Starting phenix.real_space_refine
on Fri Aug 22 12:36:56 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6r23_4708/08_2025/6r23_4708.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6r23_4708/08_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_4708/08_2025/6r23_4708.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6r23_4708/08_2025/6r23_4708.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6r23_4708/08_2025/6r23_4708.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6r23_4708/08_2025/6r23_4708.cif"
  }
  resolution = 4.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.026 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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 0.44, per 1000 atoms: 0.29
  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: 0.10
  Conformation dependent library (CDL) restraints added in 54.6 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  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: 0.03
  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: 0.10

  Time building geometry restraints manager: 0.11 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: 0.00
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:             0.240
  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:          0.020
  Check model and map are aligned:         0.000
  Set scattering table:                    0.000
  Process input model:                     2.410
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.000
  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:0.770
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    3.450
-------------------------------------------------------------------------------
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= 0.286
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.004   0.001   ARG B 191 
 TYR   0.009   0.002   TYR A 164 
 PHE   0.023   0.003   PHE B 145 
 TRP   0.009   0.002   TRP A 138 
 HIS   0.004   0.002   HIS A 170 

Details of bonding type rmsd
  covalent geometry    : bond        0.00574 ( 1552)
  covalent geometry    : angle       1.06867 ( 2092)
  hydrogen bonds       : bond        0.28955 (   64)
  hydrogen bonds       : angle       9.00361 (  192)

*********************** 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  : 0.018 
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: 0.0835
  time to fit residues: 2.1730
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  : 0.018 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 12 optimal weight:    4.9990
   chunk 13 optimal weight:    5.9990
   chunk 1 optimal weight:    4.9990
   chunk 8 optimal weight:    7.9990
   chunk 16 optimal weight:    0.6980
   chunk 15 optimal weight:    0.8980
   chunk 9 optimal weight:    7.9990
   chunk 11 optimal weight:    1.9990
   chunk 6 optimal weight:    0.0870
   chunk 4 optimal weight:    3.9990
   chunk 3 optimal weight:    3.9990
   overall best weight:    1.5362
-------------------------------------------------------------------------------
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 = 0.2998 r_free = 0.2998 target = 0.061235 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2858 r_free = 0.2858 target = 0.055157 restraints weight = 3471.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2899 r_free = 0.2899 target = 0.056710 restraints weight = 1968.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2923 r_free = 0.2923 target = 0.057766 restraints weight = 1262.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2939 r_free = 0.2939 target = 0.058496 restraints weight = 871.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.2950 r_free = 0.2950 target = 0.059030 restraints weight = 636.546|
|-----------------------------------------------------------------------------|
r_work (final): 0.2960
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7456
moved from start:          0.3526

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= 0.138
  Angle     :  0.686   6.064   2092  Z= 0.358
  Chirality :  0.036   0.116    228
  Planarity :  0.006   0.028    266
  Dihedral  :  6.300  27.890    202
  Min Nonbonded Distance : 2.606

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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.77 (0.63), residues: 178
  helix: -0.57 (0.47), residues: 104
  sheet:  None (None), residues: 0
  loop : -1.99 (0.81), residues: 74

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 133 
 TYR   0.005   0.001   TYR A 155 
 PHE   0.023   0.003   PHE A 114 
 TRP   0.002   0.001   TRP B 138 
 HIS   0.001   0.001   HIS A 170 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 1552)
  covalent geometry    : angle       0.68583 ( 2092)
  hydrogen bonds       : bond        0.03818 (   64)
  hydrogen bonds       : angle       3.82165 (  192)

