Starting phenix.real_space_refine
on Wed Jun  3 10:11:22 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9wus_66269/06_2026/9wus_66269.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9wus_66269/06_2026/9wus_66269.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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9wus_66269/06_2026/9wus_66269.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9wus_66269/06_2026/9wus_66269.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9wus_66269/06_2026/9wus_66269.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9wus_66269/06_2026/9wus_66269.map"
  }
  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=   0.000 sd=   0.003
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: 3
    Type Number    sf(0)   Gaussians
     C    1974      2.51       5
     N     552      2.21       5
     O     642      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3168
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 528
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 65, 528
          Classifications: {'peptide': 65}
          Link IDs: {'PTRANS': 5, 'TRANS': 59}
  Restraints were copied for chains:
    B, C, D, E, F
  Time building chain proxies: 0.71, per 1000 atoms: 0.22
  Number of scatterers: 3168
  At special positions: 0
  Unit cell: (89.25, 82.95, 50.4, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 3
    Type Number    sf(0)
     O     642      8.00
     N     552      7.00
     C    1974      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: 0.18
  Conformation dependent library (CDL) restraints added in 122.5 milliseconds
  

  756 Ramachandran restraints generated.
    378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  756

  Finding SS restraints...
    Secondary structure from input PDB file:
      12 helices and 6 sheets defined
      26.2% alpha, 27.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.10
  Creating SS restraints...
    Processing helix  chain 'A' and resid 33 through 42
    Processing helix  chain 'A' and resid 77 through 83
    Processing helix  chain 'B' and resid 33 through 42
    Processing helix  chain 'B' and resid 77 through 83
    Processing helix  chain 'C' and resid 33 through 42
    Processing helix  chain 'C' and resid 77 through 83
    Processing helix  chain 'D' and resid 33 through 42
    Processing helix  chain 'D' and resid 77 through 83
    Processing helix  chain 'E' and resid 33 through 42
    Processing helix  chain 'E' and resid 77 through 83
    Processing helix  chain 'F' and resid 33 through 42
    Processing helix  chain 'F' and resid 77 through 83
    Processing sheet with id=AA1, first strand: chain 'A' and resid 65 through 69
      removed outlier: 7.500A  pdb=" N   GLU A  55 " --> pdb=" O   ILE A  51 " (cutoff:3.500A)
      removed outlier: 4.915A  pdb=" N   ILE A  51 " --> pdb=" O   GLU A  55 " (cutoff:3.500A)
      removed outlier: 6.009A  pdb=" N   ASN A  57 " --> pdb=" O   ALA A  49 " (cutoff:3.500A)
      removed outlier: 3.919A  pdb=" N   ALA A  49 " --> pdb=" O   ASN A  57 " (cutoff:3.500A)
      removed outlier: 6.743A  pdb=" N   THR A  59 " --> pdb=" O   ARG A  47 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 65 through 69
      removed outlier: 7.501A  pdb=" N   GLU B  55 " --> pdb=" O   ILE B  51 " (cutoff:3.500A)
      removed outlier: 4.915A  pdb=" N   ILE B  51 " --> pdb=" O   GLU B  55 " (cutoff:3.500A)
      removed outlier: 6.010A  pdb=" N   ASN B  57 " --> pdb=" O   ALA B  49 " (cutoff:3.500A)
      removed outlier: 3.919A  pdb=" N   ALA B  49 " --> pdb=" O   ASN B  57 " (cutoff:3.500A)
      removed outlier: 6.744A  pdb=" N   THR B  59 " --> pdb=" O   ARG B  47 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 65 through 69
      removed outlier: 7.500A  pdb=" N   GLU C  55 " --> pdb=" O   ILE C  51 " (cutoff:3.500A)
      removed outlier: 4.915A  pdb=" N   ILE C  51 " --> pdb=" O   GLU C  55 " (cutoff:3.500A)
      removed outlier: 6.008A  pdb=" N   ASN C  57 " --> pdb=" O   ALA C  49 " (cutoff:3.500A)
      removed outlier: 3.919A  pdb=" N   ALA C  49 " --> pdb=" O   ASN C  57 " (cutoff:3.500A)
      removed outlier: 6.743A  pdb=" N   THR C  59 " --> pdb=" O   ARG C  47 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 65 through 69
      removed outlier: 7.501A  pdb=" N   GLU D  55 " --> pdb=" O   ILE D  51 " (cutoff:3.500A)
      removed outlier: 4.915A  pdb=" N   ILE D  51 " --> pdb=" O   GLU D  55 " (cutoff:3.500A)
      removed outlier: 6.010A  pdb=" N   ASN D  57 " --> pdb=" O   ALA D  49 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   ALA D  49 " --> pdb=" O   ASN D  57 " (cutoff:3.500A)
      removed outlier: 6.743A  pdb=" N   THR D  59 " --> pdb=" O   ARG D  47 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'E' and resid 65 through 69
      removed outlier: 7.500A  pdb=" N   GLU E  55 " --> pdb=" O   ILE E  51 " (cutoff:3.500A)
      removed outlier: 4.915A  pdb=" N   ILE E  51 " --> pdb=" O   GLU E  55 " (cutoff:3.500A)
      removed outlier: 6.009A  pdb=" N   ASN E  57 " --> pdb=" O   ALA E  49 " (cutoff:3.500A)
      removed outlier: 3.919A  pdb=" N   ALA E  49 " --> pdb=" O   ASN E  57 " (cutoff:3.500A)
      removed outlier: 6.744A  pdb=" N   THR E  59 " --> pdb=" O   ARG E  47 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'F' and resid 65 through 69
      removed outlier: 7.500A  pdb=" N   GLU F  55 " --> pdb=" O   ILE F  51 " (cutoff:3.500A)
      removed outlier: 4.915A  pdb=" N   ILE F  51 " --> pdb=" O   GLU F  55 " (cutoff:3.500A)
      removed outlier: 6.009A  pdb=" N   ASN F  57 " --> pdb=" O   ALA F  49 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   ALA F  49 " --> pdb=" O   ASN F  57 " (cutoff:3.500A)
      removed outlier: 6.743A  pdb=" N   THR F  59 " --> pdb=" O   ARG F  47 " (cutoff:3.500A)

