
REVERT: A  347 ILE cc_start: 0.8638 (mm) cc_final: 0.8188 (mt)
REVERT: A  384 TYR cc_start: 0.8939 (t80) cc_final: 0.8652 (t80)
REVERT: H   68 LYS cc_start: 0.8446 (tttt) cc_final: 0.8013 (ttpp)
REVERT: H   80 ASN cc_start: 0.8650 (t0) cc_final: 0.8354 (t0)
REVERT: L   56 TYR cc_start: 0.8856 (t80) cc_final: 0.8516 (t80)
REVERT: L   91 GLN cc_start: 0.9115 (pp30) cc_final: 0.8182 (pp30)
  outliers start: 14
  outliers final: 10
  residues processed: 134
  average time/residue: 0.1782
  time to fit residues: 29.7470
Evaluate side-chains
  118 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 108
  time to evaluate  : 0.551 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  258 CYS
Chi-restraints excluded: chain A residue  276 TYR
Chi-restraints excluded: chain A residue  289 CYS
Chi-restraints excluded: chain A residue  301 CYS
Chi-restraints excluded: chain A residue  337 ILE
Chi-restraints excluded: chain A residue  343 MET
Chi-restraints excluded: chain H residue   14 LEU
Chi-restraints excluded: chain H residue   25 CYS
Chi-restraints excluded: chain H residue   94 THR
Chi-restraints excluded: chain L residue   21 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 50 optimal weight:    0.0970
   chunk 35 optimal weight:    0.1980
   chunk 12 optimal weight:    0.9990
   chunk 29 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 14 optimal weight:    0.7980
   chunk 10 optimal weight:    0.6980
   chunk 3 optimal weight:    0.9980
   chunk 16 optimal weight:    0.9990
   chunk 49 optimal weight:    0.8980
   chunk 28 optimal weight:    0.8980
   overall best weight:    0.5378

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

Flipped N/Q/H residues before XYZ refinement:
A 183 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.123832 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.115659 restraints weight = 7657.941|
|-----------------------------------------------------------------------------|
r_work (start): 0.3403 rms_B_bonded: 1.92
r_work: 0.3314 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3208 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.3208
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8156
moved from start:          0.2414

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4740  Z= 0.178
  Angle     :  0.553   7.055   6440  Z= 0.291
  Chirality :  0.041   0.144    739
  Planarity :  0.004   0.041    788
  Dihedral  :  6.989  58.945    705
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 6.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 15.08 %
    Favored  : 80.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.81 (0.34), residues: 574
  helix:  0.59 (0.31), residues: 269
  sheet: -0.81 (0.54), residues: 91
  loop : -1.83 (0.39), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP L  95 
 HIS   0.002   0.001   HIS A  97 
 PHE   0.013   0.001   PHE A 268 
 TYR   0.011   0.001   TYR A 345 
 ARG   0.006   0.001   ARG H 111 

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

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

  1148 Ramachandran restraints generated.
    574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1148 Ramachandran restraints generated.
    574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 115
  time to evaluate  : 0.517 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  299 GLU cc_start: 0.8553 (mm-30) cc_final: 0.8343 (mm-30)
REVERT: A  305 MET cc_start: 0.8650 (mtp) cc_final: 0.8308 (mmm)
REVERT: A  310 ASP cc_start: 0.8663 (p0) cc_final: 0.8391 (p0)
REVERT: A  325 PHE cc_start: 0.9126 (m-10) cc_final: 0.8885 (m-80)
REVERT: A  333 THR cc_start: 0.9098 (m) cc_final: 0.8814 (m)
REVERT: A  347 ILE cc_start: 0.8577 (mm) cc_final: 0.8162 (mt)
REVERT: A  384 TYR cc_start: 0.8937 (t80) cc_final: 0.8651 (t80)
REVERT: H   38 HIS cc_start: 0.8310 (p90) cc_final: 0.8060 (p-80)
REVERT: H   68 LYS cc_start: 0.8399 (tttt) cc_final: 0.8012 (ttpp)
REVERT: H   80 ASN cc_start: 0.8532 (t0) cc_final: 0.8226 (t0)
REVERT: L   18 ASP cc_start: 0.8170 (m-30) cc_final: 0.7892 (m-30)
REVERT: L   56 TYR cc_start: 0.8898 (t80) cc_final: 0.8639 (t80)
REVERT: L   91 GLN cc_start: 0.9187 (pp30) cc_final: 0.8304 (pp30)
  outliers start: 21
  outliers final: 17
  residues processed: 129
  average time/residue: 0.1769
  time to fit residues: 28.6561
Evaluate side-chains
  123 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 106
  time to evaluate  : 0.504 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  243 LEU
Chi-restraints excluded: chain A residue  258 CYS
Chi-restraints excluded: chain A residue  276 TYR
Chi-restraints excluded: chain A residue  289 CYS
Chi-restraints excluded: chain A residue  297 VAL
Chi-restraints excluded: chain A residue  301 CYS
Chi-restraints excluded: chain A residue  337 ILE
Chi-restraints excluded: chain A residue  369 VAL
Chi-restraints excluded: chain H residue   15 VAL
Chi-restraints excluded: chain H residue   25 CYS
Chi-restraints excluded: chain H residue   94 THR
Chi-restraints excluded: chain H residue   96 VAL
Chi-restraints excluded: chain H residue  102 TYR
Chi-restraints excluded: chain H residue  119 ILE
Chi-restraints excluded: chain L residue   21 THR
Chi-restraints excluded: chain L residue   38 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9990
   chunk 35 optimal weight:    0.5980
   chunk 51 optimal weight:    0.8980
   chunk 30 optimal weight:    0.5980
   chunk 27 optimal weight:    1.9990
   chunk 56 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   chunk 29 optimal weight:    0.7980
   chunk 49 optimal weight:    0.9980
   chunk 8 optimal weight:    0.8980
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.3481 r_free = 0.3481 target = 0.121359 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.113170 restraints weight = 7762.029|
|-----------------------------------------------------------------------------|
r_work (start): 0.3364 rms_B_bonded: 1.92
r_work: 0.3275 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3171 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.3171
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8186
moved from start:          0.2635

