Starting phenix.real_space_refine
on Mon Feb 10 19:31:00 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jga_36228/02_2025/8jga_36228.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jga_36228/02_2025/8jga_36228.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.68
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jga_36228/02_2025/8jga_36228.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jga_36228/02_2025/8jga_36228.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jga_36228/02_2025/8jga_36228.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jga_36228/02_2025/8jga_36228.cif"
  }
  resolution = 3.68
  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=   0.002 sd=   0.022
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       7      5.16       5
     C     987      2.51       5
     N     249      2.21       5
     O     273      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 1516
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 1516
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 202, 1516
          Classifications: {'peptide': 202}
          Incomplete info: {'backbone_only': 2}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 191}
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 7
          Unresolved non-hydrogen chiralities: 2
  Time building chain proxies: 4.41, per 1000 atoms: 2.91
  Number of scatterers: 1516
  At special positions: 0
  Unit cell: (54.78, 50.63, 55.61, 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       7     16.00
     O     273      8.00
     N     249      7.00
     C     987      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 165 " - pdb=" SG  CYS A 203 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.40
  Conformation dependent library (CDL) restraints added in 207.4 milliseconds
  

  400 Ramachandran restraints generated.
    200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  362

  Finding SS restraints...
    Secondary structure from input PDB file:
      11 helices and 3 sheets defined
      58.4% alpha, 8.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.20
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2 through 11
    Processing helix  chain 'A' and resid 20 through 35
      removed outlier: 3.506A  pdb=" N   LEU A  29 " --> pdb=" O   LYS A  25 " (cutoff:3.500A)
      removed outlier: 4.023A  pdb=" N   ALA A  30 " --> pdb=" O   LYS A  26 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   VAL A  31 " --> pdb=" O   LYS A  27 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   PHE A  32 " --> pdb=" O   ALA A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 47 through 56
    Processing helix  chain 'A' and resid 56 through 62
      removed outlier: 4.314A  pdb=" N   GLU A  60 " --> pdb=" O   SER A  56 " (cutoff:3.500A)
      removed outlier: 3.942A  pdb=" N   MET A  61 " --> pdb=" O   PHE A  57 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 72 through 82
    Processing helix  chain 'A' and resid 93 through 104
    Processing helix  chain 'A' and resid 113 through 124
      removed outlier: 4.002A  pdb=" N   LYS A 119 " --> pdb=" O   THR A 115 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 132 through 137
    Processing helix  chain 'A' and resid 137 through 145
      removed outlier: 4.100A  pdb=" N   VAL A 141 " --> pdb=" O   GLY A 137 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 163 through 169
    Processing helix  chain 'A' and resid 185 through 202
      removed outlier: 3.799A  pdb=" N   ALA A 190 " --> pdb=" O   PRO A 186 " (cutoff:3.500A)
      removed outlier: 4.014A  pdb=" N   GLU A 191 " --> pdb=" O   VAL A 187 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   GLU A 198 " --> pdb=" O   LYS A 194 " (cutoff:3.500A)
      removed outlier: 4.007A  pdb=" N   LYS A 199 " --> pdb=" O   ALA A 195 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   ILE A 200 " --> pdb=" O   PHE A 196 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   ARG A 201 " --> pdb=" O   VAL A 197 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 14 through 15
      removed outlier: 6.254A  pdb=" N   ALA A  14 " --> pdb=" O   GLU A  40 " (cutoff:3.500A)
      removed outlier: 6.571A  pdb=" N   THR A  42 " --> pdb=" O   ALA A  14 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 86 through 88
      removed outlier: 3.553A  pdb=" N   MET A 108 " --> pdb=" O   ILE A  87 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 127 through 129
      removed outlier: 6.784A  pdb=" N   LEU A 128 " --> pdb=" O   VAL A 154 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3

    65 hydrogen bonds defined for protein.
    195 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.40

