Starting phenix.real_space_refine
on Tue Mar  3 12:27:56 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8cvn_27010/03_2026/8cvn_27010.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8cvn_27010/03_2026/8cvn_27010.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8cvn_27010/03_2026/8cvn_27010.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8cvn_27010/03_2026/8cvn_27010.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8cvn_27010/03_2026/8cvn_27010.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8cvn_27010/03_2026/8cvn_27010.cif"
  }
  resolution = 2.4
  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=   0.005
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: 5
    Type Number    sf(0)   Gaussians
     P       4      5.49       5
     S      30      5.16       5
     C    2560      2.51       5
     N     690      2.21       5
     O     770      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4054
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1955
      Number of conformers: 1
      Conformer: "A"
        Number of residues, atoms: 256, 1955
          Classifications: {'peptide': 256}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 249}
    Chain: "B"
      Number of atoms: 1955
      Number of conformers: 1
      Conformer: "A"
        Number of residues, atoms: 256, 1955
          Classifications: {'peptide': 256}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 249}
    Chain: "A"
      Number of atoms: 72
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 72
          Unusual residues: {'NAI': 1, 'SWL': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 72
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 72
          Unusual residues: {'NAI': 1, 'SWL': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 1.23, per 1000 atoms: 0.30
  Number of scatterers: 4054
  At special positions: 0
  Unit cell: (95.16, 69.16, 56.68, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      30     16.00
     P       4     15.00
     O     770      8.00
     N     690      7.00
     C    2560      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: 0.35
  Conformation dependent library (CDL) restraints added in 129.7 milliseconds
  

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  928

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 2 sheets defined
      60.5% alpha, 12.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.09
  Creating SS restraints...
    Processing helix  chain 'A' and resid 16 through 29
    Processing helix  chain 'A' and resid 38 through 51
    Processing helix  chain 'A' and resid 54 through 56
      No H-bonds generated for 'chain 'A' and resid 54 through 56'
    Processing helix  chain 'A' and resid 67 through 83
    Processing helix  chain 'A' and resid 99 through 108
    Processing helix  chain 'A' and resid 108 through 123
      removed outlier: 3.650A  pdb=" N   TYR A 121 " --> pdb=" O   LEU A 117 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 124 through 127
    Processing helix  chain 'A' and resid 138 through 142
    Processing helix  chain 'A' and resid 148 through 173
      removed outlier: 3.654A  pdb=" N   LEU A 167 " --> pdb=" O   ARG A 163 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 188 through 195
      removed outlier: 3.520A  pdb=" N   LEU A 191 " --> pdb=" O   THR A 188 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 196 through 201
    Processing helix  chain 'A' and resid 202 through 205
      removed outlier: 4.489A  pdb=" N   GLU A 205 " --> pdb=" O   GLN A 202 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 202 through 205'
    Processing helix  chain 'A' and resid 206 through 218
      removed outlier: 4.447A  pdb=" N   ILE A 210 " --> pdb=" O   TYR A 206 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 221 through 235
      removed outlier: 4.179A  pdb=" N   ILE A 225 " --> pdb=" O   ASP A 221 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   ALA A 226 " --> pdb=" O   PRO A 222 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   ASN A 227 " --> pdb=" O   PRO A 223 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   GLY A 228 " --> pdb=" O   LEU A 224 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   LEU A 229 " --> pdb=" O   ILE A 225 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 16 through 29
    Processing helix  chain 'B' and resid 38 through 51
    Processing helix  chain 'B' and resid 54 through 56
      No H-bonds generated for 'chain 'B' and resid 54 through 56'
    Processing helix  chain 'B' and resid 67 through 83
    Processing helix  chain 'B' and resid 99 through 108
    Processing helix  chain 'B' and resid 108 through 123
      removed outlier: 3.552A  pdb=" N   TYR B 121 " --> pdb=" O   LEU B 117 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 124 through 127
    Processing helix  chain 'B' and resid 138 through 142
    Processing helix  chain 'B' and resid 148 through 173
      removed outlier: 3.654A  pdb=" N   LEU B 167 " --> pdb=" O   ARG B 163 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 188 through 195
      removed outlier: 3.521A  pdb=" N   LEU B 191 " --> pdb=" O   THR B 188 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 196 through 201
    Processing helix  chain 'B' and resid 202 through 205
      removed outlier: 4.490A  pdb=" N   GLU B 205 " --> pdb=" O   GLN B 202 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 202 through 205'
    Processing helix  chain 'B' and resid 206 through 218
      removed outlier: 4.447A  pdb=" N   ILE B 210 " --> pdb=" O   TYR B 206 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 221 through 235
      removed outlier: 3.545A  pdb=" N   GLY B 228 " --> pdb=" O   LEU B 224 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 58 through 62
      removed outlier: 6.488A  pdb=" N   VAL A  32 " --> pdb=" O   LEU A  59 " (cutoff:3.500A)
      removed outlier: 7.866A  pdb=" N   ILE A  61 " --> pdb=" O   VAL A  32 " (cutoff:3.500A)
      removed outlier: 6.028A  pdb=" N   LEU A  34 " --> pdb=" O   ILE A  61 " (cutoff:3.500A)
      removed outlier: 6.492A  pdb=" N   VAL A   7 " --> pdb=" O   ILE A  87 " (cutoff:3.500A)
      removed outlier: 8.091A  pdb=" N   VAL A  89 " --> pdb=" O   VAL A   7 " (cutoff:3.500A)
      removed outlier: 6.450A  pdb=" N   LEU A   9 " --> pdb=" O   VAL A  89 " (cutoff:3.500A)
      removed outlier: 6.406A  pdb=" N   LEU A  88 " --> pdb=" O   ILE A 134 " (cutoff:3.500A)
      removed outlier: 7.953A  pdb=" N   MET A 136 " --> pdb=" O   LEU A  88 " (cutoff:3.500A)
      removed outlier: 7.401A  pdb=" N   ASN A  90 " --> pdb=" O   MET A 136 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 62
      removed outlier: 3.586A  pdb=" N   ASP B  36 " --> pdb=" O   ILE B  61 " (cutoff:3.500A)
      removed outlier: 6.492A  pdb=" N   VAL B   7 " --> pdb=" O   ILE B  87 " (cutoff:3.500A)
      removed outlier: 8.091A  pdb=" N   VAL B  89 " --> pdb=" O   VAL B   7 " (cutoff:3.500A)
      removed outlier: 6.449A  pdb=" N   LEU B   9 " --> pdb=" O   VAL B  89 " (cutoff:3.500A)
      removed outlier: 6.406A  pdb=" N   LEU B  88 " --> pdb=" O   ILE B 134 " (cutoff:3.500A)
      removed outlier: 7.954A  pdb=" N   MET B 136 " --> pdb=" O   LEU B  88 " (cutoff:3.500A)
      removed outlier: 7.400A  pdb=" N   ASN B  90 " --> pdb=" O   MET B 136 " (cutoff:3.500A)