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4740  Z= 0.205
  Angle     :  0.592  10.841   6440  Z= 0.303
  Chirality :  0.042   0.152    739
  Planarity :  0.004   0.041    788
  Dihedral  :  6.931  59.496    705
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.01 %
    Favored  : 95.99 %
  Rotamer:
    Outliers :  4.76 %
    Allowed  : 16.47 %
    Favored  : 78.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.41 (0.35), residues: 574
  helix:  0.94 (0.31), residues: 269
  sheet: -0.68 (0.56), residues: 91
  loop : -1.63 (0.40), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP L  95 
 HIS   0.002   0.001   HIS H  38 
 PHE   0.020   0.001   PHE A 268 
 TYR   0.014   0.001   TYR A 345 
 ARG   0.007   0.001   ARG H 111 

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

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

  1148 Ramachandran restraints generated.
    574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1148 Ramachandran restraints generated.
    574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 111
  time to evaluate  : 0.543 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  106 PHE cc_start: 0.7803 (t80) cc_final: 0.6912 (m-10)
REVERT: A  325 PHE cc_start: 0.9152 (m-10) cc_final: 0.8923 (m-80)
REVERT: A  333 THR cc_start: 0.9125 (m) cc_final: 0.8796 (m)
REVERT: A  347 ILE cc_start: 0.8759 (mm) cc_final: 0.8409 (mt)
REVERT: A  384 TYR cc_start: 0.8996 (t80) cc_final: 0.8672 (t80)
REVERT: H   49 GLU cc_start: 0.8358 (tt0) cc_final: 0.8103 (tt0)
REVERT: H   68 LYS cc_start: 0.8383 (tttt) cc_final: 0.7994 (ttpp)
REVERT: H   80 ASN cc_start: 0.8493 (t0) cc_final: 0.8186 (t0)
REVERT: L   56 TYR cc_start: 0.8938 (t80) cc_final: 0.8617 (t80)
REVERT: L   91 GLN cc_start: 0.9238 (pp30) cc_final: 0.8173 (pp30)
  outliers start: 24
  outliers final: 21
  residues processed: 127
  average time/residue: 0.1707
  time to fit residues: 27.2957
Evaluate side-chains
  124 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 103
  time to evaluate  : 0.486 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 ILE
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  258 CYS
Chi-restraints excluded: chain A residue  276 TYR
Chi-restraints excluded: chain A residue  289 CYS
Chi-restraints excluded: chain A residue  297 VAL
Chi-restraints excluded: chain A residue  301 CYS
Chi-restraints excluded: chain A residue  337 ILE
Chi-restraints excluded: chain A residue  369 VAL
Chi-restraints excluded: chain A residue  379 VAL
Chi-restraints excluded: chain H residue   14 LEU
Chi-restraints excluded: chain H residue   15 VAL
Chi-restraints excluded: chain H residue   25 CYS
Chi-restraints excluded: chain H residue   94 THR
Chi-restraints excluded: chain H residue   96 VAL
Chi-restraints excluded: chain H residue  102 TYR
Chi-restraints excluded: chain H residue  119 ILE
Chi-restraints excluded: chain L residue    6 THR
Chi-restraints excluded: chain L residue   21 THR
Chi-restraints excluded: chain L residue   38 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 10 optimal weight:    0.9990
   chunk 42 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   chunk 21 optimal weight:    4.9990
   chunk 1 optimal weight:    0.9980
   chunk 47 optimal weight:    0.0020
   chunk 51 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9990
   chunk 25 optimal weight:    1.9990
   chunk 30 optimal weight:    0.0980
   chunk 22 optimal weight:    1.9990
   overall best weight:    0.6192