*********************** 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  : 0.019 
Fit side-chains
REVERT: A  115 ASN cc_start: 0.8723 (t0) cc_final: 0.8475 (t0)
REVERT: A  161 LYS cc_start: 0.8781 (tttm) cc_final: 0.8376 (mmtt)
REVERT: A  175 LEU cc_start: 0.8377 (mm) cc_final: 0.7948 (pp)
REVERT: A  176 LYS cc_start: 0.8738 (mppt) cc_final: 0.8032 (mtpp)
REVERT: A  177 ASP cc_start: 0.9364 (m-30) cc_final: 0.9146 (m-30)
REVERT: A  179 MET cc_start: 0.8878 (mtt) cc_final: 0.8289 (mtm)
  outliers start: 1
  outliers final: 0
  residues processed: 24
  average time/residue: 0.0610
  time to fit residues: 1.5743
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  : 0.023 
-------------------------------------------------------------------------------
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 17 optimal weight:    6.9990
   chunk 9 optimal weight:    7.9990
   chunk 5 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9990
   chunk 4 optimal weight:    0.9980
   chunk 7 optimal weight:    4.9990
   chunk 10 optimal weight:    0.9990
   chunk 16 optimal weight:    4.9990
   chunk 11 optimal weight:    0.9980
   chunk 13 optimal weight:    0.5980
   overall best weight:    0.8982
-------------------------------------------------------------------------------
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 = 0.3024 r_free = 0.3024 target = 0.062418 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2877 r_free = 0.2877 target = 0.056906 restraints weight = 3455.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2915 r_free = 0.2915 target = 0.058334 restraints weight = 1992.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2940 r_free = 0.2940 target = 0.059258 restraints weight = 1263.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.2956 r_free = 0.2956 target = 0.059804 restraints weight = 871.910|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2969 r_free = 0.2969 target = 0.060317 restraints weight = 659.576|
|-----------------------------------------------------------------------------|
r_work (final): 0.2964
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7432
moved from start:          0.4461

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= 0.109
  Angle     :  0.603   6.307   2092  Z= 0.308
  Chirality :  0.034   0.109    228
  Planarity :  0.004   0.018    266
  Dihedral  :  5.260  23.885    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  :  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.46 (0.68), residues: 178
  helix:  0.63 (0.50), residues: 106
  sheet:  None (None), residues: 0
  loop : -1.74 (0.89), residues: 72

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 129 
 TYR   0.014   0.002   TYR A 183 
 PHE   0.013   0.002   PHE B 192 
 TRP   0.004   0.001   TRP B 138 
 HIS   0.001   0.000   HIS A 170 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 1552)
  covalent geometry    : angle       0.60303 ( 2092)
  hydrogen bonds       : bond        0.02726 (   64)
  hydrogen bonds       : angle       3.13912 (  192)

*********************** 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  : 0.019 
Fit side-chains
REVERT: A  141 MET cc_start: 0.4079 (ptm) cc_final: 0.3788 (mtt)
REVERT: A  153 MET cc_start: 0.8580 (tmm) cc_final: 0.8309 (tmm)
REVERT: A  161 LYS cc_start: 0.8764 (tttm) cc_final: 0.8379 (mmtt)
REVERT: A  176 LYS cc_start: 0.8671 (mppt) cc_final: 0.8460 (mtpp)
REVERT: A  177 ASP cc_start: 0.9286 (m-30) cc_final: 0.9064 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 20
  average time/residue: 0.0485
  time to fit residues: 1.0388
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  : 0.018 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 6 optimal weight:    0.0670
   chunk 13 optimal weight:    0.9990
   chunk 4 optimal weight:    1.9990
   chunk 0 optimal weight:    7.9990
   chunk 16 optimal weight:    5.9990
   chunk 12 optimal weight:    0.5980
   chunk 11 optimal weight:    0.9990
   chunk 14 optimal weight:    3.9990
   chunk 1 optimal weight:    1.9990
   chunk 17 optimal weight:    5.9990
   chunk 7 optimal weight:    4.9990
   overall best weight:    0.9324
-------------------------------------------------------------------------------
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 = 0.3017 r_free = 0.3017 target = 0.062062 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2891 r_free = 0.2891 target = 0.056699 restraints weight = 3723.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2923 r_free = 0.2923 target = 0.058061 restraints weight = 2074.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2943 r_free = 0.2943 target = 0.058923 restraints weight = 1315.082|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2958 r_free = 0.2958 target = 0.059560 restraints weight = 908.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.2963 r_free = 0.2963 target = 0.059794 restraints weight = 673.705|
|-----------------------------------------------------------------------------|
r_work (final): 0.2970
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7483
moved from start:          0.5226

