Starting phenix.real_space_refine
on Mon Feb 10 19:27:47 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6r23_4708/02_2025/6r23_4708.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6r23_4708/02_2025/6r23_4708.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6r23_4708/02_2025/6r23_4708.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6r23_4708/02_2025/6r23_4708.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6r23_4708/02_2025/6r23_4708.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6r23_4708/02_2025/6r23_4708.cif"
  }
  resolution = 4.9
  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=   0.026 sd=   0.295
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      10      5.16       5
     C     974      2.51       5
     N     260      2.21       5
     O     274      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 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: 1518
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 759
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 91, 759
          Classifications: {'peptide': 91}
          Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 83}
  Restraints were copied for chains:
    B
  Time building chain proxies: 1.60, per 1000 atoms: 1.05
  Number of scatterers: 1518
  At special positions: 0
  Unit cell: (90.72, 56.16, 47.52, 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      10     16.00
     O     274      8.00
     N     260      7.00
     C     974      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.36
  Conformation dependent library (CDL) restraints added in 175.7 milliseconds
  

  356 Ramachandran restraints generated.
    178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  356

  Finding SS restraints...
    Secondary structure from input PDB file:
      10 helices and 0 sheets defined
      68.1% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.17
  Creating SS restraints...
    Processing helix  chain 'A' and resid 109 through 119
      removed outlier: 4.046A  pdb=" N   ILE A 113 " --> pdb=" O   ASP A 109 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   THR A 118 " --> pdb=" O   PHE A 114 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   GLN A 119 " --> pdb=" O   ASN A 115 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 125 through 139
      removed outlier: 4.323A  pdb=" N   ARG A 129 " --> pdb=" O   LEU A 125 " (cutoff:3.500A)
      removed outlier: 4.030A  pdb=" N   LEU A 130 " --> pdb=" O   GLY A 126 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   ASP A 139 " --> pdb=" O   ARG A 135 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 147 through 157
      removed outlier: 3.775A  pdb=" N   TYR A 155 " --> pdb=" O   ALA A 151 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 160 through 169
      removed outlier: 3.743A  pdb=" N   MET A 169 " --> pdb=" O   ASN A 165 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 174 through 188
      removed outlier: 3.545A  pdb=" N   THR A 185 " --> pdb=" O   GLU A 181 " (cutoff:3.500A)
      removed outlier: 4.612A  pdb=" N   THR A 186 " --> pdb=" O   ALA A 182 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 109 through 119
      removed outlier: 4.046A  pdb=" N   ILE B 113 " --> pdb=" O   ASP B 109 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   THR B 118 " --> pdb=" O   PHE B 114 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   GLN B 119 " --> pdb=" O   ASN B 115 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 125 through 139
      removed outlier: 4.322A  pdb=" N   ARG B 129 " --> pdb=" O   LEU B 125 " (cutoff:3.500A)
      removed outlier: 4.030A  pdb=" N   LEU B 130 " --> pdb=" O   GLY B 126 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   ASP B 139 " --> pdb=" O   ARG B 135 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 147 through 157
      removed outlier: 3.775A  pdb=" N   TYR B 155 " --> pdb=" O   ALA B 151 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 160 through 169
      removed outlier: 3.743A  pdb=" N   MET B 169 " --> pdb=" O   ASN B 165 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 174 through 188
      removed outlier: 3.546A  pdb=" N   THR B 185 " --> pdb=" O   GLU B 181 " (cutoff:3.500A)
      removed outlier: 4.612A  pdb=" N   THR B 186 " --> pdb=" O   ALA B 182 " (cutoff:3.500A)

    64 hydrogen bonds defined for protein.
    192 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: 0.33