  Time building geometry restraints manager: 0.47 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 381
        1.33 -     1.46: 306
        1.46 -     1.58: 846
        1.58 -     1.71: 0
        1.71 -     1.83: 12
  Bond restraints: 1545
  Sorted by residual:
  bond pdb=" C   LYS A 183 "
       pdb=" O   LYS A 183 "
    ideal  model  delta    sigma   weight residual
    1.234  1.207  0.026 1.19e-02 7.06e+03 4.92e+00
  bond pdb=" C   LEU A 181 "
       pdb=" O   LEU A 181 "
    ideal  model  delta    sigma   weight residual
    1.235  1.213  0.022 1.26e-02 6.30e+03 3.15e+00
  bond pdb=" C   VAL A 182 "
       pdb=" O   VAL A 182 "
    ideal  model  delta    sigma   weight residual
    1.236  1.218  0.018 1.19e-02 7.06e+03 2.36e+00
  bond pdb=" CA  LYS A 183 "
       pdb=" C   LYS A 183 "
    ideal  model  delta    sigma   weight residual
    1.525  1.506  0.020 1.29e-02 6.01e+03 2.31e+00
  bond pdb=" CG  LEU A 173 "
       pdb=" CD1 LEU A 173 "
    ideal  model  delta    sigma   weight residual
    1.521  1.479  0.042 3.30e-02 9.18e+02 1.61e+00
  ... (remaining 1540 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.63: 1985
        1.63 -     3.27: 76
        3.27 -     4.90: 19
        4.90 -     6.54: 2
        6.54 -     8.17: 2
  Bond angle restraints: 2084
  Sorted by residual:
  angle pdb=" C   LYS A 183 "
        pdb=" N   GLY A 184 "
        pdb=" CA  GLY A 184 "
      ideal   model   delta    sigma   weight residual
     121.23  125.06   -3.83 1.34e+00 5.57e-01 8.16e+00
  angle pdb=" N   ALA A 180 "
        pdb=" CA  ALA A 180 "
        pdb=" C   ALA A 180 "
      ideal   model   delta    sigma   weight residual
     112.59  109.52    3.07 1.22e+00 6.72e-01 6.33e+00
  angle pdb=" C   ASN A  19 "
        pdb=" N   SER A  20 "
        pdb=" CA  SER A  20 "
      ideal   model   delta    sigma   weight residual
     121.54  126.00   -4.46 1.91e+00 2.74e-01 5.46e+00
  angle pdb=" CA  LEU A  55 "
        pdb=" CB  LEU A  55 "
        pdb=" CG  LEU A  55 "
      ideal   model   delta    sigma   weight residual
     116.30  124.47   -8.17 3.50e+00 8.16e-02 5.45e+00
  angle pdb=" C   VAL A 164 "
        pdb=" N   CYS A 165 "
        pdb=" CA  CYS A 165 "
      ideal   model   delta    sigma   weight residual
     121.58  117.20    4.38 1.95e+00 2.63e-01 5.04e+00
  ... (remaining 2079 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.01 -    15.82: 821
       15.82 -    31.64: 81
       31.64 -    47.46: 22
       47.46 -    63.28: 7
       63.28 -    79.10: 1
  Dihedral angle restraints: 932
    sinusoidal: 368
      harmonic: 564
  Sorted by residual:
  dihedral pdb=" CB  CYS A 165 "
           pdb=" SG  CYS A 165 "
           pdb=" SG  CYS A 203 "
           pdb=" CB  CYS A 203 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   42.70   50.30     1      1.00e+01 1.00e-02 3.47e+01
  dihedral pdb=" CA  LYS A 152 "
           pdb=" C   LYS A 152 "
           pdb=" N   PHE A 153 "
           pdb=" CA  PHE A 153 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.76  -17.24     0      5.00e+00 4.00e-02 1.19e+01
  dihedral pdb=" CA  GLY A 202 "
           pdb=" C   GLY A 202 "
           pdb=" N   CYS A 203 "
           pdb=" CA  CYS A 203 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.98  -17.02     0      5.00e+00 4.00e-02 1.16e+01
  ... (remaining 929 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 139
       0.039 -    0.079: 66
       0.079 -    0.118: 30
       0.118 -    0.157: 8
       0.157 -    0.197: 1
  Chirality restraints: 244
  Sorted by residual:
  chirality pdb=" CG  LEU A 181 "
            pdb=" CB  LEU A 181 "
            pdb=" CD1 LEU A 181 "
            pdb=" CD2 LEU A 181 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.39   -0.20 2.00e-01 2.50e+01 9.66e-01
  chirality pdb=" CA  PRO A 186 "
            pdb=" N   PRO A 186 "
            pdb=" C   PRO A 186 "
            pdb=" CB  PRO A 186 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.57    0.15 2.00e-01 2.50e+01 5.66e-01
  chirality pdb=" CA  ILE A  64 "
            pdb=" N   ILE A  64 "
            pdb=" C   ILE A  64 "
            pdb=" CB  ILE A  64 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.47e-01
  ... (remaining 241 not shown)