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= 0.106
  Angle     :  0.585   5.813   2092  Z= 0.290
  Chirality :  0.036   0.106    228
  Planarity :  0.003   0.018    266
  Dihedral  :  4.791  22.084    202
  Min Nonbonded Distance : 2.651

Molprobity Statistics.
  All-atom Clashscore : 6.21
  Ramachandran Plot:
    Outliers :  1.12 %
    Allowed  :  4.49 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.25 (0.70), residues: 178
  helix:  1.23 (0.51), residues: 106
  sheet:  None (None), residues: 0
  loop : -1.49 (0.90), residues: 72

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 129 
 TYR   0.002   0.001   TYR A 155 
 PHE   0.016   0.002   PHE B 145 
 TRP   0.002   0.000   TRP A 138 
 HIS   0.001   0.001   HIS A 170 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 1552)
  covalent geometry    : angle       0.58516 ( 2092)
  hydrogen bonds       : bond        0.02116 (   64)
  hydrogen bonds       : angle       2.96136 (  192)

*********************** 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  : 0.021 
Fit side-chains
REVERT: A  141 MET cc_start: 0.4289 (ptm) cc_final: 0.4014 (mmt)
REVERT: A  161 LYS cc_start: 0.8723 (tttm) cc_final: 0.8274 (mmtt)
REVERT: A  169 MET cc_start: 0.7950 (ptp) cc_final: 0.7358 (pmm)
  outliers start: 0
  outliers final: 0
  residues processed: 16
  average time/residue: 0.0728
  time to fit residues: 1.2636
Evaluate side-chains
  10 residues out of total 82 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 10
  time to evaluate  : 0.034 
-------------------------------------------------------------------------------
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 17 optimal weight:    5.9990
   chunk 5 optimal weight:    6.9990
   chunk 7 optimal weight:    5.9990
   chunk 13 optimal weight:    0.7980
   chunk 12 optimal weight:    0.0570
   chunk 15 optimal weight:    1.9990
   chunk 0 optimal weight:    7.9990
   chunk 6 optimal weight:    2.9990
   chunk 1 optimal weight:    4.9990
   chunk 8 optimal weight:    6.9990
   overall best weight:    1.5704
-------------------------------------------------------------------------------
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 = 0.3033 r_free = 0.3033 target = 0.062346 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.2892 r_free = 0.2892 target = 0.056752 restraints weight = 3782.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2929 r_free = 0.2929 target = 0.058172 restraints weight = 2179.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.059100 restraints weight = 1396.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2971 r_free = 0.2971 target = 0.059787 restraints weight = 962.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2983 r_free = 0.2983 target = 0.060265 restraints weight = 697.897|
|-----------------------------------------------------------------------------|
r_work (final): 0.2983
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7468
moved from start:          0.5498

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= 0.116
  Angle     :  0.603   6.087   2092  Z= 0.299
  Chirality :  0.036   0.114    228
  Planarity :  0.004   0.020    266
  Dihedral  :  4.922  22.002    202
  Min Nonbonded Distance : 2.654

Molprobity Statistics.
  All-atom Clashscore : 7.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.74 %
    Favored  : 93.26 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.30 (0.69), residues: 178
  helix:  1.20 (0.51), residues: 106
  sheet:  None (None), residues: 0
  loop : -1.34 (0.90), residues: 72

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 129 
 TYR   0.020   0.002   TYR B 155 
 PHE   0.025   0.003   PHE B 114 
 TRP   0.002   0.001   TRP A 138 
 HIS   0.001   0.001   HIS B 170 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 1552)
  covalent geometry    : angle       0.60290 ( 2092)
  hydrogen bonds       : bond        0.02586 (   64)
  hydrogen bonds       : angle       2.97859 (  192)