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

Flipped N/Q/H residues before XYZ refinement:
A 183 ASN
A 214 ASN
L  28 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.122063 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.113866 restraints weight = 7861.238|
|-----------------------------------------------------------------------------|
r_work (start): 0.3378 rms_B_bonded: 1.95
r_work: 0.3288 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3181 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.3181
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8172
moved from start:          0.2831

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4740  Z= 0.187
  Angle     :  0.579  10.069   6440  Z= 0.296
  Chirality :  0.042   0.141    739
  Planarity :  0.004   0.042    788
  Dihedral  :  6.802  58.755    705
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 7.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  4.96 %
    Allowed  : 16.87 %
    Favored  : 78.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.17 (0.35), residues: 574
  helix:  1.14 (0.32), residues: 270
  sheet: -0.56 (0.57), residues: 90
  loop : -1.53 (0.40), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP L  95 
 HIS   0.002   0.001   HIS H  38 
 PHE   0.019   0.001   PHE A 268 
 TYR   0.012   0.001   TYR A 345 
 ARG   0.004   0.001   ARG H 111 

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

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

  1148 Ramachandran restraints generated.
    574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1148 Ramachandran restraints generated.
    574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 117
  time to evaluate  : 0.539 
Fit side-chains
   revert: symmetry clash
REVERT: A  333 THR cc_start: 0.9115 (m) cc_final: 0.8808 (m)
REVERT: A  347 ILE cc_start: 0.8743 (mm) cc_final: 0.8413 (mt)
REVERT: A  384 TYR cc_start: 0.9004 (t80) cc_final: 0.8683 (t80)
REVERT: H   49 GLU cc_start: 0.8398 (tt0) cc_final: 0.8150 (tt0)
REVERT: H   68 LYS cc_start: 0.8374 (tttt) cc_final: 0.7979 (ttpp)
REVERT: H   80 ASN cc_start: 0.8479 (t0) cc_final: 0.8194 (t0)
REVERT: L    3 ILE cc_start: 0.8534 (mt) cc_final: 0.7864 (mt)
REVERT: L   18 ASP cc_start: 0.8168 (m-30) cc_final: 0.7950 (m-30)
REVERT: L   56 TYR cc_start: 0.8961 (t80) cc_final: 0.8597 (t80)
REVERT: L   91 GLN cc_start: 0.9238 (pp30) cc_final: 0.8168 (pp30)
  outliers start: 25
  outliers final: 21
  residues processed: 134
  average time/residue: 0.1726
  time to fit residues: 29.6356
Evaluate side-chains
  130 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 109
  time to evaluate  : 0.551 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 ILE
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  258 CYS
Chi-restraints excluded: chain A residue  276 TYR
Chi-restraints excluded: chain A residue  289 CYS
Chi-restraints excluded: chain A residue  297 VAL
Chi-restraints excluded: chain A residue  301 CYS
Chi-restraints excluded: chain A residue  337 ILE
Chi-restraints excluded: chain A residue  369 VAL
Chi-restraints excluded: chain A residue  379 VAL
Chi-restraints excluded: chain H residue   15 VAL
Chi-restraints excluded: chain H residue   25 CYS
Chi-restraints excluded: chain H residue   94 THR
Chi-restraints excluded: chain H residue   96 VAL
Chi-restraints excluded: chain H residue  102 TYR
Chi-restraints excluded: chain H residue  119 ILE
Chi-restraints excluded: chain L residue    6 THR
Chi-restraints excluded: chain L residue   10 SER
Chi-restraints excluded: chain L residue   21 THR
Chi-restraints excluded: chain L residue   38 GLN
Chi-restraints excluded: chain L residue   73 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 56 optimal weight:    3.9990
   chunk 22 optimal weight:    1.9990
   chunk 19 optimal weight:    0.8980
   chunk 17 optimal weight:    2.9990
   chunk 29 optimal weight:    0.5980
   chunk 2 optimal weight:    0.7980
   chunk 44 optimal weight:    5.9990
   chunk 9 optimal weight:    0.7980
   chunk 7 optimal weight:    0.7980
   chunk 42 optimal weight:    0.4980
   chunk 36 optimal weight:    0.9980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 183 ASN
L  38 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.121271 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.113010 restraints weight = 7807.880|
|-----------------------------------------------------------------------------|
r_work (start): 0.3367 rms_B_bonded: 1.94
r_work: 0.3279 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.3174 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.3174
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8182
moved from start:          0.2952