  Time building geometry restraints manager: 0.43 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 480
        1.34 -     1.46: 268
        1.46 -     1.57: 784
        1.57 -     1.69: 0
        1.69 -     1.80: 20
  Bond restraints: 1552
  Sorted by residual:
  bond pdb=" C   ASP B 144 "
       pdb=" N   PHE B 145 "
    ideal  model  delta    sigma   weight residual
    1.332  1.350 -0.017 1.40e-02 5.10e+03 1.52e+00
  bond pdb=" C   ASP A 144 "
       pdb=" N   PHE A 145 "
    ideal  model  delta    sigma   weight residual
    1.332  1.349 -0.017 1.40e-02 5.10e+03 1.48e+00
  bond pdb=" N   PHE A 145 "
       pdb=" CA  PHE A 145 "
    ideal  model  delta    sigma   weight residual
    1.457  1.473 -0.015 1.29e-02 6.01e+03 1.39e+00
  bond pdb=" N   PHE B 145 "
       pdb=" CA  PHE B 145 "
    ideal  model  delta    sigma   weight residual
    1.457  1.472 -0.015 1.29e-02 6.01e+03 1.34e+00
  bond pdb=" C   PRO B 142 "
       pdb=" N   PRO B 143 "
    ideal  model  delta    sigma   weight residual
    1.334  1.307  0.027 2.34e-02 1.83e+03 1.29e+00
  ... (remaining 1547 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.59: 1896
        1.59 -     3.18: 153
        3.18 -     4.77: 31
        4.77 -     6.36: 10
        6.36 -     7.95: 2
  Bond angle restraints: 2092
  Sorted by residual:
  angle pdb=" C   ARG B 140 "
        pdb=" N   MET B 141 "
        pdb=" CA  MET B 141 "
      ideal   model   delta    sigma   weight residual
     121.80  129.75   -7.95 2.44e+00 1.68e-01 1.06e+01
  angle pdb=" C   ARG A 140 "
        pdb=" N   MET A 141 "
        pdb=" CA  MET A 141 "
      ideal   model   delta    sigma   weight residual
     121.80  129.72   -7.92 2.44e+00 1.68e-01 1.05e+01
  angle pdb=" C   ASP B 144 "
        pdb=" N   PHE B 145 "
        pdb=" CA  PHE B 145 "
      ideal   model   delta    sigma   weight residual
     121.54  127.72   -6.18 1.91e+00 2.74e-01 1.05e+01
  angle pdb=" C   ASP A 144 "
        pdb=" N   PHE A 145 "
        pdb=" CA  PHE A 145 "
      ideal   model   delta    sigma   weight residual
     121.54  127.71   -6.17 1.91e+00 2.74e-01 1.04e+01
  angle pdb=" N   SER B 121 "
        pdb=" CA  SER B 121 "
        pdb=" C   SER B 121 "
      ideal   model   delta    sigma   weight residual
     108.24  112.30   -4.06 1.32e+00 5.74e-01 9.45e+00
  ... (remaining 2087 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.66: 820
       16.66 -    33.32: 112
       33.32 -    49.98: 28
       49.98 -    66.63: 0
       66.63 -    83.29: 6
  Dihedral angle restraints: 966
    sinusoidal: 422
      harmonic: 544
  Sorted by residual:
  dihedral pdb=" CA  ARG B 191 "
           pdb=" C   ARG B 191 "
           pdb=" N   PHE B 192 "
           pdb=" CA  PHE B 192 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  142.43   37.57     0      5.00e+00 4.00e-02 5.65e+01
  dihedral pdb=" CA  ARG A 191 "
           pdb=" C   ARG A 191 "
           pdb=" N   PHE A 192 "
           pdb=" CA  PHE A 192 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  142.44   37.56     0      5.00e+00 4.00e-02 5.64e+01
  dihedral pdb=" CA  MET B 141 "
           pdb=" C   MET B 141 "
           pdb=" N   PRO B 142 "
           pdb=" CA  PRO B 142 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  149.42   30.58     0      5.00e+00 4.00e-02 3.74e+01
  ... (remaining 963 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.034: 148
       0.034 -    0.068: 56
       0.068 -    0.102: 14
       0.102 -    0.136: 4
       0.136 -    0.169: 6
  Chirality restraints: 228
  Sorted by residual:
  chirality pdb=" CA  PRO A 108 "
            pdb=" N   PRO A 108 "
            pdb=" C   PRO A 108 "
            pdb=" CB  PRO A 108 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.55    0.17 2.00e-01 2.50e+01 7.17e-01
  chirality pdb=" CA  PRO B 108 "
            pdb=" N   PRO B 108 "
            pdb=" C   PRO B 108 "
            pdb=" CB  PRO B 108 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.55    0.17 2.00e-01 2.50e+01 7.02e-01
  chirality pdb=" CB  ILE A 127 "
            pdb=" CA  ILE A 127 "
            pdb=" CG1 ILE A 127 "
            pdb=" CG2 ILE A 127 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.48    0.16 2.00e-01 2.50e+01 6.52e-01
  ... (remaining 225 not shown)

  Planarity restraints: 266
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A 106 "   -0.028 5.00e-02 4.00e+02   4.17e-02 2.79e+00
        pdb=" N   PRO A 107 "    0.072 5.00e-02 4.00e+02
        pdb=" CA  PRO A 107 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A 107 "   -0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS B 106 "   -0.027 5.00e-02 4.00e+02   4.15e-02 2.75e+00
        pdb=" N   PRO B 107 "    0.072 5.00e-02 4.00e+02
        pdb=" CA  PRO B 107 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO B 107 "   -0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 166 "   -0.007 2.00e-02 2.50e+03   1.43e-02 2.05e+00
        pdb=" C   ILE A 166 "    0.025 2.00e-02 2.50e+03
        pdb=" O   ILE A 166 "   -0.009 2.00e-02 2.50e+03
        pdb=" N   VAL A 167 "   -0.008 2.00e-02 2.50e+03
  ... (remaining 263 not shown)