    108 hydrogen bonds defined for protein.
    306 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: 0.37

  Time building geometry restraints manager: 0.25 seconds

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

  Histogram of bond lengths:
        1.23 -     1.29: 582
        1.29 -     1.36: 516
        1.36 -     1.42: 174
        1.42 -     1.48: 474
        1.48 -     1.55: 1470
  Bond restraints: 3216
  Sorted by residual:
  bond pdb=" N   ASN E  85 "
       pdb=" CA  ASN E  85 "
    ideal  model  delta    sigma   weight residual
    1.460  1.470 -0.010 1.42e-02 4.96e+03 5.46e-01
  bond pdb=" N   ASN A  85 "
       pdb=" CA  ASN A  85 "
    ideal  model  delta    sigma   weight residual
    1.460  1.470 -0.010 1.42e-02 4.96e+03 5.24e-01
  bond pdb=" N   ASN C  85 "
       pdb=" CA  ASN C  85 "
    ideal  model  delta    sigma   weight residual
    1.460  1.470 -0.010 1.42e-02 4.96e+03 5.03e-01
  bond pdb=" N   ASN D  85 "
       pdb=" CA  ASN D  85 "
    ideal  model  delta    sigma   weight residual
    1.460  1.469 -0.010 1.42e-02 4.96e+03 4.54e-01
  bond pdb=" N   ASN F  85 "
       pdb=" CA  ASN F  85 "
    ideal  model  delta    sigma   weight residual
    1.460  1.469 -0.009 1.42e-02 4.96e+03 4.46e-01
  ... (remaining 3211 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.11: 4194
        1.11 -     2.21: 120
        2.21 -     3.32: 54
        3.32 -     4.42: 0
        4.42 -     5.53: 6
  Bond angle restraints: 4374
  Sorted by residual:
  angle pdb=" C   LYS D  84 "
        pdb=" N   ASN D  85 "
        pdb=" CA  ASN D  85 "
      ideal   model   delta    sigma   weight residual
     122.82  125.61   -2.79 1.42e+00 4.96e-01 3.87e+00
  angle pdb=" C   LYS F  84 "
        pdb=" N   ASN F  85 "
        pdb=" CA  ASN F  85 "
      ideal   model   delta    sigma   weight residual
     122.82  125.61   -2.79 1.42e+00 4.96e-01 3.86e+00
  angle pdb=" C   LYS B  84 "
        pdb=" N   ASN B  85 "
        pdb=" CA  ASN B  85 "
      ideal   model   delta    sigma   weight residual
     122.82  125.60   -2.78 1.42e+00 4.96e-01 3.83e+00
  angle pdb=" C   LYS C  84 "
        pdb=" N   ASN C  85 "
        pdb=" CA  ASN C  85 "
      ideal   model   delta    sigma   weight residual
     122.82  125.58   -2.76 1.42e+00 4.96e-01 3.79e+00
  angle pdb=" C   LYS A  84 "
        pdb=" N   ASN A  85 "
        pdb=" CA  ASN A  85 "
      ideal   model   delta    sigma   weight residual
     122.82  125.55   -2.73 1.42e+00 4.96e-01 3.69e+00
  ... (remaining 4369 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    10.24: 1703
       10.24 -    20.49: 181
       20.49 -    30.73: 96
       30.73 -    40.98: 36
       40.98 -    51.22: 12
  Dihedral angle restraints: 2028
    sinusoidal: 870
      harmonic: 1158
  Sorted by residual:
  dihedral pdb=" CB  LYS D  84 "
           pdb=" CG  LYS D  84 "
           pdb=" CD  LYS D  84 "
           pdb=" CE  LYS D  84 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  131.12   48.88     3      1.50e+01 4.44e-03 8.70e+00
  dihedral pdb=" CB  LYS E  84 "
           pdb=" CG  LYS E  84 "
           pdb=" CD  LYS E  84 "
           pdb=" CE  LYS E  84 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  131.12   48.88     3      1.50e+01 4.44e-03 8.70e+00
  dihedral pdb=" CB  LYS C  84 "
           pdb=" CG  LYS C  84 "
           pdb=" CD  LYS C  84 "
           pdb=" CE  LYS C  84 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  131.14   48.86     3      1.50e+01 4.44e-03 8.70e+00
  ... (remaining 2025 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.023: 211
       0.023 -    0.045: 132
       0.045 -    0.068: 73
       0.068 -    0.090: 30
       0.090 -    0.113: 58
  Chirality restraints: 504
  Sorted by residual:
  chirality pdb=" CA  ILE A  51 "
            pdb=" N   ILE A  51 "
            pdb=" C   ILE A  51 "
            pdb=" CB  ILE A  51 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.11 2.00e-01 2.50e+01 3.17e-01
  chirality pdb=" CA  VAL E  89 "
            pdb=" N   VAL E  89 "
            pdb=" C   VAL E  89 "
            pdb=" CB  VAL E  89 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.55   -0.11 2.00e-01 2.50e+01 3.16e-01
  chirality pdb=" CA  VAL A  89 "
            pdb=" N   VAL A  89 "
            pdb=" C   VAL A  89 "
            pdb=" CB  VAL A  89 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.55   -0.11 2.00e-01 2.50e+01 3.12e-01
  ... (remaining 501 not shown)