*********************** 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  : 0.032 
Fit side-chains
REVERT: A  161 LYS cc_start: 0.8594 (tttm) cc_final: 0.8239 (mmtt)
REVERT: A  177 ASP cc_start: 0.9220 (m-30) cc_final: 0.8966 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 15
  average time/residue: 0.0711
  time to fit residues: 1.1891
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  : 0.056 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 4 optimal weight:    0.9990
   chunk 17 optimal weight:    6.9990
   chunk 9 optimal weight:    6.9990
   chunk 13 optimal weight:    0.9990
   chunk 12 optimal weight:    0.0770
   chunk 1 optimal weight:    4.9990
   chunk 14 optimal weight:    2.9990
   chunk 6 optimal weight:    4.9990
   chunk 5 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9990
   chunk 15 optimal weight:    2.9990
   overall best weight:    1.2146
-------------------------------------------------------------------------------
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 = 0.3035 r_free = 0.3035 target = 0.062679 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2881 r_free = 0.2881 target = 0.056360 restraints weight = 3921.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2917 r_free = 0.2917 target = 0.057787 restraints weight = 2352.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2941 r_free = 0.2941 target = 0.058722 restraints weight = 1556.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.2956 r_free = 0.2956 target = 0.059372 restraints weight = 1115.591|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.2968 r_free = 0.2968 target = 0.059866 restraints weight = 841.699|
|-----------------------------------------------------------------------------|
r_work (final): 0.2970
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7502
moved from start:          0.5784

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= 0.103
  Angle     :  0.650   7.929   2092  Z= 0.308
  Chirality :  0.034   0.100    228
  Planarity :  0.003   0.019    266
  Dihedral  :  4.774  20.941    202
  Min Nonbonded Distance : 2.654

Molprobity Statistics.
  All-atom Clashscore : 5.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.74 %
    Favored  : 93.26 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.41 (0.70), residues: 178
  helix:  1.26 (0.51), residues: 106
  sheet:  None (None), residues: 0
  loop : -1.23 (0.91), residues: 72

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 1552)
  covalent geometry    : angle       0.64961 ( 2092)
  hydrogen bonds       : bond        0.01961 (   64)
  hydrogen bonds       : angle       2.80669 (  192)

*********************** 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
  16 residues out of total 82 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 16
  time to evaluate  : 0.035 
Fit side-chains
   revert: symmetry clash
REVERT: A  161 LYS cc_start: 0.8498 (tttm) cc_final: 0.8089 (mmtt)
REVERT: A  169 MET cc_start: 0.8006 (ptp) cc_final: 0.7478 (pmm)
REVERT: A  177 ASP cc_start: 0.9184 (m-30) cc_final: 0.8915 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 16
  average time/residue: 0.0532
  time to fit residues: 0.9581
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  : 0.034 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 12 optimal weight:    0.4980
   chunk 15 optimal weight:    4.9990
   chunk 7 optimal weight:    5.9990
   chunk 3 optimal weight:    0.5980
   chunk 13 optimal weight:    0.0770
   chunk 1 optimal weight:    6.9990
   chunk 9 optimal weight:    6.9990
   chunk 5 optimal weight:    0.0370
   chunk 8 optimal weight:    0.4980
   chunk 16 optimal weight:    4.9990
   chunk 17 optimal weight:    0.2980
   overall best weight:    0.2816
-------------------------------------------------------------------------------
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 = 0.3061 r_free = 0.3061 target = 0.064214 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2921 r_free = 0.2921 target = 0.058235 restraints weight = 3851.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2955 r_free = 0.2955 target = 0.059659 restraints weight = 2364.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2978 r_free = 0.2978 target = 0.060602 restraints weight = 1583.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2995 r_free = 0.2995 target = 0.061294 restraints weight = 1121.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3005 r_free = 0.3005 target = 0.061762 restraints weight = 826.860|
|-----------------------------------------------------------------------------|
r_work (final): 0.3002
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7437
moved from start:          0.6291