    223 hydrogen bonds defined for protein.
    625 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: 0.50

  Time building geometry restraints manager: 0.46 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 686
        1.30 -     1.43: 998
        1.43 -     1.55: 2380
        1.55 -     1.68: 16
        1.68 -     1.81: 48
  Bond restraints: 4128
  Sorted by residual:
  bond pdb=" O1  SWL B 302 "
       pdb=" S3  SWL B 302 "
    ideal  model  delta    sigma   weight residual
    2.267  1.645  0.622 2.00e-02 2.50e+03 9.66e+02
  bond pdb=" O1  SWL A 302 "
       pdb=" S3  SWL A 302 "
    ideal  model  delta    sigma   weight residual
    2.267  1.646  0.621 2.00e-02 2.50e+03 9.63e+02
  bond pdb=" C   SER A 123 "
       pdb=" O   SER A 123 "
    ideal  model  delta    sigma   weight residual
    1.234  1.323 -0.089 1.19e-02 7.06e+03 5.54e+01
  bond pdb=" C   SER B 123 "
       pdb=" O   SER B 123 "
    ideal  model  delta    sigma   weight residual
    1.234  1.322 -0.088 1.19e-02 7.06e+03 5.44e+01
  bond pdb=" C   CYS B  63 "
       pdb=" N   ASP B  64 "
    ideal  model  delta    sigma   weight residual
    1.330  1.416 -0.086 1.42e-02 4.96e+03 3.65e+01
  ... (remaining 4123 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.48: 5494
        4.48 -     8.95: 98
        8.95 -    13.43: 8
       13.43 -    17.90: 0
       17.90 -    22.38: 4
  Bond angle restraints: 5604
  Sorted by residual:
  angle pdb=" N   SER A 123 "
        pdb=" CA ASER A 123 "
        pdb=" C   SER A 123 "
      ideal   model   delta    sigma   weight residual
     110.23  123.25  -13.02 1.45e+00 4.76e-01 8.06e+01
  angle pdb=" N   SER B 123 "
        pdb=" CA ASER B 123 "
        pdb=" C   SER B 123 "
      ideal   model   delta    sigma   weight residual
     110.23  123.05  -12.82 1.45e+00 4.76e-01 7.81e+01
  angle pdb=" C16 SWL B 302 "
        pdb=" S3  SWL B 302 "
        pdb=" O1  SWL B 302 "
      ideal   model   delta    sigma   weight residual
      88.25  110.63  -22.38 3.00e+00 1.11e-01 5.56e+01
  angle pdb=" C16 SWL A 302 "
        pdb=" S3  SWL A 302 "
        pdb=" O1  SWL A 302 "
      ideal   model   delta    sigma   weight residual
      88.25  110.62  -22.37 3.00e+00 1.11e-01 5.56e+01
  angle pdb=" C   PRO A 222 "
        pdb=" CA  PRO A 222 "
        pdb=" CB  PRO A 222 "
      ideal   model   delta    sigma   weight residual
     110.92  119.76   -8.84 1.22e+00 6.72e-01 5.25e+01
  ... (remaining 5599 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.30: 2093
       16.30 -    32.61: 294
       32.61 -    48.91: 88
       48.91 -    65.21: 39
       65.21 -    81.51: 14
  Dihedral angle restraints: 2528
    sinusoidal: 1074
      harmonic: 1454
  Sorted by residual:
  dihedral pdb=" C   PRO A 222 "
           pdb=" N   PRO A 222 "
           pdb=" CA  PRO A 222 "
           pdb=" CB  PRO A 222 "
      ideal   model   delta  harmonic     sigma   weight residual
    -120.70 -133.98   13.28     0      2.50e+00 1.60e-01 2.82e+01
  dihedral pdb=" C   ASN B 173 "
           pdb=" N   ASN B 173 "
           pdb=" CA  ASN B 173 "
           pdb=" CB  ASN B 173 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -134.78   12.18     0      2.50e+00 1.60e-01 2.37e+01
  dihedral pdb=" C   ASN A 173 "
           pdb=" N   ASN A 173 "
           pdb=" CA  ASN A 173 "
           pdb=" CB  ASN A 173 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -134.33   11.73     0      2.50e+00 1.60e-01 2.20e+01
  ... (remaining 2525 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.569: 631
       0.569 -    1.137: 1
       1.137 -    1.706: 0
       1.706 -    2.275: 0
       2.275 -    2.844: 2
  Chirality restraints: 634
  Sorted by residual:
  chirality pdb=" S3  SWL B 302 "
            pdb=" C10 SWL B 302 "
            pdb=" C16 SWL B 302 "
            pdb=" O1  SWL B 302 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -7.07   -4.22   -2.84 2.00e-01 2.50e+01 2.02e+02
  chirality pdb=" S3  SWL A 302 "
            pdb=" C10 SWL A 302 "
            pdb=" C16 SWL A 302 "
            pdb=" O1  SWL A 302 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -7.07   -4.23   -2.84 2.00e-01 2.50e+01 2.02e+02
  chirality pdb=" CA  PRO A 222 "
            pdb=" N   PRO A 222 "
            pdb=" C   PRO A 222 "
            pdb=" CB  PRO A 222 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.10    0.62 2.00e-01 2.50e+01 9.62e+00
  ... (remaining 631 not shown)