  Planarity restraints: 588
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE F  70 "    0.005 2.00e-02 2.50e+03   9.50e-03 9.02e-01
        pdb=" C   ILE F  70 "   -0.016 2.00e-02 2.50e+03
        pdb=" O   ILE F  70 "    0.006 2.00e-02 2.50e+03
        pdb=" N   PRO F  71 "    0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN B  52 "    0.005 2.00e-02 2.50e+03   9.45e-03 8.93e-01
        pdb=" C   ASN B  52 "   -0.016 2.00e-02 2.50e+03
        pdb=" O   ASN B  52 "    0.006 2.00e-02 2.50e+03
        pdb=" N   GLY B  53 "    0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE D  70 "   -0.005 2.00e-02 2.50e+03   9.44e-03 8.92e-01
        pdb=" C   ILE D  70 "    0.016 2.00e-02 2.50e+03
        pdb=" O   ILE D  70 "   -0.006 2.00e-02 2.50e+03
        pdb=" N   PRO D  71 "   -0.006 2.00e-02 2.50e+03
  ... (remaining 585 not shown)

  Histogram of nonbonded interaction distances:
        2.44 -     2.93: 1302
        2.93 -     3.42: 2939
        3.42 -     3.92: 4824
        3.92 -     4.41: 4655
        4.41 -     4.90: 8013
  Nonbonded interactions: 21733
  Sorted by model distance:
  nonbonded pdb=" O   ASP B  33 "
            pdb=" OG1 THR B  36 "
     model   vdw
     2.441 3.040
  nonbonded pdb=" O   ASP A  33 "
            pdb=" OG1 THR A  36 "
     model   vdw
     2.441 3.040
  nonbonded pdb=" O   ASP F  33 "
            pdb=" OG1 THR F  36 "
     model   vdw
     2.441 3.040
  nonbonded pdb=" O   ASP E  33 "
            pdb=" OG1 THR E  36 "
     model   vdw
     2.441 3.040
  nonbonded pdb=" O   ASP D  33 "
            pdb=" OG1 THR D  36 "
     model   vdw
     2.442 3.040
  ... (remaining 21728 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'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
}

Set up NCS constraints
  Number of NCS constrained groups: 1
  pdb_interpretation.ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
}
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:             0.270
  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:          0.050
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     4.580
  Find NCS groups from input model:        0.030
  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:1.170
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    6.120
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6568
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      :  0.002   0.016   3216  Z= 0.106
  Angle     :  0.568   5.530   4374  Z= 0.306
  Chirality :  0.048   0.113    504
  Planarity :  0.003   0.012    588
  Dihedral  : 12.719  51.220   1272
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 12.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.94 %
    Favored  : 92.06 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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 are not related in a simple way.
  whole: -2.06 (0.42), residues: 378
  helix: -0.40 (0.53), residues: 114
  sheet: -0.97 (0.56), residues: 72
  loop : -2.16 (0.41), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG E  50 
 TYR   0.004   0.001   TYR A  66 
 PHE   0.003   0.001   PHE C  37 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00219 /  0.11 ( 3216)
  covalent geometry    : angle       0.56754 /  0.31 ( 4374)
  hydrogen bonds       : bond        0.15531 /  8.70 (  108)
  hydrogen bonds       : angle       5.61643 /  4.12 (  306)