  Histogram of nonbonded interaction distances:
        2.33 -     2.85: 491
        2.85 -     3.36: 1529
        3.36 -     3.87: 2170
        3.87 -     4.39: 2419
        4.39 -     4.90: 3859
  Nonbonded interactions: 10468
  Sorted by model distance:
  nonbonded pdb=" O   ILE B 152 "
            pdb=" OG1 THR B 156 "
     model   vdw
     2.332 3.040
  nonbonded pdb=" O   ILE A 152 "
            pdb=" OG1 THR A 156 "
     model   vdw
     2.333 3.040
  nonbonded pdb=" O   PHE A 114 "
            pdb=" OG1 THR A 118 "
     model   vdw
     2.353 3.040
  nonbonded pdb=" O   PHE B 114 "
            pdb=" OG1 THR B 118 "
     model   vdw
     2.353 3.040
  nonbonded pdb=" OE1 GLU A 122 "
            pdb=" OG1 THR A 160 "
     model   vdw
     2.395 3.040
  ... (remaining 10463 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  Number of NCS constrained groups: 1
  pdb_interpretation.ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}
Set refine NCS operators
  NCS operators will be refined.
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.180
  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:                     9.210
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.010
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.550
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.060
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7581
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      :  0.006   0.029   1552  Z= 0.368
  Angle     :  1.069   7.947   2092  Z= 0.635
  Chirality :  0.046   0.169    228
  Planarity :  0.007   0.042    266
  Dihedral  : 16.555  83.293    610
  Min Nonbonded Distance : 2.332

Molprobity Statistics.
  All-atom Clashscore : 7.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.87 %
    Favored  : 92.13 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 12.20 %
    Favored  : 87.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.19 %
    Twisted Proline : 16.67 %
    Twisted General : 1.19 %

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: -4.61 (0.51), residues: 178
  helix: -3.06 (0.33), residues: 100
  sheet:  None (None), residues: 0
  loop : -2.93 (0.71), residues: 78

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP A 138 
 HIS   0.004   0.002   HIS A 170 
 PHE   0.023   0.003   PHE B 145 
 TYR   0.009   0.002   TYR A 164 
 ARG   0.004   0.001   ARG B 191 

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

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

  356 Ramachandran restraints generated.
    178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  356 Ramachandran restraints generated.
    178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  25 residues out of total 82 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 25
  time to evaluate  : 0.099 
Fit side-chains
REVERT: A  161 LYS cc_start: 0.8804 (ttpp) cc_final: 0.8325 (mmtt)
REVERT: A  169 MET cc_start: 0.8189 (ptp) cc_final: 0.7835 (ptm)
REVERT: A  176 LYS cc_start: 0.8705 (mppt) cc_final: 0.8321 (mtpp)
REVERT: A  179 MET cc_start: 0.8828 (mtt) cc_final: 0.8601 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 25
  average time/residue: 0.2633
  time to fit residues: 6.9680
Evaluate side-chains
  13 residues out of total 82 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 13
  time to evaluate  : 0.107 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 15 optimal weight:    0.8980
   chunk 13 optimal weight:    5.9990
   chunk 7 optimal weight:    3.9990
   chunk 4 optimal weight:    3.9990
   chunk 9 optimal weight:    7.9990
   chunk 14 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 8 optimal weight:    7.9990
   chunk 10 optimal weight:    5.9990
   chunk 16 optimal weight:    0.6980
   chunk 11 optimal weight:    1.9990
   overall best weight:    1.5186
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 131 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.061466 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2859 r_free = 0.2859 target = 0.055363 restraints weight = 3484.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2902 r_free = 0.2902 target = 0.056929 restraints weight = 1984.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2927 r_free = 0.2927 target = 0.058021 restraints weight = 1263.732|
|-----------------------------------------------------------------------------|
r_work (final): 0.2934
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7467
moved from start:          0.3653

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   1552  Z= 0.209
  Angle     :  0.684   5.939   2092  Z= 0.356
  Chirality :  0.037   0.119    228
  Planarity :  0.005   0.028    266
  Dihedral  :  6.182  27.162    202
  Min Nonbonded Distance : 2.622

Molprobity Statistics.
  All-atom Clashscore : 6.54
  Ramachandran Plot:
    Outliers :  1.12 %
    Allowed  :  5.62 %
    Favored  : 93.26 %
  Rotamer:
    Outliers :  1.22 %
    Allowed  :  1.22 %
    Favored  : 97.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.19 %
    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: -1.72 (0.63), residues: 178
  helix: -0.57 (0.47), residues: 104
  sheet:  None (None), residues: 0
  loop : -1.89 (0.83), residues: 74