  Planarity restraints: 710
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU B 195 "   -0.016 2.00e-02 2.50e+03   3.36e-02 1.13e+01
        pdb=" C   GLU B 195 "    0.058 2.00e-02 2.50e+03
        pdb=" O   GLU B 195 "   -0.022 2.00e-02 2.50e+03
        pdb=" N   LYS B 196 "   -0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU A 195 "    0.014 2.00e-02 2.50e+03   2.82e-02 7.93e+00
        pdb=" C   GLU A 195 "   -0.049 2.00e-02 2.50e+03
        pdb=" O   GLU A 195 "    0.019 2.00e-02 2.50e+03
        pdb=" N   LYS A 196 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  CYS B 152 "    0.012 2.00e-02 2.50e+03   2.54e-02 6.45e+00
        pdb=" C   CYS B 152 "   -0.044 2.00e-02 2.50e+03
        pdb=" O   CYS B 152 "    0.017 2.00e-02 2.50e+03
        pdb=" N   ALA B 153 "    0.015 2.00e-02 2.50e+03
  ... (remaining 707 not shown)

  Histogram of nonbonded interaction distances:
        2.54 -     3.01: 2134
        3.01 -     3.48: 3957
        3.48 -     3.95: 6653
        3.95 -     4.43: 7969
        4.43 -     4.90: 12283
  Nonbonded interactions: 32996
  Sorted by model distance:
  nonbonded pdb=" O   LEU B 178 "
            pdb=" OD1 ASN B 179 "
     model   vdw
     2.536 3.040
  nonbonded pdb=" O   LEU A 178 "
            pdb=" OD1 ASN A 179 "
     model   vdw
     2.536 3.040
  nonbonded pdb=" O   GLN B  70 "
            pdb=" OG1 THR B  74 "
     model   vdw
     2.547 3.040
  nonbonded pdb=" O   TYR A 151 "
            pdb=" OG  SER A 154 "
     model   vdw
     2.584 3.040
  nonbonded pdb=" O   GLN A  70 "
            pdb=" OG1 THR A  74 "
     model   vdw
     2.586 3.040
  ... (remaining 32991 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  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=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             5.080
  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:          0.110
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.670
  Find NCS groups from input model:        0.030
  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:7.390
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.310
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8212
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      :  0.018   0.622   4128  Z= 0.989
  Angle     :  1.467  22.376   5604  Z= 0.909
  Chirality :  0.177   2.844    634
  Planarity :  0.005   0.034    710
  Dihedral  : 18.480  81.509   1600
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 1.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 19.81 %
    Favored  : 78.99 %
  Cbeta Deviations :  0.65 %
  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:  0.60 (0.37), residues: 508
  helix:  1.02 (0.33), residues: 258
  sheet:  0.63 (0.47), residues: 108
  loop : -0.78 (0.47), residues: 142

