Starting phenix.real_space_refine
on Wed Sep 17 02:59:25 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ik7_35505/09_2025/8ik7_35505.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ik7_35505/09_2025/8ik7_35505.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.69
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ik7_35505/09_2025/8ik7_35505.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ik7_35505/09_2025/8ik7_35505.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ik7_35505/09_2025/8ik7_35505.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ik7_35505/09_2025/8ik7_35505.map"
  }
  resolution = 3.69
  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=   0.002
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     912      2.51       5
     N     264      2.21       5
     O     312      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 22 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 1488
  Number of models: 1
  Model: ""
    Number of chains: 24
    Chain: "C"
      Number of atoms: 62
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 62
          Classifications: {'peptide': 9}
          Link IDs: {'TRANS': 8}
    Chain: "L"
      Number of atoms: 62
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 62
          Classifications: {'peptide': 9}
          Link IDs: {'TRANS': 8}
    Chain: "M"
      Number of atoms: 62
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 62
          Classifications: {'peptide': 9}
          Link IDs: {'TRANS': 8}
    Chain: "K"
      Number of atoms: 62
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 62
          Classifications: {'peptide': 9}
          Link IDs: {'TRANS': 8}
    Chain: "G"
      Number of atoms: 62
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 62
          Classifications: {'peptide': 9}
          Link IDs: {'TRANS': 8}
    Chain: "I"
      Number of atoms: 62
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 62
          Classifications: {'peptide': 9}
          Link IDs: {'TRANS': 8}
    Chain: "U"
      Number of atoms: 62
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 62
          Classifications: {'peptide': 9}
          Link IDs: {'TRANS': 8}
    Chain: "O"
      Number of atoms: 62
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 62
          Classifications: {'peptide': 9}
          Link IDs: {'TRANS': 8}
    Chain: "R"
      Number of atoms: 62
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 62
          Classifications: {'peptide': 9}
          Link IDs: {'TRANS': 8}
    Chain: "V"
      Number of atoms: 62
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 62
          Classifications: {'peptide': 9}
          Link IDs: {'TRANS': 8}
    Chain: "P"
      Number of atoms: 62
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 62
          Classifications: {'peptide': 9}
          Link IDs: {'TRANS': 8}
    Chain: "S"
      Number of atoms: 62
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 62
          Classifications: {'peptide': 9}
          Link IDs: {'TRANS': 8}
    Chain: "X"
      Number of atoms: 62
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 62
          Classifications: {'peptide': 9}
          Link IDs: {'TRANS': 8}
    Chain: "D"
      Number of atoms: 62
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 62
          Classifications: {'peptide': 9}
          Link IDs: {'TRANS': 8}
    Chain: "E"
      Number of atoms: 62
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 62
          Classifications: {'peptide': 9}
          Link IDs: {'TRANS': 8}
    Chain: "A"
      Number of atoms: 62
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 62
          Classifications: {'peptide': 9}
          Link IDs: {'TRANS': 8}
    Chain: "B"
      Number of atoms: 62
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 62
          Classifications: {'peptide': 9}
          Link IDs: {'TRANS': 8}
    Chain: "N"
      Number of atoms: 62
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 62
          Classifications: {'peptide': 9}
          Link IDs: {'TRANS': 8}
    Chain: "J"
      Number of atoms: 62
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 62
          Classifications: {'peptide': 9}
          Link IDs: {'TRANS': 8}
    Chain: "F"
      Number of atoms: 62
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 62
          Classifications: {'peptide': 9}
          Link IDs: {'TRANS': 8}
    Chain: "H"
      Number of atoms: 62
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 62
          Classifications: {'peptide': 9}
          Link IDs: {'TRANS': 8}
    Chain: "W"
      Number of atoms: 62
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 62
          Classifications: {'peptide': 9}
          Link IDs: {'TRANS': 8}
    Chain: "Q"
      Number of atoms: 62
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 62
          Classifications: {'peptide': 9}
          Link IDs: {'TRANS': 8}
    Chain: "T"
      Number of atoms: 62
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 62
          Classifications: {'peptide': 9}
          Link IDs: {'TRANS': 8}
  Time building chain proxies: 0.34, per 1000 atoms: 0.23
  Number of scatterers: 1488
  At special positions: 0
  Unit cell: (126.16, 90.47, 24.07, 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     312      8.00
     N     264      7.00
     C     912      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: 0.27
  Conformation dependent library (CDL) restraints added in 57.7 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  336 Ramachandran restraints generated.
    168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  240

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      0 helices and 0 sheets defined
      0.0% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.32
  Creating SS restraints...