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP A 138 
 HIS   0.001   0.001   HIS A 170 
 PHE   0.022   0.003   PHE A 114 
 TYR   0.004   0.001   TYR B 155 
 ARG   0.004   0.001   ARG B 133 

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

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

  356 Ramachandran restraints generated.
    178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  356 Ramachandran restraints generated.
    178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  24 residues out of total 82 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 23
  time to evaluate  : 0.085 
Fit side-chains
REVERT: A  115 ASN cc_start: 0.8714 (t0) cc_final: 0.8472 (t0)
REVERT: A  161 LYS cc_start: 0.8771 (tttm) cc_final: 0.8363 (mmtt)
REVERT: A  175 LEU cc_start: 0.8294 (mm) cc_final: 0.7999 (pp)
REVERT: A  176 LYS cc_start: 0.8746 (mppt) cc_final: 0.8413 (mtpp)
REVERT: A  179 MET cc_start: 0.8851 (mtt) cc_final: 0.8369 (mtm)
  outliers start: 1
  outliers final: 0
  residues processed: 24
  average time/residue: 0.1531
  time to fit residues: 3.9747
Evaluate side-chains
  12 residues out of total 82 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 12
  time to evaluate  : 0.097 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 3 optimal weight:    0.8980
   chunk 8 optimal weight:    7.9990
   chunk 2 optimal weight:    0.6980
   chunk 15 optimal weight:    0.9990
   chunk 16 optimal weight:    0.6980
   chunk 5 optimal weight:    4.9990
   chunk 7 optimal weight:    3.9990
   chunk 10 optimal weight:    0.2980
   chunk 9 optimal weight:    7.9990
   chunk 4 optimal weight:    0.2980
   chunk 14 optimal weight:    4.9990
   overall best weight:    0.5780
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.062508 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2880 r_free = 0.2880 target = 0.057067 restraints weight = 3438.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2916 r_free = 0.2916 target = 0.058456 restraints weight = 1932.960|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2939 r_free = 0.2939 target = 0.059284 restraints weight = 1217.615|
|-----------------------------------------------------------------------------|
r_work (final): 0.2939
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7436
moved from start:          0.4476

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   1552  Z= 0.187
  Angle     :  0.603   5.779   2092  Z= 0.307
  Chirality :  0.035   0.125    228
  Planarity :  0.004   0.021    266
  Dihedral  :  5.193  23.597    202
  Min Nonbonded Distance : 2.645

Molprobity Statistics.
  All-atom Clashscore : 4.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.62 %
    Favored  : 94.38 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.19 %
    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: -0.55 (0.68), residues: 178
  helix:  0.54 (0.50), residues: 106
  sheet:  None (None), residues: 0
  loop : -1.75 (0.88), residues: 72

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 138 
 HIS   0.001   0.000   HIS A 170 
 PHE   0.014   0.002   PHE A 192 
 TYR   0.015   0.002   TYR B 183 
 ARG   0.003   0.000   ARG B 129 

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

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

  356 Ramachandran restraints generated.
    178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  356 Ramachandran restraints generated.
    178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  20 residues out of total 82 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 20
  time to evaluate  : 0.108 
Fit side-chains
REVERT: A  141 MET cc_start: 0.4519 (ptm) cc_final: 0.4127 (mtt)
REVERT: A  153 MET cc_start: 0.8677 (tmm) cc_final: 0.8371 (tmm)
REVERT: A  161 LYS cc_start: 0.8755 (tttm) cc_final: 0.8369 (mmtt)
REVERT: A  176 LYS cc_start: 0.8685 (mppt) cc_final: 0.8467 (mtpp)
REVERT: A  177 ASP cc_start: 0.9298 (m-30) cc_final: 0.9058 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 20
  average time/residue: 0.1893
  time to fit residues: 4.0894
Evaluate side-chains
  12 residues out of total 82 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 12
  time to evaluate  : 0.098 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 1 optimal weight:    4.9990
   chunk 3 optimal weight:    4.9990
   chunk 4 optimal weight:    0.0980
   chunk 16 optimal weight:    5.9990
   chunk 6 optimal weight:    3.9990
   chunk 14 optimal weight:    0.9990
   chunk 7 optimal weight:    4.9990
   chunk 13 optimal weight:    0.0040
   chunk 11 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9990
   chunk 12 optimal weight:    0.1980
   overall best weight:    0.4596
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3027 r_free = 0.3027 target = 0.062365 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2891 r_free = 0.2891 target = 0.056699 restraints weight = 3866.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2920 r_free = 0.2920 target = 0.058000 restraints weight = 2430.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2941 r_free = 0.2941 target = 0.058875 restraints weight = 1670.729|
|-----------------------------------------------------------------------------|
r_work (final): 0.2936
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7454
moved from start:          0.5269