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  72 
 TYR   0.019   0.002   TYR A 121 
 PHE   0.035   0.003   PHE A  75 
 TRP   0.013   0.002   TRP B 100 
 HIS   0.004   0.001   HIS A 156 

Details of bonding type rmsd
  covalent geometry    : bond        0.01752 ( 4128)
  covalent geometry    : angle       1.46720 ( 5604)
  hydrogen bonds       : bond        0.21904 (  223)
  hydrogen bonds       : angle       6.53955 (  625)

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

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

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 76
  time to evaluate  : 0.156 
Fit side-chains
  outliers start: 5
  outliers final: 0
  residues processed: 77
  average time/residue: 0.7646
  time to fit residues: 60.2486
Evaluate side-chains
  38 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 38
  time to evaluate  : 0.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 24 optimal weight:    0.6980
   chunk 48 optimal weight:    0.0870
   chunk 26 optimal weight:    0.5980
   chunk 2 optimal weight:    0.0970
   chunk 16 optimal weight:    0.5980
   chunk 32 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9990
   chunk 25 optimal weight:    0.5980
   chunk 19 optimal weight:    0.9990
   chunk 30 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   overall best weight:    0.3956

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

Flipped N/Q/H residues before XYZ refinement:
A  81 HIS
A  90 ASN
A 148 GLN
B  81 HIS
B  90 ASN
B 148 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.096342 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.088098 restraints weight = 5891.110|
|-----------------------------------------------------------------------------|
r_work (start): 0.3090 rms_B_bonded: 2.09
r_work: 0.2964 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.2840 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.2840
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2828
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2828 r_free = 0.2828    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2824 r_free = 0.2824    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.57   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2824
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8256
moved from start:          0.2415

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4128  Z= 0.120
  Angle     :  0.484   5.901   5604  Z= 0.256
  Chirality :  0.041   0.126    634
  Planarity :  0.003   0.044    710
  Dihedral  :  9.430  85.064    686
  Min Nonbonded Distance : 2.618

Molprobity Statistics.
  All-atom Clashscore : 2.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 21.74 %
    Favored  : 75.12 %
  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 (0.39), residues: 508
  helix:  1.97 (0.35), residues: 260
  sheet:  0.74 (0.50), residues: 108
  loop : -0.06 (0.51), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B  84 
 TYR   0.010   0.001   TYR A 151 
 PHE   0.007   0.001   PHE A  82 
 TRP   0.006   0.001   TRP B 100 
 HIS   0.003   0.001   HIS A 252 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 4128)
  covalent geometry    : angle       0.48449 ( 5604)
  hydrogen bonds       : bond        0.04718 (  223)
  hydrogen bonds       : angle       4.31855 (  625)

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

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

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 44
  time to evaluate  : 0.143 
Fit side-chains
REVERT: A    3 VAL cc_start: 0.8422 (p) cc_final: 0.8143 (t)
REVERT: B  197 GLU cc_start: 0.7316 (OUTLIER) cc_final: 0.7078 (tm-30)
  outliers start: 13
  outliers final: 2
  residues processed: 49
  average time/residue: 0.6506
  time to fit residues: 32.8550
Evaluate side-chains
  43 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 40
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain B residue   58 THR
Chi-restraints excluded: chain B residue  197 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 18 optimal weight:    0.0470
   chunk 48 optimal weight:    0.5980
   chunk 49 optimal weight:    0.6980
   chunk 26 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9980
   chunk 45 optimal weight:    0.0370
   chunk 32 optimal weight:    1.9990
   chunk 44 optimal weight:    0.7980
   chunk 4 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   overall best weight:    0.4356

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.091926 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.084030 restraints weight = 5989.894|
|-----------------------------------------------------------------------------|
r_work (start): 0.3031 rms_B_bonded: 2.07
r_work: 0.2907 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.2783 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.2783
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2784
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2784 r_free = 0.2784    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.57   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2784 r_free = 0.2784    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.63   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2784
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8255
moved from start:          0.2942

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4128  Z= 0.112
  Angle     :  0.439   5.487   5604  Z= 0.235
  Chirality :  0.040   0.126    634
  Planarity :  0.003   0.043    710
  Dihedral  :  8.918  89.203    686
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 2.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 23.91 %
    Favored  : 73.91 %
  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:  1.92 (0.40), residues: 508
  helix:  2.22 (0.36), residues: 260
  sheet:  0.61 (0.50), residues: 108
  loop :  0.10 (0.54), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  84 
 TYR   0.007   0.001   TYR B 151 
 PHE   0.006   0.001   PHE A  82 
 TRP   0.006   0.001   TRP B 100 
 HIS   0.003   0.001   HIS A 252 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 4128)
  covalent geometry    : angle       0.43890 ( 5604)
  hydrogen bonds       : bond        0.04378 (  223)
  hydrogen bonds       : angle       3.98785 (  625)