    No hydrogen bonds 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: 0.00

  Time building geometry restraints manager: 0.31 seconds

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

  Histogram of bond lengths:
        1.22 -     1.28: 312
        1.28 -     1.35: 240
        1.35 -     1.41: 288
        1.41 -     1.47: 221
        1.47 -     1.54: 451
  Bond restraints: 1512
  Sorted by residual:
  bond pdb=" CA  PHE B 222 "
       pdb=" CB  PHE B 222 "
    ideal  model  delta    sigma   weight residual
    1.529  1.484  0.045 1.63e-02 3.76e+03 7.64e+00
  bond pdb=" CA  PHE N 216 "
       pdb=" C   PHE N 216 "
    ideal  model  delta    sigma   weight residual
    1.532  1.514  0.019 9.60e-03 1.09e+04 3.84e+00
  bond pdb=" CB  PHE U 216 "
       pdb=" CG  PHE U 216 "
    ideal  model  delta    sigma   weight residual
    1.502  1.461  0.041 2.30e-02 1.89e+03 3.24e+00
  bond pdb=" CB  PHE W 216 "
       pdb=" CG  PHE W 216 "
    ideal  model  delta    sigma   weight residual
    1.502  1.461  0.041 2.30e-02 1.89e+03 3.10e+00
  bond pdb=" CA  ASN D 215 "
       pdb=" CB  ASN D 215 "
    ideal  model  delta    sigma   weight residual
    1.530  1.506  0.025 1.50e-02 4.44e+03 2.71e+00
  ... (remaining 1507 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     6.95: 1863
        6.95 -    13.90: 69
       13.90 -    20.84: 21
       20.84 -    27.79: 8
       27.79 -    34.74: 7
  Bond angle restraints: 1968
  Sorted by residual:
  angle pdb=" N   GLY Q 211 "
        pdb=" CA  GLY Q 211 "
        pdb=" C   GLY Q 211 "
      ideal   model   delta    sigma   weight residual
     112.49  141.77  -29.28 1.21e+00 6.83e-01 5.86e+02
  angle pdb=" N   GLY T 211 "
        pdb=" CA  GLY T 211 "
        pdb=" C   GLY T 211 "
      ideal   model   delta    sigma   weight residual
     114.61  149.35  -34.74 1.49e+00 4.50e-01 5.44e+02
  angle pdb=" N   GLY R 211 "
        pdb=" CA  GLY R 211 "
        pdb=" C   GLY R 211 "
      ideal   model   delta    sigma   weight residual
     114.10  148.75  -34.65 1.51e+00 4.39e-01 5.26e+02
  angle pdb=" N   ASN I 215 "
        pdb=" CA  ASN I 215 "
        pdb=" CB  ASN I 215 "
      ideal   model   delta    sigma   weight residual
     110.47   77.33   33.14 1.66e+00 3.63e-01 3.98e+02
  angle pdb=" N   ASP I 214 "
        pdb=" CA  ASP I 214 "
        pdb=" C   ASP I 214 "
      ideal   model   delta    sigma   weight residual
     109.59   78.79   30.80 1.61e+00 3.86e-01 3.66e+02
  ... (remaining 1963 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.01 -     7.86: 453
        7.86 -    15.71: 140
       15.71 -    23.56: 49
       23.56 -    31.41: 19
       31.41 -    39.25: 11
  Dihedral angle restraints: 672
    sinusoidal: 240
      harmonic: 432
  Sorted by residual:
  dihedral pdb=" N   ASN I 215 "
           pdb=" C   ASN I 215 "
           pdb=" CA  ASN I 215 "
           pdb=" CB  ASN I 215 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80   83.55   39.25     0      2.50e+00 1.60e-01 2.47e+02
  dihedral pdb=" C   PHE B 222 "
           pdb=" N   PHE B 222 "
           pdb=" CA  PHE B 222 "
           pdb=" CB  PHE B 222 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -157.09   34.49     0      2.50e+00 1.60e-01 1.90e+02
  dihedral pdb=" C   PHE C 216 "
           pdb=" N   PHE C 216 "
           pdb=" CA  PHE C 216 "
           pdb=" CB  PHE C 216 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -156.80   34.20     0      2.50e+00 1.60e-01 1.87e+02
  ... (remaining 669 not shown)

  Histogram of chiral volume deviations from ideal:
       0.008 -    0.308: 97
       0.308 -    0.609: 13
       0.609 -    0.910: 6
       0.910 -    1.210: 1
       1.210 -    1.511: 3
  Chirality restraints: 120
  Sorted by residual:
  chirality pdb=" CA  PHE B 222 "
            pdb=" N   PHE B 222 "
            pdb=" C   PHE B 222 "
            pdb=" CB  PHE B 222 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.00    1.51 2.00e-01 2.50e+01 5.71e+01
  chirality pdb=" CA  PHE C 216 "
            pdb=" N   PHE C 216 "
            pdb=" C   PHE C 216 "
            pdb=" CB  PHE C 216 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.17    1.34 2.00e-01 2.50e+01 4.50e+01
  chirality pdb=" CA  PHE H 216 "
            pdb=" N   PHE H 216 "
            pdb=" C   PHE H 216 "
            pdb=" CB  PHE H 216 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.17    1.34 2.00e-01 2.50e+01 4.49e+01
  ... (remaining 117 not shown)

  Planarity restraints: 312
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE I 210 "    0.013 2.00e-02 2.50e+03   1.51e-02 4.01e+00
        pdb=" CG  PHE I 210 "   -0.035 2.00e-02 2.50e+03
        pdb=" CD1 PHE I 210 "    0.006 2.00e-02 2.50e+03
        pdb=" CD2 PHE I 210 "    0.012 2.00e-02 2.50e+03
        pdb=" CE1 PHE I 210 "    0.003 2.00e-02 2.50e+03
        pdb=" CE2 PHE I 210 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ  PHE I 210 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP H 214 "   -0.006 2.00e-02 2.50e+03   1.13e-02 1.29e+00
        pdb=" C   ASP H 214 "    0.020 2.00e-02 2.50e+03
        pdb=" O   ASP H 214 "   -0.007 2.00e-02 2.50e+03
        pdb=" N   ASN H 215 "   -0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE L 216 "   -0.006 2.00e-02 2.50e+03   8.06e-03 1.14e+00
        pdb=" CG  PHE L 216 "    0.018 2.00e-02 2.50e+03
        pdb=" CD1 PHE L 216 "   -0.009 2.00e-02 2.50e+03
        pdb=" CD2 PHE L 216 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE1 PHE L 216 "    0.003 2.00e-02 2.50e+03
        pdb=" CE2 PHE L 216 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ  PHE L 216 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 309 not shown)

  Histogram of nonbonded interaction distances:
        1.94 -     2.53: 47
        2.53 -     3.12: 1307
        3.12 -     3.71: 1620
        3.71 -     4.31: 2246
        4.31 -     4.90: 3071
  Nonbonded interactions: 8291
  Sorted by model distance:
  nonbonded pdb=" O   ASN P 213 "
            pdb=" OD1 ASP P 214 "
     model   vdw
     1.936 3.040
  nonbonded pdb=" O   ASN R 213 "
            pdb=" OD1 ASN R 213 "
     model   vdw
     1.964 3.040
  nonbonded pdb=" O   ASP I 214 "
            pdb=" OD1 ASP I 214 "
     model   vdw
     2.032 3.040
  nonbonded pdb=" N   ASP I 214 "
            pdb=" O   ASP I 214 "
     model   vdw
     2.042 2.496
  nonbonded pdb=" N   ASN F 215 "
            pdb=" O   ASN F 215 "
     model   vdw
     2.082 2.496
  ... (remaining 8286 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'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
  selection = chain 'I'
  selection = chain 'J'
  selection = chain 'K'
  selection = chain 'L'
  selection = chain 'M'
  selection = chain 'N'
  selection = chain 'O'
  selection = chain 'P'
  selection = chain 'Q'
  selection = chain 'R'
  selection = chain 'S'
  selection = chain 'T'
  selection = chain 'U'
  selection = chain 'V'
  selection = chain 'W'
  selection = chain 'X'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.000
  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:          0.040
  Check model and map are aligned:         0.000
  Set scattering table:                    0.010
  Process input model:                     3.110
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.690
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.910
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7453
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      :  0.009   0.045   1512  Z= 0.428
  Angle     :  3.746  34.741   1968  Z= 2.184
  Chirality :  0.340   1.511    120
  Planarity :  0.003   0.015    312
  Dihedral  : 10.510  35.419    432
  Min Nonbonded Distance : 1.936