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= 0.100
  Angle     :  0.609   6.125   2092  Z= 0.293
  Chirality :  0.033   0.088    228
  Planarity :  0.003   0.015    266
  Dihedral  :  4.303  17.363    202
  Min Nonbonded Distance : 2.647

Molprobity Statistics.
  All-atom Clashscore : 5.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.74 %
    Favored  : 93.26 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.51 (0.70), residues: 178
  helix:  1.38 (0.52), residues: 106
  sheet:  None (None), residues: 0
  loop : -1.29 (0.91), residues: 72

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 129 
 TYR   0.015   0.002   TYR A 183 
 PHE   0.013   0.002   PHE B 192 
 TRP   0.005   0.001   TRP B 138 
 HIS   0.000   0.000   HIS B 170 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 1552)
  covalent geometry    : angle       0.60927 ( 2092)
  hydrogen bonds       : bond        0.01675 (   64)
  hydrogen bonds       : angle       2.37547 (  192)

*********************** 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
  15 residues out of total 82 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 15
  time to evaluate  : 0.033 
Fit side-chains
REVERT: A  153 MET cc_start: 0.8230 (ppp) cc_final: 0.8010 (ppp)
REVERT: A  161 LYS cc_start: 0.8299 (tttm) cc_final: 0.7775 (mmtt)
REVERT: A  169 MET cc_start: 0.7916 (ptp) cc_final: 0.7439 (pmm)
REVERT: A  177 ASP cc_start: 0.9078 (m-30) cc_final: 0.8815 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 15
  average time/residue: 0.0852
  time to fit residues: 1.3834
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  : 0.031 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 4 optimal weight:    1.9990
   chunk 3 optimal weight:    0.0060
   chunk 12 optimal weight:    0.0050
   chunk 9 optimal weight:    6.9990
   chunk 2 optimal weight:    5.9990
   chunk 6 optimal weight:    0.8980
   chunk 5 optimal weight:    0.3980
   chunk 16 optimal weight:    0.9980
   chunk 14 optimal weight:    0.4980
   chunk 8 optimal weight:    7.9990
   chunk 10 optimal weight:    0.0470
   overall best weight:    0.1908
-------------------------------------------------------------------------------
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 = 0.3089 r_free = 0.3089 target = 0.065259 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2959 r_free = 0.2959 target = 0.059451 restraints weight = 3807.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2994 r_free = 0.2994 target = 0.060964 restraints weight = 2154.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3016 r_free = 0.3016 target = 0.061973 restraints weight = 1369.341|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 17)----------------|
| r_work = 0.3026 r_free = 0.3026 target = 0.062406 restraints weight = 932.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.063024 restraints weight = 719.701|
|-----------------------------------------------------------------------------|
r_work (final): 0.3035
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7411
moved from start:          0.6783

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= 0.097
  Angle     :  0.601   6.352   2092  Z= 0.287
  Chirality :  0.035   0.124    228
  Planarity :  0.003   0.016    266
  Dihedral  :  4.125  14.070    202
  Min Nonbonded Distance : 2.649

Molprobity Statistics.
  All-atom Clashscore : 6.21
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.53 (0.71), residues: 178
  helix:  1.44 (0.52), residues: 106
  sheet:  None (None), residues: 0
  loop : -1.34 (0.91), residues: 72

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 129 
 TYR   0.016   0.002   TYR A 183 
 PHE   0.007   0.001   PHE B 114 
 TRP   0.002   0.000   TRP B 138 
 HIS   0.000   0.000   HIS A 170 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 1552)
  covalent geometry    : angle       0.60130 ( 2092)
  hydrogen bonds       : bond        0.01566 (   64)
  hydrogen bonds       : angle       2.35645 (  192)