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

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

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 48
  time to evaluate  : 0.125 
Fit side-chains
REVERT: A    3 VAL cc_start: 0.8568 (p) cc_final: 0.8304 (t)
REVERT: A   84 ARG cc_start: 0.8418 (ptp90) cc_final: 0.7861 (ptt90)
REVERT: B    3 VAL cc_start: 0.8697 (p) cc_final: 0.8420 (t)
REVERT: B   84 ARG cc_start: 0.8436 (ptp90) cc_final: 0.7871 (ptt90)
  outliers start: 9
  outliers final: 5
  residues processed: 52
  average time/residue: 0.6024
  time to fit residues: 32.3834
Evaluate side-chains
  47 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 42
  time to evaluate  : 0.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 GLN
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  248 SER
Chi-restraints excluded: chain B residue   58 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 7 optimal weight:    0.8980
   chunk 24 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9990
   chunk 26 optimal weight:    1.9990
   chunk 22 optimal weight:    0.8980
   chunk 9 optimal weight:    0.0980
   chunk 37 optimal weight:    0.6980
   chunk 29 optimal weight:    0.9990
   chunk 8 optimal weight:    1.9990
   chunk 10 optimal weight:    0.6980
   chunk 14 optimal weight:    2.9990
   overall best weight:    0.6580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3098 r_free = 0.3098 target = 0.088381 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.080787 restraints weight = 6057.865|
|-----------------------------------------------------------------------------|
r_work (start): 0.2970 rms_B_bonded: 2.04
r_work: 0.2842 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.2720 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.2720
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2719
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2719 r_free = 0.2719    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.63   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2719 r_free = 0.2719    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.65   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2719
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8351
moved from start:          0.3140

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   4128  Z= 0.141
  Angle     :  0.459   5.316   5604  Z= 0.244
  Chirality :  0.040   0.125    634
  Planarity :  0.004   0.043    710
  Dihedral  :  8.925  80.689    686
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 2.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 22.22 %
    Favored  : 74.64 %
  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:  1.80 (0.40), residues: 508
  helix:  2.16 (0.35), residues: 260
  sheet:  0.41 (0.50), residues: 108
  loop :  0.08 (0.55), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  84 
 TYR   0.007   0.001   TYR B 151 
 PHE   0.006   0.001   PHE A  82 
 TRP   0.007   0.001   TRP B 100 
 HIS   0.003   0.001   HIS B 156 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 4128)
  covalent geometry    : angle       0.45859 ( 5604)
  hydrogen bonds       : bond        0.04966 (  223)
  hydrogen bonds       : angle       4.03285 (  625)

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

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

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 48
  time to evaluate  : 0.156 
Fit side-chains
REVERT: A    3 VAL cc_start: 0.8683 (p) cc_final: 0.8390 (t)
REVERT: A   84 ARG cc_start: 0.8397 (ptp90) cc_final: 0.7865 (ptt90)
REVERT: B    3 VAL cc_start: 0.8813 (p) cc_final: 0.8526 (t)
REVERT: B   84 ARG cc_start: 0.8413 (ptp90) cc_final: 0.7848 (ptt90)
  outliers start: 13
  outliers final: 6
  residues processed: 54
  average time/residue: 0.6015
  time to fit residues: 33.5810
Evaluate side-chains
  51 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 45
  time to evaluate  : 0.145 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 GLN
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  248 SER
Chi-restraints excluded: chain B residue   58 THR
Chi-restraints excluded: chain B residue  248 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 46 optimal weight:    0.0870
   chunk 47 optimal weight:    0.8980
   chunk 29 optimal weight:    0.7980
   chunk 11 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9980
   chunk 10 optimal weight:    0.5980
   chunk 4 optimal weight:    0.9990
   chunk 1 optimal weight:    1.9990
   chunk 24 optimal weight:    0.8980
   chunk 39 optimal weight:    0.8980
   chunk 5 optimal weight:    0.9990
   overall best weight:    0.6558

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.087885 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.2985 r_free = 0.2985 target = 0.080314 restraints weight = 6087.265|
|-----------------------------------------------------------------------------|
r_work (start): 0.2967 rms_B_bonded: 2.03
r_work: 0.2840 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.2718 rms_B_bonded: 4.20 restraints_weight: 0.2500
r_work (final): 0.2718
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2724
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2724 r_free = 0.2724    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.65   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2724 r_free = 0.2724    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.69   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2724
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8346
moved from start:          0.3276

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   4128  Z= 0.139
  Angle     :  0.448   5.226   5604  Z= 0.238
  Chirality :  0.040   0.123    634
  Planarity :  0.004   0.043    710
  Dihedral  :  8.726  71.557    686
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 2.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  : 22.22 %
    Favored  : 74.15 %
  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:  1.77 (0.40), residues: 508
  helix:  2.17 (0.35), residues: 260
  sheet:  0.34 (0.50), residues: 108
  loop :  0.07 (0.55), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  84 
 TYR   0.007   0.001   TYR B 151 
 PHE   0.005   0.001   PHE A  82 
 TRP   0.006   0.001   TRP B 100 
 HIS   0.003   0.001   HIS A 252 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 4128)
  covalent geometry    : angle       0.44786 ( 5604)
  hydrogen bonds       : bond        0.04794 (  223)
  hydrogen bonds       : angle       4.01543 (  625)