Molprobity Statistics.
  All-atom Clashscore : 29.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.69 %
    Favored  : 86.31 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Cbeta Deviations : 22.50 %
  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 aren not related in a simple way.
  whole: -5.90 (0.31), residues: 168
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.49 (0.24), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.035   0.002   PHE I 210 

Details of bonding type rmsd
  covalent geometry    : bond        0.00883 ( 1512)
  covalent geometry    : angle       3.74615 ( 1968)

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

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

  336 Ramachandran restraints generated.
    168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  336 Ramachandran restraints generated.
    168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 38
  time to evaluate  : 0.043 
Fit side-chains
REVERT: R  214 ASP cc_start: 0.8528 (p0) cc_final: 0.8303 (m-30)
REVERT: P  210 PHE cc_start: 0.8334 (p90) cc_final: 0.6844 (t80)
REVERT: A  222 PHE cc_start: 0.7226 (m-80) cc_final: 0.4813 (p90)
  outliers start: 0
  outliers final: 0
  residues processed: 38
  average time/residue: 0.0237
  time to fit residues: 1.1325
Evaluate side-chains
  19 residues out of total 120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 19
  time to evaluate  : 0.048 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 1
   random chunks:
   chunk 0 optimal weight:    9.9990
   overall best weight:   50.0000

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

Flipped N/Q/H residues before XYZ refinement:
** M 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 213 ASN
** F 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
W 215 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.085617 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.071021 restraints weight = 4550.212|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.071859 restraints weight = 3198.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.072370 restraints weight = 2608.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.072500 restraints weight = 2282.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.072499 restraints weight = 2190.661|
|-----------------------------------------------------------------------------|
r_work (final): 0.3272
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8629
moved from start:          0.6830

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.051   0.243   1512  Z= 2.417
  Angle     :  2.474  18.614   1968  Z= 1.377
  Chirality :  0.145   0.346    120
  Planarity :  0.016   0.047    312
  Dihedral  : 15.124  44.746    192
  Min Nonbonded Distance : 2.133

Molprobity Statistics.
  All-atom Clashscore : 64.64
  Ramachandran Plot:
    Outliers :  7.14 %
    Allowed  : 38.10 %
    Favored  : 54.76 %
  Rotamer:
    Outliers : 15.00 %
    Allowed  : 25.00 %
    Favored  : 60.00 %
  Cbeta Deviations :  0.83 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 6.25 %

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: -7.13 (0.38), residues: 168
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -5.43 (0.29), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.060   0.010   PHE Q 216 

Details of bonding type rmsd
  covalent geometry    : bond        0.05099 ( 1512)
  covalent geometry    : angle       2.47412 ( 1968)

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

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

  336 Ramachandran restraints generated.
    168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  336 Ramachandran restraints generated.
    168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  29 residues out of total 120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 11
  time to evaluate  : 0.055 
Fit side-chains
REVERT: G  210 PHE cc_start: 0.5323 (OUTLIER) cc_final: 0.4203 (p90)
REVERT: V  210 PHE cc_start: 0.9474 (OUTLIER) cc_final: 0.8738 (t80)
REVERT: H  214 ASP cc_start: 0.7086 (m-30) cc_final: 0.6613 (m-30)
REVERT: W  214 ASP cc_start: 0.8648 (OUTLIER) cc_final: 0.8364 (p0)
REVERT: W  215 ASN cc_start: 0.8871 (OUTLIER) cc_final: 0.8232 (t0)
  outliers start: 18
  outliers final: 13
  residues processed: 25
  average time/residue: 0.0248
  time to fit residues: 0.8322
Evaluate side-chains
  27 residues out of total 120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 10
  time to evaluate  : 0.051 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  219 ASN
Chi-restraints excluded: chain M residue  219 ASN
Chi-restraints excluded: chain K residue  214 ASP
Chi-restraints excluded: chain G residue  210 PHE
Chi-restraints excluded: chain G residue  214 ASP
Chi-restraints excluded: chain I residue  215 ASN
Chi-restraints excluded: chain O residue  210 PHE
Chi-restraints excluded: chain O residue  215 ASN
Chi-restraints excluded: chain V residue  210 PHE
Chi-restraints excluded: chain D residue  214 ASP
Chi-restraints excluded: chain B residue  221 ASN
Chi-restraints excluded: chain N residue  220 ASP
Chi-restraints excluded: chain F residue  210 PHE
Chi-restraints excluded: chain H residue  210 PHE
Chi-restraints excluded: chain W residue  214 ASP
Chi-restraints excluded: chain W residue  215 ASN
Chi-restraints excluded: chain W residue  216 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 1
   random chunks:
   chunk 0 optimal weight:    1.9990
   overall best weight:   50.0000

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

Flipped N/Q/H residues before XYZ refinement:
** M 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** W 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.083563 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.068629 restraints weight = 4626.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.069398 restraints weight = 3396.201|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.069834 restraints weight = 2809.310|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.069970 restraints weight = 2506.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.070307 restraints weight = 2405.474|
|-----------------------------------------------------------------------------|
r_work (final): 0.3223
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8644
moved from start:          0.7347

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.051   0.250   1512  Z= 2.418
  Angle     :  2.440  18.694   1968  Z= 1.365
  Chirality :  0.149   0.372    120
  Planarity :  0.015   0.050    312
  Dihedral  : 15.767  46.808    192
  Min Nonbonded Distance : 2.134

Molprobity Statistics.
  All-atom Clashscore : 68.54
  Ramachandran Plot:
    Outliers :  3.57 %
    Allowed  : 48.81 %
    Favored  : 47.62 %
  Rotamer:
    Outliers : 21.67 %
    Allowed  : 24.17 %
    Favored  : 54.17 %
  Cbeta Deviations :  0.83 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 6.77 %