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   1552  Z= 0.171
  Angle     :  0.582   5.788   2092  Z= 0.286
  Chirality :  0.035   0.100    228
  Planarity :  0.003   0.020    266
  Dihedral  :  4.742  21.248    202
  Min Nonbonded Distance : 2.647

Molprobity Statistics.
  All-atom Clashscore : 5.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.62 %
    Favored  : 94.38 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.88 %
    Favored  : 95.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.19 %
    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:  0.08 (0.69), residues: 178
  helix:  1.08 (0.51), residues: 106
  sheet:  None (None), residues: 0
  loop : -1.54 (0.89), residues: 72

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP A 138 
 HIS   0.001   0.000   HIS A 170 
 PHE   0.014   0.002   PHE A 192 
 TYR   0.003   0.001   TYR B 155 
 ARG   0.002   0.000   ARG A 129 

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

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

  356 Ramachandran restraints generated.
    178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  356 Ramachandran restraints generated.
    178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  16 residues out of total 82 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 16
  time to evaluate  : 0.097 
Fit side-chains
REVERT: A  141 MET cc_start: 0.4217 (ptm) cc_final: 0.3842 (mmt)
REVERT: A  161 LYS cc_start: 0.8705 (tttm) cc_final: 0.8243 (mmtt)
REVERT: A  169 MET cc_start: 0.7850 (ptp) cc_final: 0.7326 (pmm)
REVERT: A  176 LYS cc_start: 0.8858 (mppt) cc_final: 0.8591 (mtpp)
  outliers start: 0
  outliers final: 0
  residues processed: 16
  average time/residue: 0.1560
  time to fit residues: 2.7569
Evaluate side-chains
  12 residues out of total 82 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 12
  time to evaluate  : 0.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 2 optimal weight:    1.9990
   chunk 8 optimal weight:    8.9990
   chunk 0 optimal weight:    7.9990
   chunk 5 optimal weight:    7.9990
   chunk 3 optimal weight:    2.9990
   chunk 15 optimal weight:    2.9990
   chunk 4 optimal weight:    1.9990
   chunk 11 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9990
   chunk 12 optimal weight:    2.9990
   chunk 6 optimal weight:    0.5980
   overall best weight:    1.7188
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.062103 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2871 r_free = 0.2871 target = 0.056388 restraints weight = 3856.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2909 r_free = 0.2909 target = 0.057975 restraints weight = 2276.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.2933 r_free = 0.2933 target = 0.059004 restraints weight = 1461.311|
|-----------------------------------------------------------------------------|
r_work (final): 0.2919
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7487
moved from start:          0.5505

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   1552  Z= 0.200
  Angle     :  0.621   6.411   2092  Z= 0.306
  Chirality :  0.037   0.122    228
  Planarity :  0.004   0.022    266
  Dihedral  :  4.693  18.228    202
  Min Nonbonded Distance : 2.654

Molprobity Statistics.
  All-atom Clashscore : 9.16
  Ramachandran Plot:
    Outliers :  1.12 %
    Allowed  :  4.49 %
    Favored  : 94.38 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.19 %
    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:  0.07 (0.69), residues: 178
  helix:  1.04 (0.51), residues: 106
  sheet:  None (None), residues: 0
  loop : -1.48 (0.89), residues: 72

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.000   TRP A 138 
 HIS   0.001   0.001   HIS B 170 
 PHE   0.023   0.003   PHE B 114 
 TYR   0.021   0.002   TYR A 155 
 ARG   0.002   0.001   ARG B 129 

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

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

  356 Ramachandran restraints generated.
    178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  356 Ramachandran restraints generated.
    178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  15 residues out of total 82 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 15
  time to evaluate  : 0.109 
Fit side-chains
REVERT: A  141 MET cc_start: 0.4407 (ptm) cc_final: 0.4074 (mmt)
REVERT: A  161 LYS cc_start: 0.8603 (tttm) cc_final: 0.8159 (mmtt)
REVERT: A  176 LYS cc_start: 0.8836 (mppt) cc_final: 0.8593 (mtpp)
REVERT: A  177 ASP cc_start: 0.9175 (m-30) cc_final: 0.8935 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 15
  average time/residue: 0.1817
  time to fit residues: 2.9887
Evaluate side-chains
  12 residues out of total 82 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 12
  time to evaluate  : 0.168 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 1 optimal weight:    0.5980
   chunk 6 optimal weight:    4.9990
   chunk 8 optimal weight:    6.9990
   chunk 11 optimal weight:    0.9990
   chunk 12 optimal weight:    0.0970
   chunk 2 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 3 optimal weight:    0.2980
   chunk 13 optimal weight:    0.8980
   chunk 5 optimal weight:    0.0670
   overall best weight:    0.3916
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.063582 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2907 r_free = 0.2907 target = 0.057683 restraints weight = 3697.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2942 r_free = 0.2942 target = 0.059188 restraints weight = 2185.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2963 r_free = 0.2963 target = 0.060090 restraints weight = 1417.908|
|-----------------------------------------------------------------------------|
r_work (final): 0.2961
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7438
moved from start:          0.5996