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

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

  756 Ramachandran restraints generated.
    378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  756 Ramachandran restraints generated.
    378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  21 residues out of total 62 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 21
  time to evaluate  : 0.015 
Fit side-chains
REVERT: A   44 ASP cc_start: 0.8025 (t0) cc_final: 0.7729 (t70)
REVERT: A   66 TYR cc_start: 0.3311 (t80) cc_final: 0.2566 (t80)
REVERT: A   69 TYR cc_start: 0.7538 (m-80) cc_final: 0.7059 (m-80)
REVERT: A   84 LYS cc_start: 0.8755 (mttt) cc_final: 0.8502 (mtmt)
  outliers start: 0
  outliers final: 0
  residues processed: 21
  average time/residue: 0.0564
  time to fit residues: 1.2510
Evaluate side-chains
  15 residues out of total 62 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 15
  time to evaluate  : 0.025 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 24 optimal weight:    5.9990
   chunk 26 optimal weight:    4.9990
   chunk 2 optimal weight:    4.9990
   chunk 16 optimal weight:    0.0060
   chunk 32 optimal weight:    5.9990
   chunk 31 optimal weight:    1.9990
   chunk 25 optimal weight:    0.0470
   chunk 19 optimal weight:    3.9990
   chunk 30 optimal weight:    5.9990
   chunk 22 optimal weight:    0.2980
   chunk 13 optimal weight:    0.0060
   overall best weight:    0.4712
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
C  85 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 = 0.4128 r_free = 0.4128 target = 0.193598 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.158535 restraints weight = 883.286|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.162747 restraints weight = 623.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.166984 restraints weight = 485.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.170191 restraints weight = 389.667|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.172306 restraints weight = 318.517|
|-----------------------------------------------------------------------------|
r_work (final): 0.3849
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6640
moved from start:          0.0832

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.017   3216  Z= 0.096
  Angle     :  0.499   4.945   4374  Z= 0.255
  Chirality :  0.047   0.110    504
  Planarity :  0.002   0.010    588
  Dihedral  :  3.768  10.765    426
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 10.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.35 %
    Favored  : 93.65 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  :  0.00 %
    Favored  : 98.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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 are not related in a simple way.
  whole: -1.61 (0.43), residues: 378
  helix: -0.40 (0.52), residues: 114
  sheet:  0.07 (0.67), residues: 72
  loop : -1.98 (0.42), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D  54 
 TYR   0.004   0.001   TYR A  66 
 PHE   0.002   0.001   PHE B  37 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00217 /  0.10 ( 3216)
  covalent geometry    : angle       0.49855 /  0.26 ( 4374)
  hydrogen bonds       : bond        0.03706 /  2.15 (  108)
  hydrogen bonds       : angle       5.07622 /  3.74 (  306)

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

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

  630 Ramachandran restraints generated.
    315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  630 Ramachandran restraints generated.
    315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  24 residues out of total 62 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 23
  time to evaluate  : 0.013 
Fit side-chains
REVERT: C   44 ASP cc_start: 0.7944 (t0) cc_final: 0.7543 (t70)
REVERT: C   66 TYR cc_start: 0.3457 (t80) cc_final: 0.2043 (t80)
  outliers start: 1
  outliers final: 0
  residues processed: 23
  average time/residue: 0.0617
  time to fit residues: 1.4983
Evaluate side-chains
  17 residues out of total 62 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 17
  time to evaluate  : 0.021 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 9 optimal weight:    0.9980
   chunk 24 optimal weight:    6.9990
   chunk 18 optimal weight:    5.9990
   chunk 30 optimal weight:    6.9990
   chunk 4 optimal weight:    0.8980
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    0.0030
   chunk 2 optimal weight:    0.6980
   chunk 14 optimal weight:    0.6980
   chunk 8 optimal weight:    3.9990
   chunk 19 optimal weight:    5.9990
   overall best weight:    0.6590
-------------------------------------------------------------------------------
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 = 0.4194 r_free = 0.4194 target = 0.197979 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.166173 restraints weight = 806.265|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.170140 restraints weight = 587.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3925 r_free = 0.3925 target = 0.172308 restraints weight = 456.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.175238 restraints weight = 385.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.176554 restraints weight = 321.386|
|-----------------------------------------------------------------------------|
r_work (final): 0.3964
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6689
moved from start:          0.1448

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.018   3216  Z= 0.097
  Angle     :  0.511   4.891   4374  Z= 0.264
  Chirality :  0.048   0.114    504
  Planarity :  0.002   0.009    588
  Dihedral  :  3.729  11.282    426
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 12.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.76 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.84 %
    Favored  : 95.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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 are not related in a simple way.
  whole: -1.49 (0.44), residues: 378
  helix: -0.76 (0.50), residues: 114
  sheet:  0.38 (0.61), residues: 102
  loop : -2.07 (0.43), residues: 162

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D  54 
 TYR   0.004   0.001   TYR F  66 
 PHE   0.002   0.001   PHE F  37 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00219 /  0.10 ( 3216)
  covalent geometry    : angle       0.51082 /  0.26 ( 4374)
  hydrogen bonds       : bond        0.03266 /  1.93 (  108)
  hydrogen bonds       : angle       5.09825 /  3.78 (  306)