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: -7.47 (0.39), residues: 168
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -5.69 (0.30), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.051   0.009   PHE Q 216 

Details of bonding type rmsd
  covalent geometry    : bond        0.05109 ( 1512)
  covalent geometry    : angle       2.44012 ( 1968)

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

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

  336 Ramachandran restraints generated.
    168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  336 Ramachandran restraints generated.
    168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 11
  time to evaluate  : 0.053 
Fit side-chains
REVERT: V  210 PHE cc_start: 0.9218 (OUTLIER) cc_final: 0.8566 (t80)
REVERT: P  210 PHE cc_start: 0.8457 (OUTLIER) cc_final: 0.7389 (m-80)
REVERT: H  210 PHE cc_start: 0.8618 (OUTLIER) cc_final: 0.8361 (m-80)
REVERT: H  214 ASP cc_start: 0.7495 (OUTLIER) cc_final: 0.7167 (m-30)
  outliers start: 26
  outliers final: 18
  residues processed: 34
  average time/residue: 0.0254
  time to fit residues: 1.1249
Evaluate side-chains
  33 residues out of total 120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 11
  time to evaluate  : 0.077 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  219 ASN
Chi-restraints excluded: chain L residue  219 ASN
Chi-restraints excluded: chain L residue  221 ASN
Chi-restraints excluded: chain M residue  219 ASN
Chi-restraints excluded: chain K residue  214 ASP
Chi-restraints excluded: chain K residue  215 ASN
Chi-restraints excluded: chain G residue  213 ASN
Chi-restraints excluded: chain I residue  210 PHE
Chi-restraints excluded: chain I residue  215 ASN
Chi-restraints excluded: chain O residue  210 PHE
Chi-restraints excluded: chain O residue  215 ASN
Chi-restraints excluded: chain R residue  214 ASP
Chi-restraints excluded: chain V residue  210 PHE
Chi-restraints excluded: chain P residue  210 PHE
Chi-restraints excluded: chain S residue  210 PHE
Chi-restraints excluded: chain D residue  214 ASP
Chi-restraints excluded: chain B residue  221 ASN
Chi-restraints excluded: chain N residue  220 ASP
Chi-restraints excluded: chain F residue  210 PHE
Chi-restraints excluded: chain H residue  210 PHE
Chi-restraints excluded: chain H residue  214 ASP
Chi-restraints excluded: chain W residue  216 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 1
   random chunks:
   chunk 0 optimal weight:    1.9990
   overall best weight:   50.0000

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

Flipped N/Q/H residues before XYZ refinement:
** M 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
W 213 ASN
** W 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.083047 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.068454 restraints weight = 4624.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.069236 restraints weight = 3321.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.069700 restraints weight = 2726.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.070006 restraints weight = 2409.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 16)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.070078 restraints weight = 2220.443|
|-----------------------------------------------------------------------------|
r_work (final): 0.3220
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8649
moved from start:          0.7566

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.051   0.250   1512  Z= 2.419
  Angle     :  2.470  18.898   1968  Z= 1.381
  Chirality :  0.151   0.391    120
  Planarity :  0.014   0.052    312
  Dihedral  : 15.958  44.720    192
  Min Nonbonded Distance : 2.129

Molprobity Statistics.
  All-atom Clashscore : 72.04
  Ramachandran Plot:
    Outliers :  1.79 %
    Allowed  : 54.76 %
    Favored  : 43.45 %
  Rotamer:
    Outliers : 24.17 %
    Allowed  : 27.50 %
    Favored  : 48.33 %
  Cbeta Deviations :  0.83 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 7.29 %

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: -7.59 (0.39), residues: 168
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -5.78 (0.30), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.049   0.008   PHE Q 216 

Details of bonding type rmsd
  covalent geometry    : bond        0.05113 ( 1512)
  covalent geometry    : angle       2.46999 ( 1968)

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

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

  336 Ramachandran restraints generated.
    168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  336 Ramachandran restraints generated.
    168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 11
  time to evaluate  : 0.053 
Fit side-chains
   revert: symmetry clash
REVERT: V  210 PHE cc_start: 0.9209 (OUTLIER) cc_final: 0.8634 (t80)
REVERT: P  210 PHE cc_start: 0.8592 (OUTLIER) cc_final: 0.7415 (p90)
  outliers start: 29
  outliers final: 20
  residues processed: 36
  average time/residue: 0.0252
  time to fit residues: 1.1852
Evaluate side-chains
  33 residues out of total 120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 11
  time to evaluate  : 0.049 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  219 ASN
Chi-restraints excluded: chain L residue  219 ASN
Chi-restraints excluded: chain M residue  219 ASN
Chi-restraints excluded: chain K residue  214 ASP
Chi-restraints excluded: chain K residue  215 ASN
Chi-restraints excluded: chain G residue  210 PHE
Chi-restraints excluded: chain G residue  213 ASN
Chi-restraints excluded: chain I residue  210 PHE
Chi-restraints excluded: chain I residue  214 ASP
Chi-restraints excluded: chain I residue  215 ASN
Chi-restraints excluded: chain O residue  210 PHE
Chi-restraints excluded: chain O residue  214 ASP
Chi-restraints excluded: chain R residue  214 ASP
Chi-restraints excluded: chain V residue  210 PHE
Chi-restraints excluded: chain P residue  210 PHE
Chi-restraints excluded: chain D residue  214 ASP
Chi-restraints excluded: chain D residue  216 PHE
Chi-restraints excluded: chain B residue  221 ASN
Chi-restraints excluded: chain N residue  220 ASP
Chi-restraints excluded: chain F residue  210 PHE
Chi-restraints excluded: chain H residue  214 ASP
Chi-restraints excluded: chain W residue  216 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 1
   random chunks:
   chunk 0 optimal weight:    0.9990
   overall best weight:   50.0000

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

Flipped N/Q/H residues before XYZ refinement:
** M 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** W 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.082690 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.068174 restraints weight = 4581.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.068948 restraints weight = 3311.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.069380 restraints weight = 2721.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.069380 restraints weight = 2414.520|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.069380 restraints weight = 2414.520|
|-----------------------------------------------------------------------------|
r_work (final): 0.3208
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8660
moved from start:          0.7656