*********************** 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
  14 residues out of total 82 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 14
  time to evaluate  : 0.032 
Fit side-chains
REVERT: A  115 ASN cc_start: 0.8541 (m110) cc_final: 0.8154 (t0)
REVERT: A  161 LYS cc_start: 0.8340 (tttm) cc_final: 0.7784 (mmtt)
REVERT: A  169 MET cc_start: 0.7912 (ptp) cc_final: 0.7454 (pmm)
REVERT: A  177 ASP cc_start: 0.9145 (m-30) cc_final: 0.8883 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 14
  average time/residue: 0.0666
  time to fit residues: 1.0307
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  : 0.032 
-------------------------------------------------------------------------------
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:    0.5980
   chunk 16 optimal weight:    4.9990
   chunk 9 optimal weight:    5.9990
   chunk 10 optimal weight:    3.9990
   chunk 2 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9980
   chunk 1 optimal weight:    0.0270
   chunk 12 optimal weight:    0.9990
   chunk 8 optimal weight:    8.9990
   chunk 7 optimal weight:    0.9990
   chunk 14 optimal weight:    8.9990
   overall best weight:    0.7242
-------------------------------------------------------------------------------
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 = 0.3107 r_free = 0.3107 target = 0.066191 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2985 r_free = 0.2985 target = 0.060758 restraints weight = 3709.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.062242 restraints weight = 2145.820|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3044 r_free = 0.3044 target = 0.063233 restraints weight = 1355.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3058 r_free = 0.3058 target = 0.063887 restraints weight = 915.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3066 r_free = 0.3066 target = 0.064237 restraints weight = 649.964|
|-----------------------------------------------------------------------------|
r_work (final): 0.3057
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7409
moved from start:          0.6944

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= 0.093
  Angle     :  0.598   6.450   2092  Z= 0.285
  Chirality :  0.034   0.100    228
  Planarity :  0.003   0.019    266
  Dihedral  :  3.946  12.533    202
  Min Nonbonded Distance : 2.629

Molprobity Statistics.
  All-atom Clashscore : 6.87
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.53 (0.69), residues: 178
  helix:  1.51 (0.51), residues: 106
  sheet:  None (None), residues: 0
  loop : -1.47 (0.87), residues: 72

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 129 
 TYR   0.016   0.002   TYR B 183 
 PHE   0.007   0.001   PHE A 145 
 TRP   0.001   0.000   TRP A 138 
 HIS   0.000   0.000   HIS B 170 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 1552)
  covalent geometry    : angle       0.59788 ( 2092)
  hydrogen bonds       : bond        0.01483 (   64)
  hydrogen bonds       : angle       2.30542 (  192)

*********************** 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  : 0.036 
Fit side-chains
   revert: symmetry clash
REVERT: A  161 LYS cc_start: 0.8191 (tttm) cc_final: 0.7685 (mmtt)
REVERT: A  169 MET cc_start: 0.7916 (ptp) cc_final: 0.7485 (pmm)
REVERT: A  177 ASP cc_start: 0.9119 (m-30) cc_final: 0.8866 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 15
  average time/residue: 0.0676
  time to fit residues: 1.1153
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  : 0.030 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 3 optimal weight:    4.9990
   chunk 14 optimal weight:    0.0970
   chunk 6 optimal weight:    0.6980
   chunk 15 optimal weight:    0.7980
   chunk 8 optimal weight:   10.0000
   chunk 5 optimal weight:    0.0170
   chunk 12 optimal weight:    0.9990
   chunk 11 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9990
   chunk 4 optimal weight:    0.9980
   chunk 17 optimal weight:    4.9990
   overall best weight:    0.5216
-------------------------------------------------------------------------------
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 = 0.3093 r_free = 0.3093 target = 0.065124 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2960 r_free = 0.2960 target = 0.059312 restraints weight = 3669.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2999 r_free = 0.2999 target = 0.060925 restraints weight = 2107.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3024 r_free = 0.3024 target = 0.061984 restraints weight = 1337.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.062663 restraints weight = 906.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.3046 r_free = 0.3046 target = 0.062969 restraints weight = 651.430|
|-----------------------------------------------------------------------------|
r_work (final): 0.3043
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7416
moved from start:          0.7037