  Planarity restraints: 263
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 185 "    0.030 5.00e-02 4.00e+02   4.49e-02 3.23e+00
        pdb=" N   PRO A 186 "   -0.078 5.00e-02 4.00e+02
        pdb=" CA  PRO A 186 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO A 186 "    0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET A 108 "    0.029 5.00e-02 4.00e+02   4.42e-02 3.13e+00
        pdb=" N   PRO A 109 "   -0.077 5.00e-02 4.00e+02
        pdb=" CA  PRO A 109 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO A 109 "    0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS A 183 "    0.007 2.00e-02 2.50e+03   1.40e-02 1.95e+00
        pdb=" C   LYS A 183 "   -0.024 2.00e-02 2.50e+03
        pdb=" O   LYS A 183 "    0.009 2.00e-02 2.50e+03
        pdb=" N   GLY A 184 "    0.008 2.00e-02 2.50e+03
  ... (remaining 260 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 254
        2.76 -     3.30: 1514
        3.30 -     3.83: 2527
        3.83 -     4.37: 2950
        4.37 -     4.90: 5061
  Nonbonded interactions: 12306
  Sorted by model distance:
  nonbonded pdb=" O   ASP A  49 "
            pdb=" OG  SER A  82 "
     model   vdw
     2.230 3.040
  nonbonded pdb=" OG  SER A  89 "
            pdb=" OH  TYR A 107 "
     model   vdw
     2.252 3.040
  nonbonded pdb=" OG1 THR A 126 "
            pdb=" O   ASN A 150 "
     model   vdw
     2.257 3.040
  nonbonded pdb=" OG  SER A  97 "
            pdb=" NE2 HIS A 125 "
     model   vdw
     2.266 3.120
  nonbonded pdb=" NZ  LYS A  27 "
            pdb=" O   GLY A 184 "
     model   vdw
     2.383 3.120
  ... (remaining 12301 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             5.460
  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:          0.060
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     12.490
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.970
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.030
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7938
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      :  0.005   0.042   1545  Z= 0.320
  Angle     :  0.811   8.171   2084  Z= 0.452
  Chirality :  0.054   0.197    244
  Planarity :  0.006   0.045    263
  Dihedral  : 14.340  79.102    567
  Min Nonbonded Distance : 2.230

Molprobity Statistics.
  All-atom Clashscore : 16.80
  Ramachandran Plot:
    Outliers :  0.50 %
    Allowed  :  7.00 %
    Favored  : 92.50 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  :  0.62 %
    Favored  : 98.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.18 (0.60), residues: 200
  helix: -1.12 (0.51), residues: 108
  sheet: -1.53 (0.88), residues: 30
  loop : -1.61 (0.84), residues: 62

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP A 167 
 HIS   0.002   0.001   HIS A  91 
 PHE   0.017   0.002   PHE A  99 
 TYR   0.005   0.001   TYR A 107 
 ARG   0.009   0.002   ARG A  77 

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

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

  400 Ramachandran restraints generated.
    200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  400 Ramachandran restraints generated.
    200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  28 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 26
  time to evaluate  : 0.180 
Fit side-chains
  outliers start: 2
  outliers final: 1
  residues processed: 28
  average time/residue: 0.1931
  time to fit residues: 6.0642
Evaluate side-chains
  21 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 20
  time to evaluate  : 0.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  183 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 20
   random chunks:
   chunk 16 optimal weight:    0.9980
   chunk 15 optimal weight:    0.7980
   chunk 8 optimal weight:    6.9990
   chunk 5 optimal weight:    5.9990
   chunk 10 optimal weight:    0.7980
   chunk 6 optimal weight:    4.9990
   chunk 9 optimal weight:    5.9990
   chunk 11 optimal weight:    0.3980
   chunk 18 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9990
   chunk 19 optimal weight:    0.7980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 150 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.107786 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.091200 restraints weight = 2156.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.094374 restraints weight = 1296.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.096745 restraints weight = 893.570|
|-----------------------------------------------------------------------------|
r_work (final): 0.3179
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7865
moved from start:          0.1198