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   1552  Z= 0.182
  Angle     :  0.657   8.156   2092  Z= 0.304
  Chirality :  0.035   0.095    228
  Planarity :  0.003   0.018    266
  Dihedral  :  4.249  14.238    202
  Min Nonbonded Distance : 2.649

Molprobity Statistics.
  All-atom Clashscore : 4.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.62 %
    Favored  : 94.38 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.19 %
    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:  0.20 (0.70), residues: 178
  helix:  1.16 (0.51), residues: 106
  sheet:  None (None), residues: 0
  loop : -1.46 (0.90), residues: 72

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 138 
 HIS   0.000   0.000   HIS A 170 
 PHE   0.012   0.002   PHE B 145 
 TYR   0.017   0.002   TYR B 183 
 ARG   0.002   0.000   ARG B 129 

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

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

  356 Ramachandran restraints generated.
    178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  356 Ramachandran restraints generated.
    178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  17 residues out of total 82 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 17
  time to evaluate  : 0.094 
Fit side-chains
   revert: symmetry clash
REVERT: A  161 LYS cc_start: 0.8268 (tttm) cc_final: 0.7803 (mmtt)
REVERT: A  169 MET cc_start: 0.8030 (ptp) cc_final: 0.7470 (pmm)
REVERT: A  176 LYS cc_start: 0.8808 (mppt) cc_final: 0.8480 (mtpp)
REVERT: A  177 ASP cc_start: 0.9156 (m-30) cc_final: 0.8871 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 17
  average time/residue: 0.1520
  time to fit residues: 2.8458
Evaluate side-chains
  13 residues out of total 82 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 13
  time to evaluate  : 0.099 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 6 optimal weight:    2.9990
   chunk 0 optimal weight:    5.9990
   chunk 9 optimal weight:    6.9990
   chunk 7 optimal weight:    0.4980
   chunk 12 optimal weight:    0.0970
   chunk 17 optimal weight:    0.4980
   chunk 3 optimal weight:    0.6980
   chunk 13 optimal weight:    2.9990
   chunk 10 optimal weight:    0.8980
   chunk 2 optimal weight:    0.0770
   chunk 8 optimal weight:    6.9990
   overall best weight:    0.3736
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.064754 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2944 r_free = 0.2944 target = 0.059005 restraints weight = 3552.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2978 r_free = 0.2978 target = 0.060380 restraints weight = 2148.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.061377 restraints weight = 1397.850|
|-----------------------------------------------------------------------------|
r_work (final): 0.3007
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7408
moved from start:          0.6203

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   1552  Z= 0.180
  Angle     :  0.604   6.631   2092  Z= 0.291
  Chirality :  0.036   0.129    228
  Planarity :  0.003   0.017    266
  Dihedral  :  3.966  11.922    202
  Min Nonbonded Distance : 2.649

Molprobity Statistics.
  All-atom Clashscore : 5.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.62 %
    Favored  : 94.38 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.19 %
    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:  0.28 (0.70), residues: 178
  helix:  1.26 (0.53), residues: 106
  sheet:  None (None), residues: 0
  loop : -1.50 (0.88), residues: 72

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 138 
 HIS   0.000   0.000   HIS A 170 
 PHE   0.011   0.001   PHE B 114 
 TYR   0.016   0.002   TYR B 183 
 ARG   0.002   0.000   ARG B 129 