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   4740  Z= 0.200
  Angle     :  0.578   6.891   6440  Z= 0.298
  Chirality :  0.042   0.150    739
  Planarity :  0.004   0.042    788
  Dihedral  :  6.741  58.231    705
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 7.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.01 %
    Favored  : 95.99 %
  Rotamer:
    Outliers :  5.16 %
    Allowed  : 18.06 %
    Favored  : 76.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.03 (0.35), residues: 574
  helix:  1.29 (0.32), residues: 270
  sheet: -0.54 (0.57), residues: 90
  loop : -1.47 (0.40), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP L  95 
 HIS   0.002   0.001   HIS H  38 
 PHE   0.017   0.001   PHE A 268 
 TYR   0.012   0.001   TYR A 345 
 ARG   0.008   0.001   ARG H 111 

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

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

  1148 Ramachandran restraints generated.
    574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1148 Ramachandran restraints generated.
    574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 114
  time to evaluate  : 0.540 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  305 MET cc_start: 0.8693 (mtp) cc_final: 0.8352 (mmm)
REVERT: A  333 THR cc_start: 0.9122 (m) cc_final: 0.8813 (m)
REVERT: A  347 ILE cc_start: 0.8706 (mm) cc_final: 0.8428 (mt)
REVERT: A  384 TYR cc_start: 0.9002 (t80) cc_final: 0.8624 (t80)
REVERT: H   49 GLU cc_start: 0.8416 (tt0) cc_final: 0.8148 (tt0)
REVERT: H   68 LYS cc_start: 0.8377 (tttt) cc_final: 0.7978 (ttpp)
REVERT: H   80 ASN cc_start: 0.8488 (t0) cc_final: 0.8201 (t0)
REVERT: L   18 ASP cc_start: 0.8198 (m-30) cc_final: 0.7931 (m-30)
REVERT: L   56 TYR cc_start: 0.8979 (t80) cc_final: 0.8612 (t80)
REVERT: L   73 THR cc_start: 0.8993 (OUTLIER) cc_final: 0.8592 (p)
REVERT: L   91 GLN cc_start: 0.9259 (pp30) cc_final: 0.8194 (pp30)
  outliers start: 26
  outliers final: 21
  residues processed: 131
  average time/residue: 0.1802
  time to fit residues: 30.0162
Evaluate side-chains
  131 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 109
  time to evaluate  : 0.503 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 ILE
Chi-restraints excluded: chain A residue   89 TYR
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  258 CYS
Chi-restraints excluded: chain A residue  276 TYR
Chi-restraints excluded: chain A residue  289 CYS
Chi-restraints excluded: chain A residue  297 VAL
Chi-restraints excluded: chain A residue  301 CYS
Chi-restraints excluded: chain A residue  337 ILE
Chi-restraints excluded: chain A residue  369 VAL
Chi-restraints excluded: chain A residue  379 VAL
Chi-restraints excluded: chain H residue   14 LEU
Chi-restraints excluded: chain H residue   15 VAL
Chi-restraints excluded: chain H residue   25 CYS
Chi-restraints excluded: chain H residue   94 THR
Chi-restraints excluded: chain H residue   96 VAL
Chi-restraints excluded: chain H residue  102 TYR
Chi-restraints excluded: chain H residue  119 ILE
Chi-restraints excluded: chain L residue    6 THR
Chi-restraints excluded: chain L residue   10 SER
Chi-restraints excluded: chain L residue   38 GLN
Chi-restraints excluded: chain L residue   73 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 50 optimal weight:    1.9990
   chunk 0 optimal weight:    6.9990
   chunk 42 optimal weight:    4.9990
   chunk 55 optimal weight:    0.9980
   chunk 3 optimal weight:    0.5980
   chunk 39 optimal weight:    1.9990
   chunk 44 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9980
   chunk 47 optimal weight:    9.9990
   chunk 15 optimal weight:    0.4980
   chunk 54 optimal weight:    0.8980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 183 ASN
A 214 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.120869 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.112596 restraints weight = 7765.843|
|-----------------------------------------------------------------------------|
r_work (start): 0.3365 rms_B_bonded: 1.93
r_work: 0.3276 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.3169 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.3169
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8192
moved from start:          0.2989