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   1545  Z= 0.206
  Angle     :  0.695   9.635   2084  Z= 0.339
  Chirality :  0.048   0.132    244
  Planarity :  0.005   0.046    263
  Dihedral  :  5.781  26.949    209
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 10.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.50 %
    Favored  : 94.50 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 11.18 %
    Favored  : 85.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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: -1.96 (0.61), residues: 200
  helix: -0.99 (0.51), residues: 108
  sheet: -1.24 (0.95), residues: 30
  loop : -1.53 (0.83), residues: 62

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.002   TRP A 167 
 HIS   0.001   0.001   HIS A  91 
 PHE   0.009   0.001   PHE A 168 
 TYR   0.005   0.001   TYR A 107 
 ARG   0.002   0.000   ARG A  17 

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

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

  400 Ramachandran restraints generated.
    200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  400 Ramachandran restraints generated.
    200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  26 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 21
  time to evaluate  : 0.178 
Fit side-chains
  outliers start: 5
  outliers final: 4
  residues processed: 23
  average time/residue: 0.1785
  time to fit residues: 4.6848
Evaluate side-chains
  23 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 19
  time to evaluate  : 0.179 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 ILE
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  126 THR
Chi-restraints excluded: chain A residue  183 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 20
   random chunks:
   chunk 4 optimal weight:    6.9990
   chunk 6 optimal weight:    7.9990
   chunk 2 optimal weight:    6.9990
   chunk 15 optimal weight:    4.9990
   chunk 7 optimal weight:    1.9990
   chunk 0 optimal weight:    9.9990
   chunk 12 optimal weight:    0.7980
   chunk 18 optimal weight:    3.9990
   chunk 3 optimal weight:    0.7980
   chunk 14 optimal weight:    0.1980
   chunk 17 optimal weight:    0.4980
   overall best weight:    0.8582

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.121927 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.107314 restraints weight = 2086.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.110288 restraints weight = 1234.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.112267 restraints weight = 840.410|
|-----------------------------------------------------------------------------|
r_work (final): 0.3413
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7880
moved from start:          0.1494

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   1545  Z= 0.191
  Angle     :  0.641   9.118   2084  Z= 0.314
  Chirality :  0.047   0.133    244
  Planarity :  0.005   0.044    263
  Dihedral  :  5.534  29.854    209
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 10.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.00 %
    Favored  : 95.00 %
  Rotamer:
    Outliers :  4.35 %
    Allowed  : 13.04 %
    Favored  : 82.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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: -1.69 (0.61), residues: 200
  helix: -0.74 (0.51), residues: 109
  sheet: -1.25 (0.96), residues: 30
  loop : -1.38 (0.86), residues: 61

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.002   TRP A 167 
 HIS   0.001   0.001   HIS A  91 
 PHE   0.020   0.002   PHE A  32 
 TYR   0.004   0.001   TYR A 107 
 ARG   0.001   0.000   ARG A  17 

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

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

  400 Ramachandran restraints generated.
    200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  400 Ramachandran restraints generated.
    200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  27 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 20
  time to evaluate  : 0.163 
Fit side-chains
  outliers start: 7
  outliers final: 6
  residues processed: 23
  average time/residue: 0.1679
  time to fit residues: 4.4034
Evaluate side-chains
  26 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 20
  time to evaluate  : 0.178 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 MET
Chi-restraints excluded: chain A residue   65 ILE
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  126 THR
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  183 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 20
   random chunks:
   chunk 3 optimal weight:    6.9990
   chunk 19 optimal weight:    0.9980
   chunk 14 optimal weight:    4.9990
   chunk 16 optimal weight:    0.8980
   chunk 9 optimal weight:    3.9990
   chunk 1 optimal weight:    0.9980
   chunk 11 optimal weight:    5.9990
   chunk 8 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9980
   chunk 7 optimal weight:    4.9990
   overall best weight:    0.9782