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.051   0.246   1512  Z= 2.412
  Angle     :  2.489  19.063   1968  Z= 1.392
  Chirality :  0.151   0.397    120
  Planarity :  0.014   0.047    312
  Dihedral  : 16.043  44.867    192
  Min Nonbonded Distance : 2.121

Molprobity Statistics.
  All-atom Clashscore : 72.43
  Ramachandran Plot:
    Outliers :  2.38 %
    Allowed  : 57.14 %
    Favored  : 40.48 %
  Rotamer:
    Outliers : 25.83 %
    Allowed  : 30.00 %
    Favored  : 44.17 %
  Cbeta Deviations :  0.83 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 8.33 %

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: -7.67 (0.38), residues: 168
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -5.84 (0.29), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.048   0.008   PHE Q 216 

Details of bonding type rmsd
  covalent geometry    : bond        0.05099 ( 1512)
  covalent geometry    : angle       2.48913 ( 1968)

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

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

  336 Ramachandran restraints generated.
    168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  336 Ramachandran restraints generated.
    168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 11
  time to evaluate  : 0.053 
Fit side-chains
   revert: symmetry clash
REVERT: V  210 PHE cc_start: 0.9204 (OUTLIER) cc_final: 0.8629 (t80)
REVERT: P  210 PHE cc_start: 0.8584 (OUTLIER) cc_final: 0.7389 (p90)
REVERT: H  210 PHE cc_start: 0.8700 (OUTLIER) cc_final: 0.8392 (m-80)
  outliers start: 31
  outliers final: 25
  residues processed: 37
  average time/residue: 0.0234
  time to fit residues: 1.1324
Evaluate side-chains
  39 residues out of total 120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 11
  time to evaluate  : 0.050 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  219 ASN
Chi-restraints excluded: chain L residue  219 ASN
Chi-restraints excluded: chain L residue  221 ASN
Chi-restraints excluded: chain M residue  219 ASN
Chi-restraints excluded: chain K residue  214 ASP
Chi-restraints excluded: chain K residue  215 ASN
Chi-restraints excluded: chain G residue  210 PHE
Chi-restraints excluded: chain G residue  213 ASN
Chi-restraints excluded: chain G residue  214 ASP
Chi-restraints excluded: chain I residue  210 PHE
Chi-restraints excluded: chain I residue  214 ASP
Chi-restraints excluded: chain I residue  215 ASN
Chi-restraints excluded: chain O residue  210 PHE
Chi-restraints excluded: chain O residue  214 ASP
Chi-restraints excluded: chain O residue  215 ASN
Chi-restraints excluded: chain R residue  214 ASP
Chi-restraints excluded: chain V residue  210 PHE
Chi-restraints excluded: chain P residue  210 PHE
Chi-restraints excluded: chain D residue  214 ASP
Chi-restraints excluded: chain D residue  216 PHE
Chi-restraints excluded: chain A residue  220 ASP
Chi-restraints excluded: chain B residue  221 ASN
Chi-restraints excluded: chain N residue  220 ASP
Chi-restraints excluded: chain F residue  210 PHE
Chi-restraints excluded: chain H residue  210 PHE
Chi-restraints excluded: chain H residue  214 ASP
Chi-restraints excluded: chain W residue  213 ASN
Chi-restraints excluded: chain W residue  216 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 1
   random chunks:
   chunk 0 optimal weight:    0.9990
   overall best weight:   50.0000

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

Flipped N/Q/H residues before XYZ refinement:
** M 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** W 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.082360 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.067806 restraints weight = 4635.070|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.068559 restraints weight = 3331.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.069045 restraints weight = 2739.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.069286 restraints weight = 2424.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.069286 restraints weight = 2257.844|
|-----------------------------------------------------------------------------|
r_work (final): 0.3208
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8656
moved from start:          0.7711

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.051   0.245   1512  Z= 2.412
  Angle     :  2.496  19.013   1968  Z= 1.397
  Chirality :  0.151   0.399    120
  Planarity :  0.014   0.047    312
  Dihedral  : 16.128  45.043    192
  Min Nonbonded Distance : 2.122

Molprobity Statistics.
  All-atom Clashscore : 73.60
  Ramachandran Plot:
    Outliers :  2.38 %
    Allowed  : 55.36 %
    Favored  : 42.26 %
  Rotamer:
    Outliers : 28.33 %
    Allowed  : 28.33 %
    Favored  : 43.33 %
  Cbeta Deviations :  0.83 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 9.38 %

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: -7.64 (0.38), residues: 168
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -5.82 (0.29), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.047   0.009   PHE Q 216 

Details of bonding type rmsd
  covalent geometry    : bond        0.05097 ( 1512)
  covalent geometry    : angle       2.49580 ( 1968)

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

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

  336 Ramachandran restraints generated.
    168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  336 Ramachandran restraints generated.
    168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 12
  time to evaluate  : 0.055 
Fit side-chains
   revert: symmetry clash
REVERT: M  222 PHE cc_start: 0.9083 (OUTLIER) cc_final: 0.8774 (m-80)
REVERT: V  210 PHE cc_start: 0.9201 (OUTLIER) cc_final: 0.8690 (t80)
REVERT: P  210 PHE cc_start: 0.8563 (OUTLIER) cc_final: 0.7443 (p90)
  outliers start: 34
  outliers final: 25
  residues processed: 41
  average time/residue: 0.0240
  time to fit residues: 1.2808
Evaluate side-chains
  40 residues out of total 120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 12
  time to evaluate  : 0.050 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  219 ASN
Chi-restraints excluded: chain L residue  219 ASN
Chi-restraints excluded: chain L residue  221 ASN
Chi-restraints excluded: chain M residue  219 ASN
Chi-restraints excluded: chain M residue  222 PHE
Chi-restraints excluded: chain K residue  214 ASP
Chi-restraints excluded: chain K residue  215 ASN
Chi-restraints excluded: chain G residue  210 PHE
Chi-restraints excluded: chain G residue  213 ASN
Chi-restraints excluded: chain I residue  210 PHE
Chi-restraints excluded: chain I residue  214 ASP
Chi-restraints excluded: chain I residue  215 ASN
Chi-restraints excluded: chain U residue  214 ASP
Chi-restraints excluded: chain O residue  210 PHE
Chi-restraints excluded: chain O residue  214 ASP
Chi-restraints excluded: chain O residue  215 ASN
Chi-restraints excluded: chain R residue  214 ASP
Chi-restraints excluded: chain V residue  210 PHE
Chi-restraints excluded: chain P residue  210 PHE
Chi-restraints excluded: chain D residue  214 ASP
Chi-restraints excluded: chain D residue  216 PHE
Chi-restraints excluded: chain A residue  220 ASP
Chi-restraints excluded: chain B residue  221 ASN
Chi-restraints excluded: chain N residue  220 ASP
Chi-restraints excluded: chain F residue  210 PHE
Chi-restraints excluded: chain H residue  214 ASP
Chi-restraints excluded: chain W residue  213 ASN
Chi-restraints excluded: chain W residue  216 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 1
   random chunks:
   chunk 0 optimal weight:    1.9990
   overall best weight:   50.0000