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   4740  Z= 0.213
  Angle     :  0.591   7.497   6440  Z= 0.304
  Chirality :  0.042   0.149    739
  Planarity :  0.004   0.040    788
  Dihedral  :  6.720  57.364    705
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 7.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  5.16 %
    Allowed  : 19.05 %
    Favored  : 75.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.05 (0.35), residues: 574
  helix:  1.22 (0.32), residues: 273
  sheet: -0.58 (0.56), residues: 90
  loop : -1.44 (0.40), residues: 211

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP L  95 
 HIS   0.002   0.001   HIS H  38 
 PHE   0.017   0.001   PHE A 268 
 TYR   0.013   0.001   TYR A 345 
 ARG   0.007   0.001   ARG H 111 

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

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

  1148 Ramachandran restraints generated.
    574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1148 Ramachandran restraints generated.
    574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 110
  time to evaluate  : 0.464 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  333 THR cc_start: 0.9129 (m) cc_final: 0.8821 (m)
REVERT: A  347 ILE cc_start: 0.8732 (mm) cc_final: 0.8480 (mt)
REVERT: A  384 TYR cc_start: 0.9037 (t80) cc_final: 0.8685 (t80)
REVERT: H   49 GLU cc_start: 0.8444 (tt0) cc_final: 0.8175 (tt0)
REVERT: H   68 LYS cc_start: 0.8387 (tttt) cc_final: 0.8036 (ttpp)
REVERT: H   80 ASN cc_start: 0.8492 (t0) cc_final: 0.8203 (t0)
REVERT: L   18 ASP cc_start: 0.8233 (m-30) cc_final: 0.7945 (m-30)
REVERT: L   56 TYR cc_start: 0.8981 (t80) cc_final: 0.8632 (t80)
  outliers start: 26
  outliers final: 26
  residues processed: 126
  average time/residue: 0.1717
  time to fit residues: 27.3753
Evaluate side-chains
  134 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 108
  time to evaluate  : 0.507 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 ILE
Chi-restraints excluded: chain A residue   89 TYR
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  258 CYS
Chi-restraints excluded: chain A residue  276 TYR
Chi-restraints excluded: chain A residue  289 CYS
Chi-restraints excluded: chain A residue  297 VAL
Chi-restraints excluded: chain A residue  301 CYS
Chi-restraints excluded: chain A residue  328 CYS
Chi-restraints excluded: chain A residue  337 ILE
Chi-restraints excluded: chain A residue  369 VAL
Chi-restraints excluded: chain A residue  379 VAL
Chi-restraints excluded: chain H residue   14 LEU
Chi-restraints excluded: chain H residue   15 VAL
Chi-restraints excluded: chain H residue   25 CYS
Chi-restraints excluded: chain H residue   94 THR
Chi-restraints excluded: chain H residue   96 VAL
Chi-restraints excluded: chain H residue  102 TYR
Chi-restraints excluded: chain H residue  119 ILE
Chi-restraints excluded: chain L residue    6 THR
Chi-restraints excluded: chain L residue    7 GLN
Chi-restraints excluded: chain L residue   10 SER
Chi-restraints excluded: chain L residue   21 THR
Chi-restraints excluded: chain L residue   38 GLN
Chi-restraints excluded: chain L residue   73 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 37 optimal weight:    0.9980
   chunk 42 optimal weight:    1.9990
   chunk 36 optimal weight:    0.4980
   chunk 56 optimal weight:    2.9990
   chunk 40 optimal weight:    0.8980
   chunk 54 optimal weight:    3.9990
   chunk 48 optimal weight:    3.9990
   chunk 32 optimal weight:    1.9990
   chunk 21 optimal weight:    6.9990
   chunk 53 optimal weight:    0.9990
   chunk 29 optimal weight:    0.9990
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
A 214 ASN
L  38 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.119730 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.111333 restraints weight = 7776.667|
|-----------------------------------------------------------------------------|
r_work (start): 0.3346 rms_B_bonded: 1.95
r_work: 0.3257 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.3149 rms_B_bonded: 4.21 restraints_weight: 0.2500
r_work (final): 0.3149
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8204
moved from start:          0.3032

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   4740  Z= 0.226
  Angle     :  0.597   7.180   6440  Z= 0.308
  Chirality :  0.043   0.157    739
  Planarity :  0.004   0.040    788
  Dihedral  :  6.740  57.320    705
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 7.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.18 %
    Favored  : 95.82 %
  Rotamer:
    Outliers :  5.95 %
    Allowed  : 18.85 %
    Favored  : 75.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.00 (0.35), residues: 574
  helix:  1.25 (0.32), residues: 273
  sheet: -0.51 (0.57), residues: 90
  loop : -1.41 (0.40), residues: 211

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP L  95 
 HIS   0.002   0.001   HIS H  38 
 PHE   0.016   0.001   PHE A 268 
 TYR   0.013   0.001   TYR A 345 
 ARG   0.008   0.001   ARG H 111 