-------------------------------------------------------------------------------
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 = 0.3346 r_free = 0.3346 target = 0.109017 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.092906 restraints weight = 2061.038|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.095836 restraints weight = 1273.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.097733 restraints weight = 895.155|
|-----------------------------------------------------------------------------|
r_work (final): 0.3226
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7867
moved from start:          0.1718

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   1545  Z= 0.184
  Angle     :  0.602   8.095   2084  Z= 0.298
  Chirality :  0.047   0.135    244
  Planarity :  0.005   0.042    263
  Dihedral  :  5.292  29.666    209
  Min Nonbonded Distance : 2.626

Molprobity Statistics.
  All-atom Clashscore : 9.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.50 %
    Favored  : 94.50 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  : 16.77 %
    Favored  : 79.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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: -1.50 (0.62), residues: 200
  helix: -0.53 (0.52), residues: 109
  sheet: -1.20 (0.94), residues: 30
  loop : -1.41 (0.85), residues: 61

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.002   TRP A 167 
 HIS   0.001   0.001   HIS A  91 
 PHE   0.015   0.002   PHE A  32 
 TYR   0.003   0.001   TYR A 107 
 ARG   0.002   0.001   ARG A  77 

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

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

  400 Ramachandran restraints generated.
    200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  400 Ramachandran restraints generated.
    200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  28 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 22
  time to evaluate  : 0.179 
Fit side-chains
  outliers start: 6
  outliers final: 2
  residues processed: 25
  average time/residue: 0.1300
  time to fit residues: 3.8660
Evaluate side-chains
  21 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 19
  time to evaluate  : 0.179 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  183 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 20
   random chunks:
   chunk 13 optimal weight:    0.9990
   chunk 0 optimal weight:    8.9990
   chunk 7 optimal weight:    8.9990
   chunk 11 optimal weight:    4.9990
   chunk 2 optimal weight:    7.9990
   chunk 18 optimal weight:    0.9990
   chunk 3 optimal weight:    0.8980
   chunk 12 optimal weight:    1.9990
   chunk 1 optimal weight:    3.9990
   chunk 5 optimal weight:    2.9990
   chunk 15 optimal weight:    0.8980
   overall best weight:    1.1586

-------------------------------------------------------------------------------
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 = 0.3342 r_free = 0.3342 target = 0.109221 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.092295 restraints weight = 2120.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.095376 restraints weight = 1292.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.097603 restraints weight = 900.760|
|-----------------------------------------------------------------------------|
r_work (final): 0.3196
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7877
moved from start:          0.1807

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   1545  Z= 0.204
  Angle     :  0.619   6.733   2084  Z= 0.307
  Chirality :  0.046   0.136    244
  Planarity :  0.004   0.040    263
  Dihedral  :  5.190  28.734    209
  Min Nonbonded Distance : 2.627

Molprobity Statistics.
  All-atom Clashscore : 10.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.00 %
    Favored  : 94.00 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  : 17.39 %
    Favored  : 78.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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: -1.44 (0.62), residues: 200
  helix: -0.49 (0.52), residues: 109
  sheet: -1.15 (0.94), residues: 30
  loop : -1.37 (0.86), residues: 61

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 167 
 HIS   0.001   0.000   HIS A  91 
 PHE   0.012   0.001   PHE A  32 
 TYR   0.003   0.001   TYR A 107 
 ARG   0.002   0.000   ARG A  77 