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

Flipped N/Q/H residues before XYZ refinement:
** M 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** W 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.082327 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.067825 restraints weight = 4616.766|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.068603 restraints weight = 3307.343|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.069037 restraints weight = 2706.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.069341 restraints weight = 2395.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.069341 restraints weight = 2210.053|
|-----------------------------------------------------------------------------|
r_work (final): 0.3211
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8658
moved from start:          0.7743

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.051   0.243   1512  Z= 2.413
  Angle     :  2.494  19.062   1968  Z= 1.398
  Chirality :  0.150   0.400    120
  Planarity :  0.014   0.048    312
  Dihedral  : 16.203  46.630    192
  Min Nonbonded Distance : 2.121

Molprobity Statistics.
  All-atom Clashscore : 72.82
  Ramachandran Plot:
    Outliers :  2.38 %
    Allowed  : 56.55 %
    Favored  : 41.07 %
  Rotamer:
    Outliers : 27.50 %
    Allowed  : 29.17 %
    Favored  : 43.33 %
  Cbeta Deviations :  1.67 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 9.90 %

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: -7.65 (0.38), residues: 168
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -5.83 (0.29), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.047   0.009   PHE Q 216 

Details of bonding type rmsd
  covalent geometry    : bond        0.05101 ( 1512)
  covalent geometry    : angle       2.49444 ( 1968)

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

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

  336 Ramachandran restraints generated.
    168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  336 Ramachandran restraints generated.
    168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 12
  time to evaluate  : 0.057 
Fit side-chains
   revert: symmetry clash
REVERT: M  222 PHE cc_start: 0.9085 (OUTLIER) cc_final: 0.8771 (m-80)
REVERT: V  210 PHE cc_start: 0.9202 (OUTLIER) cc_final: 0.8690 (t80)
REVERT: P  210 PHE cc_start: 0.8571 (OUTLIER) cc_final: 0.7496 (p90)
REVERT: H  210 PHE cc_start: 0.8763 (OUTLIER) cc_final: 0.8483 (m-80)
  outliers start: 33
  outliers final: 26
  residues processed: 40
  average time/residue: 0.0241
  time to fit residues: 1.2504
Evaluate side-chains
  42 residues out of total 120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 12
  time to evaluate  : 0.057 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  219 ASN
Chi-restraints excluded: chain L residue  219 ASN
Chi-restraints excluded: chain L residue  221 ASN
Chi-restraints excluded: chain M residue  219 ASN
Chi-restraints excluded: chain M residue  222 PHE
Chi-restraints excluded: chain K residue  214 ASP
Chi-restraints excluded: chain K residue  215 ASN
Chi-restraints excluded: chain G residue  210 PHE
Chi-restraints excluded: chain G residue  213 ASN
Chi-restraints excluded: chain G residue  214 ASP
Chi-restraints excluded: chain I residue  210 PHE
Chi-restraints excluded: chain I residue  214 ASP
Chi-restraints excluded: chain I residue  215 ASN
Chi-restraints excluded: chain U residue  214 ASP
Chi-restraints excluded: chain O residue  210 PHE
Chi-restraints excluded: chain O residue  214 ASP
Chi-restraints excluded: chain O residue  215 ASN
Chi-restraints excluded: chain R residue  214 ASP
Chi-restraints excluded: chain V residue  210 PHE
Chi-restraints excluded: chain P residue  210 PHE
Chi-restraints excluded: chain D residue  214 ASP
Chi-restraints excluded: chain D residue  216 PHE
Chi-restraints excluded: chain A residue  220 ASP
Chi-restraints excluded: chain B residue  221 ASN
Chi-restraints excluded: chain N residue  220 ASP
Chi-restraints excluded: chain F residue  210 PHE
Chi-restraints excluded: chain H residue  210 PHE
Chi-restraints excluded: chain H residue  214 ASP
Chi-restraints excluded: chain W residue  213 ASN
Chi-restraints excluded: chain W residue  216 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 1
   random chunks:
   chunk 0 optimal weight:    0.9990
   overall best weight:   50.0000

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

Flipped N/Q/H residues before XYZ refinement:
** M 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** W 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.082125 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.067659 restraints weight = 4481.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.068281 restraints weight = 3254.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.068838 restraints weight = 2726.138|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.069110 restraints weight = 2399.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.069125 restraints weight = 2222.637|
|-----------------------------------------------------------------------------|
r_work (final): 0.3208
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8657
moved from start:          0.7763

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.051   0.243   1512  Z= 2.413
  Angle     :  2.497  19.032   1968  Z= 1.399
  Chirality :  0.150   0.399    120
  Planarity :  0.014   0.046    312
  Dihedral  : 16.220  47.957    192
  Min Nonbonded Distance : 2.122

Molprobity Statistics.
  All-atom Clashscore : 72.82
  Ramachandran Plot:
    Outliers :  2.38 %
    Allowed  : 55.95 %
    Favored  : 41.67 %
  Rotamer:
    Outliers : 29.17 %
    Allowed  : 28.33 %
    Favored  : 42.50 %
  Cbeta Deviations :  1.67 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 9.90 %

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: -7.62 (0.38), residues: 168
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -5.80 (0.29), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.047   0.009   PHE Q 216 