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

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

  1148 Ramachandran restraints generated.
    574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1148 Ramachandran restraints generated.
    574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 108
  time to evaluate  : 0.513 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  106 PHE cc_start: 0.7889 (t80) cc_final: 0.6910 (m-10)
REVERT: A  253 GLN cc_start: 0.8009 (tt0) cc_final: 0.7802 (tt0)
REVERT: A  271 GLN cc_start: 0.9018 (OUTLIER) cc_final: 0.7573 (mt0)
REVERT: A  305 MET cc_start: 0.8822 (mmm) cc_final: 0.8216 (mtp)
REVERT: A  333 THR cc_start: 0.9132 (m) cc_final: 0.8833 (m)
REVERT: A  347 ILE cc_start: 0.8798 (mm) cc_final: 0.8595 (mt)
REVERT: A  384 TYR cc_start: 0.9057 (t80) cc_final: 0.8664 (t80)
REVERT: H   49 GLU cc_start: 0.8465 (tt0) cc_final: 0.8184 (tt0)
REVERT: H   68 LYS cc_start: 0.8424 (tttt) cc_final: 0.8052 (ttpp)
REVERT: H   80 ASN cc_start: 0.8524 (t0) cc_final: 0.8231 (t0)
REVERT: L   56 TYR cc_start: 0.9023 (t80) cc_final: 0.8737 (t80)
REVERT: L   91 GLN cc_start: 0.9136 (pp30) cc_final: 0.8437 (pp30)
  outliers start: 30
  outliers final: 27
  residues processed: 127
  average time/residue: 0.1785
  time to fit residues: 28.8832
Evaluate side-chains
  135 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 107
  time to evaluate  : 0.557 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 ILE
Chi-restraints excluded: chain A residue   89 TYR
Chi-restraints excluded: chain A residue  152 THR
Chi-restraints excluded: chain A residue  154 ASN
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  258 CYS
Chi-restraints excluded: chain A residue  271 GLN
Chi-restraints excluded: chain A residue  276 TYR
Chi-restraints excluded: chain A residue  289 CYS
Chi-restraints excluded: chain A residue  297 VAL
Chi-restraints excluded: chain A residue  301 CYS
Chi-restraints excluded: chain A residue  328 CYS
Chi-restraints excluded: chain A residue  337 ILE
Chi-restraints excluded: chain A residue  369 VAL
Chi-restraints excluded: chain A residue  379 VAL
Chi-restraints excluded: chain H residue   14 LEU
Chi-restraints excluded: chain H residue   15 VAL
Chi-restraints excluded: chain H residue   25 CYS
Chi-restraints excluded: chain H residue   94 THR
Chi-restraints excluded: chain H residue   96 VAL
Chi-restraints excluded: chain H residue  102 TYR
Chi-restraints excluded: chain H residue  119 ILE
Chi-restraints excluded: chain L residue    6 THR
Chi-restraints excluded: chain L residue    7 GLN
Chi-restraints excluded: chain L residue   10 SER
Chi-restraints excluded: chain L residue   21 THR
Chi-restraints excluded: chain L residue   38 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 29 optimal weight:    0.8980
   chunk 8 optimal weight:    0.6980
   chunk 26 optimal weight:    3.9990
   chunk 38 optimal weight:    3.9990
   chunk 7 optimal weight:    1.9990
   chunk 19 optimal weight:    0.5980
   chunk 28 optimal weight:    0.5980
   chunk 34 optimal weight:    0.9980
   chunk 17 optimal weight:    0.9990
   chunk 12 optimal weight:    0.6980
   chunk 20 optimal weight:    0.6980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 = 0.3480 r_free = 0.3480 target = 0.121076 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.112660 restraints weight = 7805.333|
|-----------------------------------------------------------------------------|
r_work (start): 0.3360 rms_B_bonded: 1.97
r_work: 0.3273 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.3167 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.3167
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8186
moved from start:          0.3098

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4740  Z= 0.199
  Angle     :  0.595   9.963   6440  Z= 0.303
  Chirality :  0.042   0.149    739
  Planarity :  0.004   0.040    788
  Dihedral  :  6.660  56.799    705
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 7.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  5.95 %
    Allowed  : 19.84 %
    Favored  : 74.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.11 (0.35), residues: 574
  helix:  1.33 (0.32), residues: 273
  sheet: -0.46 (0.58), residues: 90
  loop : -1.33 (0.40), residues: 211

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP L  95 
 HIS   0.002   0.001   HIS H  38 
 PHE   0.016   0.001   PHE A 268 
 TYR   0.012   0.001   TYR A 345 
 ARG   0.005   0.001   ARG H 111 