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

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

  400 Ramachandran restraints generated.
    200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  400 Ramachandran restraints generated.
    200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  26 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 20
  time to evaluate  : 0.159 
Fit side-chains
  outliers start: 6
  outliers final: 4
  residues processed: 22
  average time/residue: 0.1359
  time to fit residues: 3.5440
Evaluate side-chains
  24 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 20
  time to evaluate  : 0.182 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 MET
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  126 THR
Chi-restraints excluded: chain A residue  183 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 20
   random chunks:
   chunk 1 optimal weight:    0.9980
   chunk 3 optimal weight:    0.9990
   chunk 13 optimal weight:    0.8980
   chunk 17 optimal weight:    1.9990
   chunk 9 optimal weight:    4.9990
   chunk 6 optimal weight:    0.1980
   chunk 10 optimal weight:    2.9990
   chunk 14 optimal weight:    0.8980
   chunk 12 optimal weight:    0.6980
   chunk 15 optimal weight:    0.7980
   chunk 11 optimal weight:    3.9990
   overall best weight:    0.6980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.121302 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.107300 restraints weight = 2200.178|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.110104 restraints weight = 1336.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.112076 restraints weight = 925.710|
|-----------------------------------------------------------------------------|
r_work (final): 0.3427
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7837
moved from start:          0.2080

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   1545  Z= 0.174
  Angle     :  0.589   6.763   2084  Z= 0.292
  Chirality :  0.046   0.136    244
  Planarity :  0.004   0.039    263
  Dihedral  :  5.018  27.797    209
  Min Nonbonded Distance : 2.632

Molprobity Statistics.
  All-atom Clashscore : 11.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.00 %
    Favored  : 95.00 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 19.88 %
    Favored  : 77.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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: -1.30 (0.62), residues: 200
  helix: -0.42 (0.53), residues: 109
  sheet: -1.10 (0.91), residues: 32
  loop : -1.20 (0.88), residues: 59

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP A 167 
 HIS   0.001   0.000   HIS A  91 
 PHE   0.011   0.001   PHE A  32 
 TYR   0.003   0.001   TYR A 107 
 ARG   0.002   0.000   ARG A  77 

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

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

  400 Ramachandran restraints generated.
    200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  400 Ramachandran restraints generated.
    200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  26 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 21
  time to evaluate  : 0.185 
Fit side-chains
  outliers start: 5
  outliers final: 2
  residues processed: 23
  average time/residue: 0.1399
  time to fit residues: 3.8125
Evaluate side-chains
  21 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 19
  time to evaluate  : 0.188 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 MET
Chi-restraints excluded: chain A residue  115 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 20
   random chunks:
   chunk 11 optimal weight:    2.9990
   chunk 5 optimal weight:    6.9990
   chunk 8 optimal weight:    0.3980
   chunk 3 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 4 optimal weight:    5.9990
   chunk 12 optimal weight:    0.9980
   chunk 19 optimal weight:    2.9990
   chunk 0 optimal weight:    7.9990
   chunk 1 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9990
   overall best weight:    1.2786

-------------------------------------------------------------------------------
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 = 0.3570 r_free = 0.3570 target = 0.123196 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.109388 restraints weight = 2116.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.112345 restraints weight = 1291.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.114355 restraints weight = 894.748|
|-----------------------------------------------------------------------------|
r_work (final): 0.3405
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7879
moved from start:          0.2146

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   1545  Z= 0.217
  Angle     :  0.605   5.516   2084  Z= 0.298
  Chirality :  0.047   0.134    244
  Planarity :  0.004   0.039    263
  Dihedral  :  4.585  13.769    205
  Min Nonbonded Distance : 2.637

Molprobity Statistics.
  All-atom Clashscore : 11.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.00 %
    Favored  : 95.00 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 21.74 %
    Favored  : 76.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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: -1.23 (0.62), residues: 200
  helix: -0.42 (0.52), residues: 109
  sheet: -1.04 (0.88), residues: 32
  loop : -1.10 (0.88), residues: 59

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.002   TRP A 167 
 HIS   0.001   0.001   HIS A  10 
 PHE   0.009   0.002   PHE A  32 
 TYR   0.003   0.001   TYR A 107 
 ARG   0.002   0.001   ARG A  77 