Details of bonding type rmsd
  covalent geometry    : bond        0.05103 ( 1512)
  covalent geometry    : angle       2.49674 ( 1968)

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

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

  336 Ramachandran restraints generated.
    168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  336 Ramachandran restraints generated.
    168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 12
  time to evaluate  : 0.050 
Fit side-chains
   revert: symmetry clash
REVERT: M  222 PHE cc_start: 0.9084 (OUTLIER) cc_final: 0.8772 (m-80)
REVERT: G  210 PHE cc_start: 0.5249 (OUTLIER) cc_final: 0.4837 (p90)
REVERT: V  210 PHE cc_start: 0.9199 (OUTLIER) cc_final: 0.8683 (t80)
REVERT: P  210 PHE cc_start: 0.8566 (OUTLIER) cc_final: 0.7506 (p90)
REVERT: H  210 PHE cc_start: 0.8815 (OUTLIER) cc_final: 0.8481 (m-80)
  outliers start: 35
  outliers final: 26
  residues processed: 41
  average time/residue: 0.0256
  time to fit residues: 1.3454
Evaluate side-chains
  43 residues out of total 120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 12
  time to evaluate  : 0.061 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  219 ASN
Chi-restraints excluded: chain L residue  219 ASN
Chi-restraints excluded: chain L residue  221 ASN
Chi-restraints excluded: chain M residue  219 ASN
Chi-restraints excluded: chain M residue  222 PHE
Chi-restraints excluded: chain K residue  214 ASP
Chi-restraints excluded: chain K residue  215 ASN
Chi-restraints excluded: chain G residue  210 PHE
Chi-restraints excluded: chain G residue  213 ASN
Chi-restraints excluded: chain G residue  214 ASP
Chi-restraints excluded: chain I residue  210 PHE
Chi-restraints excluded: chain I residue  214 ASP
Chi-restraints excluded: chain I residue  215 ASN
Chi-restraints excluded: chain U residue  214 ASP
Chi-restraints excluded: chain O residue  210 PHE
Chi-restraints excluded: chain O residue  214 ASP
Chi-restraints excluded: chain O residue  215 ASN
Chi-restraints excluded: chain R residue  214 ASP
Chi-restraints excluded: chain V residue  210 PHE
Chi-restraints excluded: chain P residue  210 PHE
Chi-restraints excluded: chain X residue  216 PHE
Chi-restraints excluded: chain D residue  214 ASP
Chi-restraints excluded: chain D residue  216 PHE
Chi-restraints excluded: chain A residue  220 ASP
Chi-restraints excluded: chain B residue  221 ASN
Chi-restraints excluded: chain N residue  220 ASP
Chi-restraints excluded: chain F residue  210 PHE
Chi-restraints excluded: chain H residue  210 PHE
Chi-restraints excluded: chain H residue  214 ASP
Chi-restraints excluded: chain W residue  213 ASN
Chi-restraints excluded: chain W residue  216 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 1
   random chunks:
   chunk 0 optimal weight:    1.9990
   overall best weight:   50.0000

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

Flipped N/Q/H residues before XYZ refinement:
** M 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** W 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.082173 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.067642 restraints weight = 4548.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.068415 restraints weight = 3287.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.068816 restraints weight = 2701.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.068816 restraints weight = 2408.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.068816 restraints weight = 2408.954|
|-----------------------------------------------------------------------------|
r_work (final): 0.3201
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8661
moved from start:          0.7774

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.051   0.242   1512  Z= 2.413
  Angle     :  2.493  19.044   1968  Z= 1.397
  Chirality :  0.150   0.399    120
  Planarity :  0.014   0.047    312
  Dihedral  : 16.233  48.638    192
  Min Nonbonded Distance : 2.122

Molprobity Statistics.
  All-atom Clashscore : 72.43
  Ramachandran Plot:
    Outliers :  2.38 %
    Allowed  : 56.55 %
    Favored  : 41.07 %
  Rotamer:
    Outliers : 28.33 %
    Allowed  : 29.17 %
    Favored  : 42.50 %
  Cbeta Deviations :  1.67 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 9.90 %

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: -7.59 (0.38), residues: 168
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -5.78 (0.29), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.046   0.009   PHE Q 216 

Details of bonding type rmsd
  covalent geometry    : bond        0.05102 ( 1512)
  covalent geometry    : angle       2.49301 ( 1968)

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

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

  336 Ramachandran restraints generated.
    168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  336 Ramachandran restraints generated.
    168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 12
  time to evaluate  : 0.065 
Fit side-chains
   revert: symmetry clash
REVERT: M  222 PHE cc_start: 0.9085 (OUTLIER) cc_final: 0.8771 (m-80)
REVERT: G  210 PHE cc_start: 0.5240 (OUTLIER) cc_final: 0.4892 (p90)
REVERT: V  210 PHE cc_start: 0.9200 (OUTLIER) cc_final: 0.8684 (t80)
REVERT: P  210 PHE cc_start: 0.8576 (OUTLIER) cc_final: 0.7518 (p90)
  outliers start: 34
  outliers final: 27
  residues processed: 39
  average time/residue: 0.0250
  time to fit residues: 1.2659
Evaluate side-chains
  43 residues out of total 120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 12
  time to evaluate  : 0.050 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  219 ASN
Chi-restraints excluded: chain L residue  219 ASN
Chi-restraints excluded: chain L residue  221 ASN
Chi-restraints excluded: chain M residue  219 ASN
Chi-restraints excluded: chain M residue  222 PHE
Chi-restraints excluded: chain K residue  214 ASP
Chi-restraints excluded: chain K residue  215 ASN
Chi-restraints excluded: chain G residue  210 PHE
Chi-restraints excluded: chain G residue  213 ASN
Chi-restraints excluded: chain G residue  214 ASP
Chi-restraints excluded: chain I residue  210 PHE
Chi-restraints excluded: chain I residue  214 ASP
Chi-restraints excluded: chain I residue  215 ASN
Chi-restraints excluded: chain U residue  214 ASP
Chi-restraints excluded: chain O residue  210 PHE
Chi-restraints excluded: chain O residue  214 ASP
Chi-restraints excluded: chain O residue  215 ASN
Chi-restraints excluded: chain R residue  214 ASP
Chi-restraints excluded: chain V residue  210 PHE
Chi-restraints excluded: chain P residue  210 PHE
Chi-restraints excluded: chain X residue  216 PHE
Chi-restraints excluded: chain D residue  214 ASP
Chi-restraints excluded: chain D residue  216 PHE
Chi-restraints excluded: chain A residue  220 ASP
Chi-restraints excluded: chain B residue  221 ASN
Chi-restraints excluded: chain N residue  220 ASP
Chi-restraints excluded: chain J residue  213 ASN
Chi-restraints excluded: chain F residue  210 PHE
Chi-restraints excluded: chain H residue  214 ASP
Chi-restraints excluded: chain W residue  213 ASN
Chi-restraints excluded: chain W residue  216 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 1
   random chunks:
   chunk 0 optimal weight:    1.9990
   overall best weight:   50.0000