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

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

  1148 Ramachandran restraints generated.
    574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1148 Ramachandran restraints generated.
    574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 109
  time to evaluate  : 0.545 
Fit side-chains
   revert: symmetry clash
REVERT: A  271 GLN cc_start: 0.8976 (OUTLIER) cc_final: 0.7543 (mt0)
REVERT: A  305 MET cc_start: 0.8796 (mmm) cc_final: 0.8420 (mtp)
REVERT: A  333 THR cc_start: 0.9135 (m) cc_final: 0.8836 (m)
REVERT: A  347 ILE cc_start: 0.8737 (mm) cc_final: 0.8513 (mt)
REVERT: A  384 TYR cc_start: 0.9062 (t80) cc_final: 0.8687 (t80)
REVERT: H   49 GLU cc_start: 0.8430 (tt0) cc_final: 0.8171 (tt0)
REVERT: H   68 LYS cc_start: 0.8413 (tttt) cc_final: 0.8038 (ttpp)
REVERT: H   80 ASN cc_start: 0.8513 (t0) cc_final: 0.8246 (t0)
REVERT: L   56 TYR cc_start: 0.8994 (t80) cc_final: 0.8655 (t80)
REVERT: L   91 GLN cc_start: 0.9153 (pp30) cc_final: 0.8401 (pp30)
  outliers start: 30
  outliers final: 28
  residues processed: 129
  average time/residue: 0.1702
  time to fit residues: 27.8155
Evaluate side-chains
  133 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 104
  time to evaluate  : 0.546 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 ILE
Chi-restraints excluded: chain A residue   89 TYR
Chi-restraints excluded: chain A residue  154 ASN
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  243 LEU
Chi-restraints excluded: chain A residue  258 CYS
Chi-restraints excluded: chain A residue  271 GLN
Chi-restraints excluded: chain A residue  276 TYR
Chi-restraints excluded: chain A residue  289 CYS
Chi-restraints excluded: chain A residue  297 VAL
Chi-restraints excluded: chain A residue  301 CYS
Chi-restraints excluded: chain A residue  328 CYS
Chi-restraints excluded: chain A residue  337 ILE
Chi-restraints excluded: chain A residue  343 MET
Chi-restraints excluded: chain A residue  369 VAL
Chi-restraints excluded: chain A residue  379 VAL
Chi-restraints excluded: chain H residue   14 LEU
Chi-restraints excluded: chain H residue   15 VAL
Chi-restraints excluded: chain H residue   25 CYS
Chi-restraints excluded: chain H residue   94 THR
Chi-restraints excluded: chain H residue   96 VAL
Chi-restraints excluded: chain H residue  102 TYR
Chi-restraints excluded: chain H residue  119 ILE
Chi-restraints excluded: chain L residue    6 THR
Chi-restraints excluded: chain L residue    7 GLN
Chi-restraints excluded: chain L residue   10 SER
Chi-restraints excluded: chain L residue   21 THR
Chi-restraints excluded: chain L residue   38 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 3 optimal weight:    0.9980
   chunk 12 optimal weight:    0.5980
   chunk 41 optimal weight:    1.9990
   chunk 45 optimal weight:    0.5980
   chunk 51 optimal weight:    0.8980
   chunk 29 optimal weight:    0.6980
   chunk 54 optimal weight:    0.9990
   chunk 52 optimal weight:    0.7980
   chunk 7 optimal weight:    0.0970
   chunk 43 optimal weight:    3.9990
   chunk 2 optimal weight:    1.9990
   overall best weight:    0.5578

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

Flipped N/Q/H residues before XYZ refinement:
A 395 ASN
L  39 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.122632 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.114225 restraints weight = 7722.278|
|-----------------------------------------------------------------------------|
r_work (start): 0.3384 rms_B_bonded: 1.96
r_work: 0.3296 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.3189 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.3189
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8166
moved from start:          0.3196

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4740  Z= 0.183
  Angle     :  0.571   7.185   6440  Z= 0.294
  Chirality :  0.041   0.139    739
  Planarity :  0.004   0.041    788
  Dihedral  :  6.561  57.430    705
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.18 %
    Favored  : 95.82 %
  Rotamer:
    Outliers :  6.15 %
    Allowed  : 20.24 %
    Favored  : 73.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.24 (0.35), residues: 574
  helix:  1.43 (0.32), residues: 272
  sheet: -0.41 (0.58), residues: 90
  loop : -1.23 (0.40), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP L  95 
 HIS   0.002   0.001   HIS A 180 
 PHE   0.016   0.001   PHE A 268 
 TYR   0.011   0.001   TYR A 345 
 ARG   0.006   0.001   ARG H 111 