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

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

  400 Ramachandran restraints generated.
    200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  400 Ramachandran restraints generated.
    200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  21 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 18
  time to evaluate  : 0.181 
Fit side-chains
  outliers start: 3
  outliers final: 2
  residues processed: 19
  average time/residue: 0.1328
  time to fit residues: 3.0688
Evaluate side-chains
  20 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 18
  time to evaluate  : 0.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 MET
Chi-restraints excluded: chain A residue  115 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 20
   random chunks:
   chunk 8 optimal weight:    8.9990
   chunk 4 optimal weight:    0.9990
   chunk 5 optimal weight:    3.9990
   chunk 14 optimal weight:    1.9990
   chunk 9 optimal weight:    5.9990
   chunk 3 optimal weight:    0.6980
   chunk 0 optimal weight:    0.7980
   chunk 12 optimal weight:    0.9980
   chunk 11 optimal weight:    0.0970
   chunk 10 optimal weight:    6.9990
   chunk 15 optimal weight:    0.9980
   overall best weight:    0.7178

-------------------------------------------------------------------------------
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 = 0.3520 r_free = 0.3520 target = 0.119066 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.104467 restraints weight = 2078.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.107487 restraints weight = 1196.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.109592 restraints weight = 806.385|
|-----------------------------------------------------------------------------|
r_work (final): 0.3418
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7824
moved from start:          0.2329

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   1545  Z= 0.171
  Angle     :  0.597   6.200   2084  Z= 0.290
  Chirality :  0.046   0.132    244
  Planarity :  0.004   0.037    263
  Dihedral  :  4.456  13.132    205
  Min Nonbonded Distance : 2.646

Molprobity Statistics.
  All-atom Clashscore : 10.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.50 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 22.36 %
    Favored  : 75.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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: -1.17 (0.61), residues: 200
  helix: -0.32 (0.52), residues: 109
  sheet: -1.04 (0.87), residues: 32
  loop : -1.14 (0.87), residues: 59

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP A 167 
 HIS   0.001   0.000   HIS A  91 
 PHE   0.011   0.001   PHE A  32 
 TYR   0.002   0.001   TYR A 107 
 ARG   0.002   0.001   ARG A  77 

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

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

  400 Ramachandran restraints generated.
    200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  400 Ramachandran restraints generated.
    200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  23 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 19
  time to evaluate  : 0.185 
Fit side-chains
  outliers start: 4
  outliers final: 2
  residues processed: 21
  average time/residue: 0.1170
  time to fit residues: 3.0414
Evaluate side-chains
  21 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 19
  time to evaluate  : 0.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 MET
Chi-restraints excluded: chain A residue  115 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 20
   random chunks:
   chunk 14 optimal weight:    3.9990
   chunk 15 optimal weight:    0.9980
   chunk 13 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9980
   chunk 6 optimal weight:    7.9990
   chunk 4 optimal weight:    0.0040
   chunk 7 optimal weight:    5.9990
   chunk 17 optimal weight:    4.9990
   chunk 12 optimal weight:    0.9990
   chunk 9 optimal weight:    2.9990
   overall best weight:    0.9996

-------------------------------------------------------------------------------
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 = 0.3565 r_free = 0.3565 target = 0.122618 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.108572 restraints weight = 2133.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.111497 restraints weight = 1316.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.113566 restraints weight = 917.922|
|-----------------------------------------------------------------------------|
r_work (final): 0.3484
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7848
moved from start:          0.2351

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   1545  Z= 0.192
  Angle     :  0.625   7.449   2084  Z= 0.297
  Chirality :  0.047   0.133    244
  Planarity :  0.004   0.037    263
  Dihedral  :  4.486  13.570    205
  Min Nonbonded Distance : 2.652

Molprobity Statistics.
  All-atom Clashscore : 10.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.00 %
    Favored  : 95.00 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  : 22.98 %
    Favored  : 75.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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: -1.17 (0.61), residues: 200
  helix: -0.35 (0.52), residues: 109
  sheet: -1.03 (0.86), residues: 32
  loop : -1.07 (0.87), residues: 59

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.002   TRP A 167 
 HIS   0.001   0.000   HIS A  91 
 PHE   0.009   0.001   PHE A  32 
 TYR   0.002   0.001   TYR A 107 
 ARG   0.002   0.000   ARG A  77 