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

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

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 45
  time to evaluate  : 0.101 
Fit side-chains
REVERT: A    3 VAL cc_start: 0.8704 (p) cc_final: 0.8400 (t)
REVERT: A   84 ARG cc_start: 0.8383 (ptp90) cc_final: 0.7864 (ptt90)
REVERT: B    3 VAL cc_start: 0.8804 (p) cc_final: 0.8496 (t)
REVERT: B   84 ARG cc_start: 0.8407 (ptp90) cc_final: 0.7844 (ptt90)
  outliers start: 15
  outliers final: 7
  residues processed: 53
  average time/residue: 0.6007
  time to fit residues: 32.8635
Evaluate side-chains
  51 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 44
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   63 CYS
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  248 SER
Chi-restraints excluded: chain B residue   58 THR
Chi-restraints excluded: chain B residue  219 ILE
Chi-restraints excluded: chain B residue  248 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 42 optimal weight:    0.0770
   chunk 0 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9990
   chunk 23 optimal weight:    1.9990
   chunk 47 optimal weight:    0.3980
   chunk 10 optimal weight:    0.9980
   chunk 45 optimal weight:    0.6980
   chunk 33 optimal weight:    0.7980
   chunk 9 optimal weight:    1.9990
   chunk 41 optimal weight:    0.5980
   overall best weight:    0.5138

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.088961 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2998 r_free = 0.2998 target = 0.081317 restraints weight = 6214.981|
|-----------------------------------------------------------------------------|
r_work (start): 0.2989 rms_B_bonded: 2.06
r_work: 0.2861 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.2739 rms_B_bonded: 4.28 restraints_weight: 0.2500
r_work (final): 0.2739
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2739
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2739 r_free = 0.2739    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.69   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2739 r_free = 0.2739    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.68   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2739
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8301
moved from start:          0.3358

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   4128  Z= 0.117
  Angle     :  0.419   5.171   5604  Z= 0.224
  Chirality :  0.040   0.125    634
  Planarity :  0.004   0.043    710
  Dihedral  :  8.409  63.159    686
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 3.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.18 %
    Favored  : 98.82 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 23.19 %
    Favored  : 73.91 %
  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:  1.85 (0.40), residues: 508
  helix:  2.28 (0.35), residues: 260
  sheet:  0.35 (0.51), residues: 108
  loop :  0.01 (0.55), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  84 
 TYR   0.006   0.001   TYR B 151 
 PHE   0.006   0.001   PHE A  82 
 TRP   0.006   0.001   TRP B 100 
 HIS   0.003   0.001   HIS A 252 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 4128)
  covalent geometry    : angle       0.41890 ( 5604)
  hydrogen bonds       : bond        0.04312 (  223)
  hydrogen bonds       : angle       3.87427 (  625)

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

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

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 46
  time to evaluate  : 0.151 
Fit side-chains
REVERT: A    3 VAL cc_start: 0.8698 (p) cc_final: 0.8383 (t)
REVERT: A   84 ARG cc_start: 0.8383 (ptp90) cc_final: 0.7811 (ptt90)
REVERT: B    3 VAL cc_start: 0.8788 (p) cc_final: 0.8471 (t)
REVERT: B   84 ARG cc_start: 0.8391 (ptp90) cc_final: 0.7832 (ptt90)
  outliers start: 12
  outliers final: 7
  residues processed: 51
  average time/residue: 0.5479
  time to fit residues: 28.8952
Evaluate side-chains
  51 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 44
  time to evaluate  : 0.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   63 CYS
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  248 SER
Chi-restraints excluded: chain B residue   58 THR
Chi-restraints excluded: chain B residue  213 MET
Chi-restraints excluded: chain B residue  248 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 16 optimal weight:    0.9980
   chunk 29 optimal weight:    0.9990
   chunk 23 optimal weight:    0.8980
   chunk 25 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   chunk 30 optimal weight:    0.0980
   chunk 0 optimal weight:    2.9990
   chunk 17 optimal weight:    0.5980
   chunk 20 optimal weight:    0.9980
   chunk 14 optimal weight:    1.9990
   chunk 11 optimal weight:    0.5980
   overall best weight:    0.6380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.087933 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2989 r_free = 0.2989 target = 0.080340 restraints weight = 6274.940|
|-----------------------------------------------------------------------------|
r_work (start): 0.2965 rms_B_bonded: 2.06
r_work: 0.2836 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.2714 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.2714
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2718
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2718 r_free = 0.2718    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.68   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2718 r_free = 0.2718    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.69   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2718
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8380
moved from start:          0.3367