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

Flipped N/Q/H residues before XYZ refinement:
** M 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** W 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.082098 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.067572 restraints weight = 4582.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.068311 restraints weight = 3323.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.068837 restraints weight = 2728.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.069120 restraints weight = 2387.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.069226 restraints weight = 2204.774|
|-----------------------------------------------------------------------------|
r_work (final): 0.3210
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8655
moved from start:          0.7776

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.051   0.242   1512  Z= 2.413
  Angle     :  2.495  19.045   1968  Z= 1.398
  Chirality :  0.151   0.399    120
  Planarity :  0.014   0.048    312
  Dihedral  : 16.230  48.762    192
  Min Nonbonded Distance : 2.122

Molprobity Statistics.
  All-atom Clashscore : 73.21
  Ramachandran Plot:
    Outliers :  2.38 %
    Allowed  : 55.95 %
    Favored  : 41.67 %
  Rotamer:
    Outliers : 27.50 %
    Allowed  : 30.00 %
    Favored  : 42.50 %
  Cbeta Deviations :  1.67 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 9.90 %

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: -7.57 (0.39), residues: 168
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -5.77 (0.29), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.046   0.009   PHE Q 216 

Details of bonding type rmsd
  covalent geometry    : bond        0.05103 ( 1512)
  covalent geometry    : angle       2.49501 ( 1968)

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

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

  336 Ramachandran restraints generated.
    168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  336 Ramachandran restraints generated.
    168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 12
  time to evaluate  : 0.092 
Fit side-chains
   revert: symmetry clash
REVERT: M  222 PHE cc_start: 0.9086 (OUTLIER) cc_final: 0.8774 (m-80)
REVERT: G  210 PHE cc_start: 0.5256 (OUTLIER) cc_final: 0.4898 (p90)
REVERT: V  210 PHE cc_start: 0.9198 (OUTLIER) cc_final: 0.8680 (t80)
REVERT: P  210 PHE cc_start: 0.8564 (OUTLIER) cc_final: 0.7537 (p90)
  outliers start: 33
  outliers final: 27
  residues processed: 38
  average time/residue: 0.0257
  time to fit residues: 1.2942
Evaluate side-chains
  43 residues out of total 120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 12
  time to evaluate  : 0.050 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  219 ASN
Chi-restraints excluded: chain L residue  219 ASN
Chi-restraints excluded: chain L residue  221 ASN
Chi-restraints excluded: chain M residue  219 ASN
Chi-restraints excluded: chain M residue  222 PHE
Chi-restraints excluded: chain K residue  214 ASP
Chi-restraints excluded: chain K residue  215 ASN
Chi-restraints excluded: chain G residue  210 PHE
Chi-restraints excluded: chain G residue  213 ASN
Chi-restraints excluded: chain G residue  214 ASP
Chi-restraints excluded: chain I residue  210 PHE
Chi-restraints excluded: chain I residue  214 ASP
Chi-restraints excluded: chain I residue  215 ASN
Chi-restraints excluded: chain U residue  214 ASP
Chi-restraints excluded: chain O residue  210 PHE
Chi-restraints excluded: chain O residue  214 ASP
Chi-restraints excluded: chain O residue  215 ASN
Chi-restraints excluded: chain R residue  214 ASP
Chi-restraints excluded: chain V residue  210 PHE
Chi-restraints excluded: chain P residue  210 PHE
Chi-restraints excluded: chain X residue  216 PHE
Chi-restraints excluded: chain D residue  214 ASP
Chi-restraints excluded: chain D residue  216 PHE
Chi-restraints excluded: chain A residue  220 ASP
Chi-restraints excluded: chain B residue  221 ASN
Chi-restraints excluded: chain N residue  220 ASP
Chi-restraints excluded: chain J residue  213 ASN
Chi-restraints excluded: chain F residue  210 PHE
Chi-restraints excluded: chain H residue  214 ASP
Chi-restraints excluded: chain W residue  213 ASN
Chi-restraints excluded: chain W residue  216 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 1
   random chunks:
   chunk 0 optimal weight:    1.9990
   overall best weight:   50.0000

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

Flipped N/Q/H residues before XYZ refinement:
** M 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** W 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.081962 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.067460 restraints weight = 4582.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.068034 restraints weight = 3299.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.068639 restraints weight = 2785.226|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.068877 restraints weight = 2435.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.068877 restraints weight = 2264.718|
|-----------------------------------------------------------------------------|
r_work (final): 0.3203
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8659
moved from start:          0.7778

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.051   0.242   1512  Z= 2.415
  Angle     :  2.496  19.047   1968  Z= 1.398
  Chirality :  0.151   0.399    120
  Planarity :  0.014   0.046    312
  Dihedral  : 16.247  48.907    192
  Min Nonbonded Distance : 2.122

Molprobity Statistics.
  All-atom Clashscore : 73.21
  Ramachandran Plot:
    Outliers :  2.38 %
    Allowed  : 55.36 %
    Favored  : 42.26 %
  Rotamer:
    Outliers : 27.50 %
    Allowed  : 30.00 %
    Favored  : 42.50 %
  Cbeta Deviations :  1.67 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 9.90 %

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: -7.56 (0.39), residues: 168
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -5.76 (0.30), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.046   0.009   PHE Q 216 

Details of bonding type rmsd
  covalent geometry    : bond        0.05107 ( 1512)
  covalent geometry    : angle       2.49589 ( 1968)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 328.49 seconds
wall clock time: 7 minutes 22.43 seconds (442.43 seconds total)