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= 0.099
  Angle     :  0.647   6.769   2092  Z= 0.302
  Chirality :  0.034   0.100    228
  Planarity :  0.003   0.018    266
  Dihedral  :  3.854  13.069    202
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 6.54
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.62 (0.69), residues: 178
  helix:  1.55 (0.51), residues: 106
  sheet:  None (None), residues: 0
  loop : -1.38 (0.89), residues: 72

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 129 
 TYR   0.015   0.001   TYR A 183 
 PHE   0.009   0.001   PHE A 114 
 TRP   0.003   0.001   TRP B 138 
 HIS   0.000   0.000   HIS B 170 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 1552)
  covalent geometry    : angle       0.64691 ( 2092)
  hydrogen bonds       : bond        0.01427 (   64)
  hydrogen bonds       : angle       2.32551 (  192)

********************** 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
  14 residues out of total 82 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 14
  time to evaluate  : 0.033 
Fit side-chains
   revert: symmetry clash
REVERT: A  161 LYS cc_start: 0.8195 (tttm) cc_final: 0.7674 (mmtt)
REVERT: A  169 MET cc_start: 0.7953 (ptp) cc_final: 0.7493 (pmm)
REVERT: A  177 ASP cc_start: 0.9157 (m-30) cc_final: 0.8893 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 14
  average time/residue: 0.0773
  time to fit residues: 1.1938
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  : 0.046 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 7 optimal weight:    3.9990
   chunk 6 optimal weight:    0.7980
   chunk 2 optimal weight:    0.9990
   chunk 13 optimal weight:    0.8980
   chunk 11 optimal weight:    0.9990
   chunk 17 optimal weight:    4.9990
   chunk 5 optimal weight:    2.9990
   chunk 9 optimal weight:    6.9990
   chunk 16 optimal weight:    1.9990
   chunk 12 optimal weight:    0.3980
   chunk 1 optimal weight:    0.0570
   overall best weight:    0.6300
-------------------------------------------------------------------------------
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 = 0.3112 r_free = 0.3112 target = 0.066323 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.2986 r_free = 0.2986 target = 0.060665 restraints weight = 3649.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.062266 restraints weight = 2120.750|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3046 r_free = 0.3046 target = 0.063274 restraints weight = 1332.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3061 r_free = 0.3061 target = 0.063930 restraints weight = 901.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3073 r_free = 0.3073 target = 0.064438 restraints weight = 649.989|
|-----------------------------------------------------------------------------|
r_work (final): 0.3069
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7406
moved from start:          0.7106

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= 0.096
  Angle     :  0.630   6.688   2092  Z= 0.294
  Chirality :  0.034   0.096    228
  Planarity :  0.003   0.018    266
  Dihedral  :  3.725  11.336    202
  Min Nonbonded Distance : 2.626

Molprobity Statistics.
  All-atom Clashscore : 6.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.99 %
    Favored  : 91.01 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.77 (0.70), residues: 178
  helix:  1.65 (0.51), residues: 106
  sheet:  None (None), residues: 0
  loop : -1.28 (0.90), residues: 72

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 129 
 TYR   0.014   0.001   TYR A 183 
 PHE   0.007   0.001   PHE A 145 
 TRP   0.001   0.000   TRP B 138 
 HIS   0.000   0.000   HIS A 170 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 1552)
  covalent geometry    : angle       0.62984 ( 2092)
  hydrogen bonds       : bond        0.01437 (   64)
  hydrogen bonds       : angle       2.33032 (  192)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 501.55 seconds
wall clock time: 9 minutes 27.81 seconds (567.81 seconds total)