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   4128  Z= 0.136
  Angle     :  0.435   5.189   5604  Z= 0.231
  Chirality :  0.040   0.123    634
  Planarity :  0.004   0.043    710
  Dihedral  :  8.262  62.231    686
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 3.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 23.67 %
    Favored  : 73.67 %
  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:  1.80 (0.40), residues: 508
  helix:  2.27 (0.35), residues: 260
  sheet:  0.27 (0.50), residues: 108
  loop : -0.02 (0.55), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  84 
 TYR   0.007   0.001   TYR B 151 
 PHE   0.004   0.001   PHE A  82 
 TRP   0.006   0.001   TRP B 100 
 HIS   0.003   0.001   HIS A 156 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 4128)
  covalent geometry    : angle       0.43513 ( 5604)
  hydrogen bonds       : bond        0.04687 (  223)
  hydrogen bonds       : angle       3.94100 (  625)

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

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

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 45
  time to evaluate  : 0.131 
Fit side-chains
REVERT: A    3 VAL cc_start: 0.8749 (p) cc_final: 0.8431 (t)
REVERT: A   84 ARG cc_start: 0.8411 (ptp90) cc_final: 0.7873 (ptt90)
REVERT: B    3 VAL cc_start: 0.8839 (p) cc_final: 0.8518 (t)
REVERT: B   84 ARG cc_start: 0.8422 (ptp90) cc_final: 0.7895 (ptt90)
  outliers start: 11
  outliers final: 9
  residues processed: 50
  average time/residue: 0.6034
  time to fit residues: 31.1581
Evaluate side-chains
  53 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 44
  time to evaluate  : 0.173 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   63 CYS
Chi-restraints excluded: chain A residue  172 MET
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  248 SER
Chi-restraints excluded: chain B residue   58 THR
Chi-restraints excluded: chain B residue  213 MET
Chi-restraints excluded: chain B residue  219 ILE
Chi-restraints excluded: chain B residue  248 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 1 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9990
   chunk 24 optimal weight:    0.8980
   chunk 31 optimal weight:    0.9990
   chunk 10 optimal weight:    0.9990
   chunk 12 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 7 optimal weight:    0.7980
   chunk 42 optimal weight:    0.0170
   chunk 48 optimal weight:    0.9980
   chunk 11 optimal weight:    0.6980
   overall best weight:    0.6818

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.087490 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.080015 restraints weight = 6071.659|
|-----------------------------------------------------------------------------|
r_work (start): 0.2963 rms_B_bonded: 2.00
r_work: 0.2838 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.2716 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.2716
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2706
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2706 r_free = 0.2706    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.69   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2706 r_free = 0.2706    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.67   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2706
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8316
moved from start:          0.3379

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   4128  Z= 0.142
  Angle     :  0.440   5.176   5604  Z= 0.234
  Chirality :  0.040   0.124    634
  Planarity :  0.004   0.043    710
  Dihedral  :  8.229  61.958    686
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 3.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 22.95 %
    Favored  : 73.67 %
  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:  1.77 (0.40), residues: 508
  helix:  2.25 (0.35), residues: 260
  sheet:  0.27 (0.50), residues: 108
  loop : -0.05 (0.54), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  84 
 TYR   0.007   0.001   TYR B 151 
 PHE   0.005   0.001   PHE A  82 
 TRP   0.006   0.001   TRP B 100 
 HIS   0.003   0.001   HIS B 156 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 4128)
  covalent geometry    : angle       0.44007 ( 5604)
  hydrogen bonds       : bond        0.04833 (  223)
  hydrogen bonds       : angle       3.97977 (  625)

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

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

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 44
  time to evaluate  : 0.152 
Fit side-chains
REVERT: A    3 VAL cc_start: 0.8691 (p) cc_final: 0.8375 (t)
REVERT: A   84 ARG cc_start: 0.8368 (ptp90) cc_final: 0.7815 (ptt90)
REVERT: A  243 MET cc_start: 0.9281 (ttm) cc_final: 0.9062 (ttm)
REVERT: B    3 VAL cc_start: 0.8780 (p) cc_final: 0.8460 (t)
REVERT: B   84 ARG cc_start: 0.8373 (ptp90) cc_final: 0.7825 (ptt90)
REVERT: B  198 GLU cc_start: 0.7556 (mp0) cc_final: 0.7330 (pm20)
  outliers start: 14
  outliers final: 9
  residues processed: 52
  average time/residue: 0.5959
  time to fit residues: 31.9872
Evaluate side-chains
  53 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 44
  time to evaluate  : 0.108 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   63 CYS
Chi-restraints excluded: chain A residue  172 MET
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  248 SER
Chi-restraints excluded: chain B residue   58 THR
Chi-restraints excluded: chain B residue  213 MET
Chi-restraints excluded: chain B residue  219 ILE
Chi-restraints excluded: chain B residue  248 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 32 optimal weight:    0.8980
   chunk 13 optimal weight:    0.7980
   chunk 47 optimal weight:    0.5980
   chunk 19 optimal weight:    1.9990
   chunk 14 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 49 optimal weight:    1.9990
   chunk 42 optimal weight:    0.1980
   chunk 46 optimal weight:    0.9990
   chunk 6 optimal weight:    0.4980
   overall best weight:    0.5980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3098 r_free = 0.3098 target = 0.088067 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 22)----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.080459 restraints weight = 6195.792|
|-----------------------------------------------------------------------------|
r_work (start): 0.2969 rms_B_bonded: 2.04
r_work: 0.2842 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.2719 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.2719
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2712
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2712 r_free = 0.2712    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.67   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2712 r_free = 0.2712    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.66   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2712
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8317
moved from start:          0.3411