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

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

  400 Ramachandran restraints generated.
    200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  400 Ramachandran restraints generated.
    200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  20 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 18
  time to evaluate  : 0.166 
Fit side-chains
  outliers start: 2
  outliers final: 2
  residues processed: 19
  average time/residue: 0.1283
  time to fit residues: 2.9695
Evaluate side-chains
  20 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 18
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 MET
Chi-restraints excluded: chain A residue  115 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 20
   random chunks:
   chunk 7 optimal weight:    2.9990
   chunk 18 optimal weight:    4.9990
   chunk 13 optimal weight:    0.9990
   chunk 8 optimal weight:    0.9980
   chunk 16 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9990
   chunk 17 optimal weight:    0.9980
   chunk 10 optimal weight:    0.0980
   chunk 12 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9980
   chunk 2 optimal weight:    0.9990
   overall best weight:    0.8182

-------------------------------------------------------------------------------
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 = 0.3562 r_free = 0.3562 target = 0.122279 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.108219 restraints weight = 2141.197|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.110969 restraints weight = 1324.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.112959 restraints weight = 925.224|
|-----------------------------------------------------------------------------|
r_work (final): 0.3440
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7823
moved from start:          0.2446

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   1545  Z= 0.178
  Angle     :  0.619   7.257   2084  Z= 0.295
  Chirality :  0.046   0.131    244
  Planarity :  0.004   0.036    263
  Dihedral  :  4.445  13.263    205
  Min Nonbonded Distance : 2.649

Molprobity Statistics.
  All-atom Clashscore : 9.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.50 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 22.36 %
    Favored  : 75.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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: -1.18 (0.61), residues: 200
  helix: -0.37 (0.52), residues: 109
  sheet: -1.01 (0.87), residues: 32
  loop : -1.07 (0.87), residues: 59

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.002   TRP A 167 
 HIS   0.001   0.000   HIS A  91 
 PHE   0.010   0.001   PHE A  32 
 TYR   0.002   0.001   TYR A 107 
 ARG   0.002   0.001   ARG A  77 

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

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

  400 Ramachandran restraints generated.
    200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  400 Ramachandran restraints generated.
    200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  22 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 19
  time to evaluate  : 0.166 
Fit side-chains
REVERT: A   77 ARG cc_start: 0.8038 (tpp80) cc_final: 0.7838 (tpp80)
  outliers start: 3
  outliers final: 3
  residues processed: 21
  average time/residue: 0.0959
  time to fit residues: 2.4822
Evaluate side-chains
  23 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 20
  time to evaluate  : 0.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 MET
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  181 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 20
   random chunks:
   chunk 7 optimal weight:    4.9990
   chunk 4 optimal weight:    0.1980
   chunk 9 optimal weight:    3.9990
   chunk 11 optimal weight:    0.0570
   chunk 5 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9980
   chunk 13 optimal weight:    0.9990
   chunk 8 optimal weight:    4.9990
   chunk 3 optimal weight:    0.9980
   chunk 2 optimal weight:    0.9990
   chunk 12 optimal weight:    1.9990
   overall best weight:    0.6500

-------------------------------------------------------------------------------
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 = 0.3559 r_free = 0.3559 target = 0.122171 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.107442 restraints weight = 2200.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.110617 restraints weight = 1254.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.112704 restraints weight = 835.238|
|-----------------------------------------------------------------------------|
r_work (final): 0.3449
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7799
moved from start:          0.2554

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.018   1545  Z= 0.158
  Angle     :  0.625  10.001   2084  Z= 0.290
  Chirality :  0.046   0.130    244
  Planarity :  0.004   0.036    263
  Dihedral  :  4.374  12.981    205
  Min Nonbonded Distance : 2.639

Molprobity Statistics.
  All-atom Clashscore : 9.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.50 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 22.98 %
    Favored  : 75.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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: -1.11 (0.61), residues: 200
  helix: -0.33 (0.51), residues: 109
  sheet: -0.98 (0.87), residues: 32
  loop : -1.01 (0.88), residues: 59

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.002   TRP A 167 
 HIS   0.001   0.000   HIS A  91 
 PHE   0.010   0.001   PHE A  32 
 TYR   0.001   0.001   TYR A 107 
 ARG   0.001   0.000   ARG A  77 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1378.84 seconds
wall clock time: 25 minutes 11.33 seconds (1511.33 seconds total)