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

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

  1148 Ramachandran restraints generated.
    574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1148 Ramachandran restraints generated.
    574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 111
  time to evaluate  : 0.492 
Fit side-chains
   revert: symmetry clash
REVERT: A  271 GLN cc_start: 0.8981 (OUTLIER) cc_final: 0.7468 (mt0)
REVERT: A  305 MET cc_start: 0.8807 (mmm) cc_final: 0.8523 (mtp)
REVERT: A  333 THR cc_start: 0.9125 (m) cc_final: 0.8834 (m)
REVERT: A  347 ILE cc_start: 0.8687 (mm) cc_final: 0.8460 (mt)
REVERT: A  384 TYR cc_start: 0.9042 (t80) cc_final: 0.8669 (t80)
REVERT: H   49 GLU cc_start: 0.8371 (tt0) cc_final: 0.8124 (tt0)
REVERT: H   68 LYS cc_start: 0.8433 (tttt) cc_final: 0.7987 (ttpp)
REVERT: H   80 ASN cc_start: 0.8505 (t0) cc_final: 0.8212 (t0)
REVERT: L   56 TYR cc_start: 0.8965 (t80) cc_final: 0.8642 (t80)
REVERT: L   91 GLN cc_start: 0.9165 (pp30) cc_final: 0.8423 (pp30)
  outliers start: 31
  outliers final: 28
  residues processed: 132
  average time/residue: 0.1824
  time to fit residues: 30.1769
Evaluate side-chains
  138 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 109
  time to evaluate  : 0.584 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 ILE
Chi-restraints excluded: chain A residue   89 TYR
Chi-restraints excluded: chain A residue  152 THR
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  243 LEU
Chi-restraints excluded: chain A residue  258 CYS
Chi-restraints excluded: chain A residue  271 GLN
Chi-restraints excluded: chain A residue  276 TYR
Chi-restraints excluded: chain A residue  289 CYS
Chi-restraints excluded: chain A residue  297 VAL
Chi-restraints excluded: chain A residue  301 CYS
Chi-restraints excluded: chain A residue  328 CYS
Chi-restraints excluded: chain A residue  337 ILE
Chi-restraints excluded: chain A residue  343 MET
Chi-restraints excluded: chain A residue  369 VAL
Chi-restraints excluded: chain A residue  379 VAL
Chi-restraints excluded: chain H residue   14 LEU
Chi-restraints excluded: chain H residue   15 VAL
Chi-restraints excluded: chain H residue   25 CYS
Chi-restraints excluded: chain H residue   94 THR
Chi-restraints excluded: chain H residue   96 VAL
Chi-restraints excluded: chain H residue  102 TYR
Chi-restraints excluded: chain H residue  119 ILE
Chi-restraints excluded: chain L residue    6 THR
Chi-restraints excluded: chain L residue    7 GLN
Chi-restraints excluded: chain L residue   10 SER
Chi-restraints excluded: chain L residue   21 THR
Chi-restraints excluded: chain L residue   38 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 19 optimal weight:    0.6980
   chunk 8 optimal weight:    0.6980
   chunk 18 optimal weight:    1.9990
   chunk 13 optimal weight:    0.8980
   chunk 11 optimal weight:    0.7980
   chunk 22 optimal weight:    0.7980
   chunk 38 optimal weight:    0.9990
   chunk 31 optimal weight:    6.9990
   chunk 0 optimal weight:    5.9990
   chunk 45 optimal weight:    1.9990
   chunk 15 optimal weight:    0.6980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 395 ASN
L  38 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.121166 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.112653 restraints weight = 7857.280|
|-----------------------------------------------------------------------------|
r_work (start): 0.3359 rms_B_bonded: 1.98
r_work: 0.3271 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.3167 rms_B_bonded: 4.21 restraints_weight: 0.2500
r_work (final): 0.3167
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8189
moved from start:          0.3226

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   4740  Z= 0.208
  Angle     :  0.597   9.924   6440  Z= 0.305
  Chirality :  0.042   0.148    739
  Planarity :  0.004   0.042    788
  Dihedral  :  6.575  57.255    705
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  6.15 %
    Allowed  : 20.44 %
    Favored  : 73.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.21 (0.35), residues: 574
  helix:  1.39 (0.32), residues: 273
  sheet: -0.40 (0.58), residues: 90
  loop : -1.26 (0.40), residues: 211

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP L  95 
 HIS   0.002   0.001   HIS H  38 
 PHE   0.016   0.001   PHE A 268 
 TYR   0.013   0.001   TYR A 345 
 ARG   0.008   0.000   ARG H 111 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2492.87 seconds
wall clock time: 45 minutes 1.63 seconds (2701.63 seconds total)