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

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

  630 Ramachandran restraints generated.
    315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  630 Ramachandran restraints generated.
    315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  23 residues out of total 62 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 23
  time to evaluate  : 0.014 
Fit side-chains
REVERT: C   39 GLN cc_start: 0.7741 (pp30) cc_final: 0.7394 (pp30)
REVERT: C   44 ASP cc_start: 0.7949 (t0) cc_final: 0.7545 (t70)
REVERT: C   66 TYR cc_start: 0.3473 (t80) cc_final: 0.2013 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 23
  average time/residue: 0.0642
  time to fit residues: 1.5567
Evaluate side-chains
  17 residues out of total 62 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 17
  time to evaluate  : 0.013 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 3 optimal weight:    0.5980
   chunk 10 optimal weight:    0.9980
   chunk 22 optimal weight:    0.4980
   chunk 0 optimal weight:    6.9990
   chunk 18 optimal weight:    5.9990
   chunk 8 optimal weight:    5.9990
   chunk 4 optimal weight:    0.7980
   chunk 27 optimal weight:    0.0010
   chunk 14 optimal weight:    4.9990
   chunk 25 optimal weight:    8.9990
   chunk 35 optimal weight:    5.9990
   overall best weight:    0.5786
-------------------------------------------------------------------------------
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 = 0.4088 r_free = 0.4088 target = 0.190680 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.160670 restraints weight = 829.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.165283 restraints weight = 549.345|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.168940 restraints weight = 401.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.171633 restraints weight = 310.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3925 r_free = 0.3925 target = 0.173772 restraints weight = 250.311|
|-----------------------------------------------------------------------------|
r_work (final): 0.3897
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6569
moved from start:          0.1780

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.017   3216  Z= 0.099
  Angle     :  0.517   4.809   4374  Z= 0.273
  Chirality :  0.048   0.114    504
  Planarity :  0.002   0.009    588
  Dihedral  :  3.798  11.204    426
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 9.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.94 %
    Favored  : 92.06 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.56 (0.44), residues: 378
  helix: -0.77 (0.50), residues: 114
  sheet:  0.29 (0.61), residues: 102
  loop : -2.10 (0.43), residues: 162

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG F  54 
 TYR   0.004   0.001   TYR D  66 
 PHE   0.001   0.001   PHE B  37 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00224 /  0.10 ( 3216)
  covalent geometry    : angle       0.51731 /  0.27 ( 4374)
  hydrogen bonds       : bond        0.02973 /  1.77 (  108)
  hydrogen bonds       : angle       4.93417 /  3.68 (  306)

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

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

  504 Ramachandran restraints generated.
    252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  504 Ramachandran restraints generated.
    252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  20 residues out of total 62 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 20
  time to evaluate  : 0.025 
Fit side-chains
REVERT: D   44 ASP cc_start: 0.8106 (t0) cc_final: 0.7857 (t70)
REVERT: D   66 TYR cc_start: 0.3281 (t80) cc_final: 0.2670 (t80)
REVERT: D   69 TYR cc_start: 0.7427 (m-80) cc_final: 0.6921 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 20
  average time/residue: 0.0594
  time to fit residues: 1.2717
Evaluate side-chains
  17 residues out of total 62 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 17
  time to evaluate  : 0.013 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 24 optimal weight:    6.9990
   chunk 2 optimal weight:    0.5980
   chunk 29 optimal weight:    0.9990
   chunk 22 optimal weight:    0.0570
   chunk 8 optimal weight:    0.4980
   chunk 17 optimal weight:    0.9990
   chunk 20 optimal weight:    0.5980
   chunk 1 optimal weight:    4.9990
   chunk 25 optimal weight:    5.9990
   chunk 30 optimal weight:    6.9990
   chunk 33 optimal weight:    0.0270
   overall best weight:    0.3556
-------------------------------------------------------------------------------
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 = 0.4173 r_free = 0.4173 target = 0.197868 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.167876 restraints weight = 770.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.171624 restraints weight = 547.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.174720 restraints weight = 421.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.176808 restraints weight = 334.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.178585 restraints weight = 281.982|
|-----------------------------------------------------------------------------|
r_work (final): 0.3960
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6681
moved from start:          0.1853

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   3216  Z= 0.098
  Angle     :  0.516   4.658   4374  Z= 0.268
  Chirality :  0.048   0.115    504
  Planarity :  0.002   0.009    588
  Dihedral  :  3.792  10.342    426
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 11.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.35 %
    Favored  : 93.65 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.70 (0.44), residues: 378
  helix: -0.89 (0.49), residues: 114
  sheet:  0.27 (0.63), residues: 102
  loop : -2.23 (0.42), residues: 162

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG F  50 
 TYR   0.004   0.001   TYR C  66 
 PHE   0.002   0.001   PHE B  37 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00221 /  0.10 ( 3216)
  covalent geometry    : angle       0.51646 /  0.27 ( 4374)
  hydrogen bonds       : bond        0.02825 /  1.71 (  108)
  hydrogen bonds       : angle       4.83659 /  3.60 (  306)