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

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

  356 Ramachandran restraints generated.
    178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  356 Ramachandran restraints generated.
    178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  16 residues out of total 82 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 16
  time to evaluate  : 0.089 
Fit side-chains
   revert: symmetry clash
REVERT: A  141 MET cc_start: 0.4511 (ttp) cc_final: 0.3966 (mmt)
REVERT: A  161 LYS cc_start: 0.8335 (tttm) cc_final: 0.7795 (mmtt)
REVERT: A  169 MET cc_start: 0.7911 (ptp) cc_final: 0.7463 (pmm)
REVERT: A  175 LEU cc_start: 0.8496 (mm) cc_final: 0.7949 (pp)
REVERT: A  176 LYS cc_start: 0.8721 (mppt) cc_final: 0.8384 (mtpp)
REVERT: A  179 MET cc_start: 0.8870 (mmp) cc_final: 0.7398 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 16
  average time/residue: 0.2114
  time to fit residues: 3.6423
Evaluate side-chains
  11 residues out of total 82 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 11
  time to evaluate  : 0.089 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 3 optimal weight:    2.9990
   chunk 0 optimal weight:    5.9990
   chunk 16 optimal weight:    0.9990
   chunk 4 optimal weight:    2.9990
   chunk 11 optimal weight:    5.9990
   chunk 10 optimal weight:    0.0270
   chunk 13 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9980
   chunk 14 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9980
   chunk 17 optimal weight:    6.9990
   overall best weight:    1.0042
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.063965 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2922 r_free = 0.2922 target = 0.058422 restraints weight = 3364.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2958 r_free = 0.2958 target = 0.059861 restraints weight = 1959.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.060770 restraints weight = 1238.078|
|-----------------------------------------------------------------------------|
r_work (final): 0.2990
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7434
moved from start:          0.6278

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   1552  Z= 0.173
  Angle     :  0.585   5.972   2092  Z= 0.284
  Chirality :  0.037   0.124    228
  Planarity :  0.004   0.022    266
  Dihedral  :  3.980  12.111    202
  Min Nonbonded Distance : 2.652

Molprobity Statistics.
  All-atom Clashscore : 5.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.87 %
    Favored  : 92.13 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.19 %
    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:  0.62 (0.72), residues: 178
  helix:  1.55 (0.55), residues: 106
  sheet:  None (None), residues: 0
  loop : -1.37 (0.89), residues: 72

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   0.000   TRP B 138 
 HIS   0.001   0.001   HIS B 170 
 PHE   0.011   0.002   PHE B 114 
 TYR   0.016   0.002   TYR A 183 
 ARG   0.004   0.000   ARG B 129 

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

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

  356 Ramachandran restraints generated.
    178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  356 Ramachandran restraints generated.
    178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  15 residues out of total 82 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 15
  time to evaluate  : 0.097 
Fit side-chains
   revert: symmetry clash
REVERT: A  141 MET cc_start: 0.4588 (ttp) cc_final: 0.4046 (mmm)
REVERT: A  161 LYS cc_start: 0.8318 (tttm) cc_final: 0.7741 (mmtt)
REVERT: A  169 MET cc_start: 0.7891 (ptp) cc_final: 0.7470 (pmm)
REVERT: A  175 LEU cc_start: 0.8505 (mm) cc_final: 0.8239 (pp)
REVERT: A  176 LYS cc_start: 0.8645 (mppt) cc_final: 0.8379 (mtpp)
  outliers start: 0
  outliers final: 0
  residues processed: 15
  average time/residue: 0.2008
  time to fit residues: 3.2545
Evaluate side-chains
  12 residues out of total 82 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 12
  time to evaluate  : 0.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 15 optimal weight:    0.0050
   chunk 6 optimal weight:    0.0040
   chunk 8 optimal weight:    0.0870
   chunk 11 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9990
   chunk 10 optimal weight:    0.7980
   chunk 12 optimal weight:    0.0060
   chunk 5 optimal weight:    0.0370
   chunk 17 optimal weight:    4.9990
   chunk 7 optimal weight:    5.9990
   chunk 14 optimal weight:    9.9990
   overall best weight:    0.0278
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3105 r_free = 0.3105 target = 0.066206 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2975 r_free = 0.2975 target = 0.060385 restraints weight = 3617.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3010 r_free = 0.3010 target = 0.061928 restraints weight = 2235.326|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3033 r_free = 0.3033 target = 0.062967 restraints weight = 1474.158|
|-----------------------------------------------------------------------------|
r_work (final): 0.3027
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7387
moved from start:          0.6647

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   1552  Z= 0.181
  Angle     :  0.588   6.266   2092  Z= 0.283
  Chirality :  0.036   0.102    228
  Planarity :  0.003   0.015    266
  Dihedral  :  3.625  10.419    202
  Min Nonbonded Distance : 2.648

Molprobity Statistics.
  All-atom Clashscore : 5.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.62 %
    Favored  : 94.38 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.19 %
    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 (0.70), residues: 178
  helix:  1.41 (0.53), residues: 106
  sheet:  None (None), residues: 0
  loop : -1.52 (0.88), residues: 72

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 138 
 HIS   0.000   0.000   HIS A 170 
 PHE   0.006   0.001   PHE A 114 
 TYR   0.015   0.001   TYR B 183 
 ARG   0.001   0.000   ARG B 133 

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

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

  356 Ramachandran restraints generated.
    178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  356 Ramachandran restraints generated.
    178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  15 residues out of total 82 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 15
  time to evaluate  : 0.101 
Fit side-chains
REVERT: A  141 MET cc_start: 0.4826 (ttp) cc_final: 0.4323 (mmm)
REVERT: A  161 LYS cc_start: 0.8319 (tttm) cc_final: 0.7741 (mmtt)
REVERT: A  169 MET cc_start: 0.7842 (ptp) cc_final: 0.7514 (pmm)
REVERT: A  175 LEU cc_start: 0.8498 (mm) cc_final: 0.8131 (pp)
  outliers start: 0
  outliers final: 0
  residues processed: 15
  average time/residue: 0.1846
  time to fit residues: 3.0335
Evaluate side-chains
  11 residues out of total 82 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 11
  time to evaluate  : 0.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 1 optimal weight:    0.9980
   chunk 14 optimal weight:    6.9990
   chunk 4 optimal weight:    0.4980
   chunk 17 optimal weight:    6.9990
   chunk 8 optimal weight:    8.9990
   chunk 2 optimal weight:    0.9980
   chunk 10 optimal weight:    0.7980
   chunk 9 optimal weight:    6.9990
   chunk 12 optimal weight:    0.9980
   chunk 16 optimal weight:    2.9990
   chunk 3 optimal weight:    0.9980
   overall best weight:    0.8580
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.065843 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2975 r_free = 0.2975 target = 0.060016 restraints weight = 3618.309|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.061507 restraints weight = 2126.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.062561 restraints weight = 1374.373|
|-----------------------------------------------------------------------------|
r_work (final): 0.3036
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7409
moved from start:          0.7044

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   1552  Z= 0.171
  Angle     :  0.613   6.629   2092  Z= 0.292
  Chirality :  0.037   0.099    228
  Planarity :  0.003   0.019    266
  Dihedral  :  3.755  11.333    202
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 6.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.62 %
    Favored  : 94.38 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.19 %
    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:  0.48 (0.71), residues: 178
  helix:  1.51 (0.54), residues: 106
  sheet:  None (None), residues: 0
  loop : -1.57 (0.86), residues: 72

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   0.000   TRP B 138 
 HIS   0.000   0.000   HIS A 170 
 PHE   0.010   0.001   PHE B 145 
 TYR   0.016   0.002   TYR A 183 
 ARG   0.001   0.000   ARG A 133 

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

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

  356 Ramachandran restraints generated.
    178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  356 Ramachandran restraints generated.
    178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  13 residues out of total 82 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 13
  time to evaluate  : 0.096 
Fit side-chains
   revert: symmetry clash
REVERT: A  161 LYS cc_start: 0.8165 (tttm) cc_final: 0.7619 (mmtt)
REVERT: A  169 MET cc_start: 0.7847 (ptp) cc_final: 0.7480 (pmm)
REVERT: A  175 LEU cc_start: 0.8568 (mm) cc_final: 0.8127 (pp)
REVERT: A  177 ASP cc_start: 0.8967 (m-30) cc_final: 0.8730 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 13
  average time/residue: 0.1687
  time to fit residues: 2.4313
Evaluate side-chains
  11 residues out of total 82 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 11
  time to evaluate  : 0.095 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 0 optimal weight:    6.9990
   chunk 2 optimal weight:    1.9990
   chunk 11 optimal weight:    3.9990
   chunk 12 optimal weight:    0.5980
   chunk 7 optimal weight:    0.7980
   chunk 14 optimal weight:    0.9990
   chunk 3 optimal weight:    0.9990
   chunk 10 optimal weight:    2.9990
   chunk 1 optimal weight:    0.6980
   chunk 17 optimal weight:    5.9990
   chunk 13 optimal weight:    0.9990
   overall best weight:    0.8184
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3094 r_free = 0.3094 target = 0.065393 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2958 r_free = 0.2958 target = 0.059194 restraints weight = 3801.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2992 r_free = 0.2992 target = 0.060653 restraints weight = 2313.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.061756 restraints weight = 1519.550|
|-----------------------------------------------------------------------------|
r_work (final): 0.3011
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7437
moved from start:          0.7052

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   1552  Z= 0.170
  Angle     :  0.605   6.626   2092  Z= 0.288
  Chirality :  0.036   0.103    228
  Planarity :  0.003   0.021    266
  Dihedral  :  3.604  11.865    202
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 7.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.87 %
    Favored  : 92.13 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.19 %
    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:  0.51 (0.70), residues: 178
  helix:  1.53 (0.52), residues: 106
  sheet:  None (None), residues: 0
  loop : -1.56 (0.87), residues: 72

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 138 
 HIS   0.000   0.000   HIS A 170 
 PHE   0.006   0.001   PHE A 145 
 TYR   0.015   0.001   TYR B 183 
 ARG   0.001   0.000   ARG B 133 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 920.30 seconds
wall clock time: 17 minutes 0.09 seconds (1020.09 seconds total)