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

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

  504 Ramachandran restraints generated.
    252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  504 Ramachandran restraints generated.
    252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  21 residues out of total 62 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 21
  time to evaluate  : 0.028 
Fit side-chains
REVERT: C   44 ASP cc_start: 0.7938 (t0) cc_final: 0.7579 (t70)
REVERT: C   66 TYR cc_start: 0.3473 (t80) cc_final: 0.2025 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 21
  average time/residue: 0.0534
  time to fit residues: 1.2004
Evaluate side-chains
  17 residues out of total 62 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 17
  time to evaluate  : 0.022 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 26 optimal weight:    0.9990
   chunk 35 optimal weight:    0.9980
   chunk 5 optimal weight:    0.4980
   chunk 16 optimal weight:    2.9990
   chunk 30 optimal weight:    6.9990
   chunk 14 optimal weight:    0.0770
   chunk 7 optimal weight:    6.9990
   chunk 18 optimal weight:    6.9990
   chunk 9 optimal weight:    0.0030
   chunk 23 optimal weight:    0.4980
   chunk 6 optimal weight:    5.9990
   overall best weight:    0.4148
-------------------------------------------------------------------------------
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 = 0.4213 r_free = 0.4213 target = 0.201377 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.170748 restraints weight = 782.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.174587 restraints weight = 555.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.177253 restraints weight = 421.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.179478 restraints weight = 340.470|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 16)----------------|
| r_work = 0.4022 r_free = 0.4022 target = 0.180372 restraints weight = 284.319|
|-----------------------------------------------------------------------------|
r_work (final): 0.3979
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6675
moved from start:          0.2132

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   3216  Z= 0.112
  Angle     :  0.546   4.919   4374  Z= 0.297
  Chirality :  0.050   0.134    504
  Planarity :  0.002   0.009    588
  Dihedral  :  3.930  10.772    426
  Min Nonbonded Distance : 2.384

Molprobity Statistics.
  All-atom Clashscore : 12.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.35 %
    Favored  : 93.65 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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 are not related in a simple way.
  whole: -1.81 (0.44), residues: 378
  helix: -0.98 (0.48), residues: 114
  sheet:  0.16 (0.62), residues: 102
  loop : -2.26 (0.41), residues: 162

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG B  47 
 TYR   0.004   0.001   TYR E  66 
 PHE   0.002   0.001   PHE D  37 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00246 /  0.11 ( 3216)
  covalent geometry    : angle       0.54577 /  0.30 ( 4374)
  hydrogen bonds       : bond        0.02758 /  1.65 (  108)
  hydrogen bonds       : angle       4.73374 /  3.51 (  306)

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

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

  504 Ramachandran restraints generated.
    252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  504 Ramachandran restraints generated.
    252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  21 residues out of total 62 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 21
  time to evaluate  : 0.021 
Fit side-chains
REVERT: C   44 ASP cc_start: 0.7948 (t0) cc_final: 0.7566 (t70)
REVERT: C   66 TYR cc_start: 0.3583 (t80) cc_final: 0.1969 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 21
  average time/residue: 0.0604
  time to fit residues: 1.3458
Evaluate side-chains
  18 residues out of total 62 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 18
  time to evaluate  : 0.013 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 34 optimal weight:    0.2980
   chunk 26 optimal weight:    0.4980
   chunk 7 optimal weight:    4.9990
   chunk 5 optimal weight:    0.9980
   chunk 29 optimal weight:    1.9990
   chunk 20 optimal weight:    2.9990
   chunk 11 optimal weight:    1.9990
   chunk 18 optimal weight:    6.9990
   chunk 15 optimal weight:    0.0050
   chunk 27 optimal weight:    0.3980
   chunk 2 optimal weight:    2.9990
   overall best weight:    0.4394
-------------------------------------------------------------------------------
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 = 0.4092 r_free = 0.4092 target = 0.192863 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.162242 restraints weight = 874.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.167126 restraints weight = 580.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.170620 restraints weight = 422.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.173098 restraints weight = 328.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.174766 restraints weight = 270.283|
|-----------------------------------------------------------------------------|
r_work (final): 0.3870
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6593
moved from start:          0.2250

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   3216  Z= 0.096
  Angle     :  0.523   5.053   4374  Z= 0.271
  Chirality :  0.049   0.115    504
  Planarity :  0.002   0.010    588
  Dihedral  :  3.800  10.615    426
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 10.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.94 %
    Favored  : 92.06 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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 are not related in a simple way.
  whole: -1.84 (0.43), residues: 378
  helix: -0.98 (0.48), residues: 114
  sheet:  0.05 (0.62), residues: 102
  loop : -2.22 (0.41), residues: 162

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG A  54 
 TYR   0.003   0.001   TYR D  66 
 PHE   0.002   0.001   PHE B  37 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00218 /  0.10 ( 3216)
  covalent geometry    : angle       0.52294 /  0.27 ( 4374)
  hydrogen bonds       : bond        0.02672 /  1.61 (  108)
  hydrogen bonds       : angle       4.56740 /  3.38 (  306)

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

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

  504 Ramachandran restraints generated.
    252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  504 Ramachandran restraints generated.
    252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  21 residues out of total 62 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 21
  time to evaluate  : 0.023 
Fit side-chains
REVERT: D   66 TYR cc_start: 0.3997 (t80) cc_final: 0.2546 (t80)
REVERT: D   69 TYR cc_start: 0.7339 (m-80) cc_final: 0.6899 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 21
  average time/residue: 0.0695
  time to fit residues: 1.5474
Evaluate side-chains
  16 residues out of total 62 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 16
  time to evaluate  : 0.021 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 10 optimal weight:    0.9980
   chunk 2 optimal weight:    0.1980
   chunk 30 optimal weight:    6.9990
   chunk 33 optimal weight:    0.4980
   chunk 24 optimal weight:    6.9990
   chunk 18 optimal weight:    6.9990
   chunk 13 optimal weight:    0.0870
   chunk 1 optimal weight:    0.0870
   chunk 29 optimal weight:    0.7980
   chunk 11 optimal weight:    0.2980
   chunk 28 optimal weight:    0.8980
   overall best weight:    0.2336
-------------------------------------------------------------------------------
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 = 0.4079 r_free = 0.4079 target = 0.192013 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.157314 restraints weight = 970.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.163095 restraints weight = 646.558|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 19)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.167028 restraints weight = 473.612|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.169704 restraints weight = 368.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.171644 restraints weight = 303.619|
|-----------------------------------------------------------------------------|
r_work (final): 0.3798
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6619
moved from start:          0.2471

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.017   3216  Z= 0.114
  Angle     :  0.543   4.838   4374  Z= 0.283
  Chirality :  0.051   0.116    504
  Planarity :  0.002   0.010    588
  Dihedral  :  3.943  10.523    426
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 12.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.35 %
    Favored  : 93.65 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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 are not related in a simple way.
  whole: -1.78 (0.44), residues: 378
  helix: -0.80 (0.50), residues: 114
  sheet: -0.06 (0.61), residues: 102
  loop : -2.18 (0.42), residues: 162

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D  65 
 TYR   0.005   0.001   TYR D  66 
 PHE   0.006   0.002   PHE F  37 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00248 /  0.11 ( 3216)
  covalent geometry    : angle       0.54278 /  0.28 ( 4374)
  hydrogen bonds       : bond        0.03322 /  1.92 (  108)
  hydrogen bonds       : angle       4.86020 /  3.53 (  306)

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

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

  504 Ramachandran restraints generated.
    252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  504 Ramachandran restraints generated.
    252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  20 residues out of total 62 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 20
  time to evaluate  : 0.016 
Fit side-chains
REVERT: D   66 TYR cc_start: 0.4292 (t80) cc_final: 0.2753 (t80)
REVERT: D   69 TYR cc_start: 0.7308 (m-80) cc_final: 0.6881 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 20
  average time/residue: 0.0580
  time to fit residues: 1.2285
Evaluate side-chains
  16 residues out of total 62 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 16
  time to evaluate  : 0.023 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 23 optimal weight:    0.0040
   chunk 9 optimal weight:    0.3980
   chunk 28 optimal weight:    2.9990
   chunk 1 optimal weight:    0.8980
   chunk 24 optimal weight:    6.9990
   chunk 3 optimal weight:    0.9980
   chunk 18 optimal weight:    6.9990
   chunk 32 optimal weight:    0.0370
   chunk 27 optimal weight:    0.8980
   chunk 29 optimal weight:    0.0170
   chunk 33 optimal weight:    0.8980
   overall best weight:    0.2708
-------------------------------------------------------------------------------
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 = 0.4108 r_free = 0.4108 target = 0.194340 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.161866 restraints weight = 926.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.167653 restraints weight = 611.304|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.171624 restraints weight = 440.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.174258 restraints weight = 341.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 18)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.175975 restraints weight = 278.884|
|-----------------------------------------------------------------------------|
r_work (final): 0.3854
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6578
moved from start:          0.2508

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.017   3216  Z= 0.108
  Angle     :  0.535   4.842   4374  Z= 0.277
  Chirality :  0.050   0.116    504
  Planarity :  0.003   0.011    588
  Dihedral  :  3.619  10.537    426
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 10.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.94 %
    Favored  : 92.06 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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 are not related in a simple way.
  whole: -1.88 (0.43), residues: 378
  helix: -0.79 (0.51), residues: 114
  sheet: -0.19 (0.59), residues: 102
  loop : -2.26 (0.41), residues: 162

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  50 
 TYR   0.002   0.000   TYR C  66 
 PHE   0.002   0.001   PHE F  37 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00235 /  0.11 ( 3216)
  covalent geometry    : angle       0.53469 /  0.28 ( 4374)
  hydrogen bonds       : bond        0.02842 /  1.69 (  108)
  hydrogen bonds       : angle       4.56384 /  3.33 (  306)

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

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

  504 Ramachandran restraints generated.
    252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  504 Ramachandran restraints generated.
    252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  20 residues out of total 62 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 20
  time to evaluate  : 0.014 
Fit side-chains
REVERT: D   66 TYR cc_start: 0.3747 (t80) cc_final: 0.2778 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 20
  average time/residue: 0.0561
  time to fit residues: 1.1959
Evaluate side-chains
  17 residues out of total 62 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 17
  time to evaluate  : 0.013 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 4 optimal weight:    3.9990
   chunk 26 optimal weight:   10.0000
   chunk 18 optimal weight:    6.9990
   chunk 2 optimal weight:    0.2980
   chunk 16 optimal weight:    3.9990
   chunk 0 optimal weight:    6.9990
   chunk 1 optimal weight:    0.5980
   chunk 10 optimal weight:    3.9990
   chunk 21 optimal weight:    0.0370
   chunk 11 optimal weight:    1.9990
   chunk 25 optimal weight:    0.4980
   overall best weight:    0.6860
-------------------------------------------------------------------------------
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 = 0.4090 r_free = 0.4090 target = 0.192138 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.160844 restraints weight = 874.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.165852 restraints weight = 577.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.169588 restraints weight = 421.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.172120 restraints weight = 322.007|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.174085 restraints weight = 260.315|
|-----------------------------------------------------------------------------|
r_work (final): 0.3838
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6597
moved from start:          0.2846

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.016   3216  Z= 0.112
  Angle     :  0.548   4.863   4374  Z= 0.288
  Chirality :  0.051   0.116    504
  Planarity :  0.002   0.009    588
  Dihedral  :  3.824  10.470    426
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 11.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.35 %
    Favored  : 93.65 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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 are not related in a simple way.
  whole: -2.00 (0.43), residues: 378
  helix: -0.77 (0.51), residues: 114
  sheet: -0.45 (0.60), residues: 102
  loop : -2.30 (0.41), residues: 162

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG E  54 
 TYR   0.006   0.001   TYR F  66 
 PHE   0.002   0.001   PHE B  37 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00254 /  0.11 ( 3216)
  covalent geometry    : angle       0.54756 /  0.29 ( 4374)
  hydrogen bonds       : bond        0.03119 /  1.79 (  108)
  hydrogen bonds       : angle       4.68877 /  3.37 (  306)

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

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

  504 Ramachandran restraints generated.
    252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  504 Ramachandran restraints generated.
    252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  20 residues out of total 62 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 20
  time to evaluate  : 0.022 
Fit side-chains
REVERT: D   66 TYR cc_start: 0.4197 (t80) cc_final: 0.2723 (t80)
REVERT: D   69 TYR cc_start: 0.7235 (m-80) cc_final: 0.6851 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 20
  average time/residue: 0.0630
  time to fit residues: 1.3409
Evaluate side-chains
  17 residues out of total 62 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 17
  time to evaluate  : 0.021 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 6 optimal weight:    5.9990
   chunk 24 optimal weight:    6.9990
   chunk 31 optimal weight:    0.3980
   chunk 8 optimal weight:    0.7980
   chunk 21 optimal weight:    0.6980
   chunk 33 optimal weight:    0.1980
   chunk 13 optimal weight:    4.9990
   chunk 14 optimal weight:    0.9980
   chunk 28 optimal weight:    0.0470
   chunk 18 optimal weight:    6.9990
   chunk 26 optimal weight:    0.0670
   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 = 0.4031 r_free = 0.4031 target = 0.186757 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.157761 restraints weight = 884.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.162336 restraints weight = 610.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.165945 restraints weight = 455.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.168481 restraints weight = 358.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.170516 restraints weight = 294.959|
|-----------------------------------------------------------------------------|
r_work (final): 0.3840
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6588
moved from start:          0.2877

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.015   3216  Z= 0.108
  Angle     :  0.536   4.895   4374  Z= 0.278
  Chirality :  0.051   0.118    504
  Planarity :  0.002   0.010    588
  Dihedral  :  3.487  10.248    426
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 10.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.94 %
    Favored  : 92.06 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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 are not related in a simple way.
  whole: -1.97 (0.42), residues: 378
  helix: -0.77 (0.50), residues: 114
  sheet: -0.27 (0.58), residues: 102
  loop : -2.38 (0.40), residues: 162

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG F  54 
 TYR   0.003   0.000   TYR F  66 
 PHE   0.002   0.001   PHE E  37 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00235 /  0.11 ( 3216)
  covalent geometry    : angle       0.53570 /  0.28 ( 4374)
  hydrogen bonds       : bond        0.02864 /  1.72 (  108)
  hydrogen bonds       : angle       4.43407 /  3.20 (  306)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 631.17 seconds
wall clock time: 11 minutes 40.26 seconds (700.26 seconds total)