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   4128  Z= 0.129
  Angle     :  0.430   5.163   5604  Z= 0.229
  Chirality :  0.040   0.123    634
  Planarity :  0.004   0.043    710
  Dihedral  :  8.091  60.534    686
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 3.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 23.19 %
    Favored  : 74.40 %
  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 (0.40), residues: 508
  helix:  2.30 (0.35), residues: 260
  sheet:  0.29 (0.50), residues: 108
  loop : -0.07 (0.54), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  84 
 TYR   0.006   0.001   TYR B 151 
 PHE   0.004   0.001   PHE B  82 
 TRP   0.006   0.001   TRP B 100 
 HIS   0.002   0.001   HIS A 252 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 4128)
  covalent geometry    : angle       0.42980 ( 5604)
  hydrogen bonds       : bond        0.04582 (  223)
  hydrogen bonds       : angle       3.91165 (  625)

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

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

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 43
  time to evaluate  : 0.129 
Fit side-chains
REVERT: A    3 VAL cc_start: 0.8706 (p) cc_final: 0.8385 (t)
REVERT: A   84 ARG cc_start: 0.8376 (ptp90) cc_final: 0.7825 (ptt90)
REVERT: A  243 MET cc_start: 0.9290 (ttm) cc_final: 0.9089 (ttm)
REVERT: B    3 VAL cc_start: 0.8805 (p) cc_final: 0.8477 (t)
REVERT: B   84 ARG cc_start: 0.8388 (ptp90) cc_final: 0.7564 (ptm160)
REVERT: B  198 GLU cc_start: 0.7540 (mp0) cc_final: 0.7315 (pm20)
  outliers start: 10
  outliers final: 8
  residues processed: 48
  average time/residue: 0.5893
  time to fit residues: 29.1901
Evaluate side-chains
  51 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 43
  time to evaluate  : 0.112 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   63 CYS
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  248 SER
Chi-restraints excluded: chain B residue   58 THR
Chi-restraints excluded: chain B residue  213 MET
Chi-restraints excluded: chain B residue  219 ILE
Chi-restraints excluded: chain B residue  248 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 45 optimal weight:    0.6980
   chunk 46 optimal weight:    0.8980
   chunk 8 optimal weight:    1.9990
   chunk 35 optimal weight:    0.0050
   chunk 1 optimal weight:    1.9990
   chunk 39 optimal weight:    0.5980
   chunk 11 optimal weight:    0.5980
   chunk 3 optimal weight:    0.6980
   chunk 22 optimal weight:    1.9990
   chunk 34 optimal weight:    3.9990
   chunk 21 optimal weight:    0.9990
   overall best weight:    0.5194

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.088661 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.2999 r_free = 0.2999 target = 0.081101 restraints weight = 6102.439|
|-----------------------------------------------------------------------------|
r_work (start): 0.2979 rms_B_bonded: 2.02
r_work: 0.2855 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.2734 rms_B_bonded: 4.20 restraints_weight: 0.2500
r_work (final): 0.2734
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2756
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2756 r_free = 0.2756    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.66   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2756 r_free = 0.2756    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.62   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2756
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8297
moved from start:          0.3431

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   4128  Z= 0.117
  Angle     :  0.415   5.132   5604  Z= 0.222
  Chirality :  0.040   0.124    634
  Planarity :  0.004   0.043    710
  Dihedral  :  7.911  58.493    686
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 3.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 23.43 %
    Favored  : 74.15 %
  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:  1.86 (0.40), residues: 508
  helix:  2.35 (0.35), residues: 260
  sheet:  0.31 (0.50), residues: 108
  loop : -0.07 (0.54), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  84 
 TYR   0.006   0.001   TYR B 151 
 PHE   0.005   0.001   PHE B  82 
 TRP   0.006   0.001   TRP B 100 
 HIS   0.003   0.001   HIS B 252 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 4128)
  covalent geometry    : angle       0.41514 ( 5604)
  hydrogen bonds       : bond        0.04312 (  223)
  hydrogen bonds       : angle       3.84739 (  625)

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

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

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 45
  time to evaluate  : 0.137 
Fit side-chains
REVERT: A    3 VAL cc_start: 0.8695 (p) cc_final: 0.8370 (t)
REVERT: A   84 ARG cc_start: 0.8373 (ptp90) cc_final: 0.7813 (ptt90)
REVERT: B    3 VAL cc_start: 0.8802 (p) cc_final: 0.8472 (t)
REVERT: B   84 ARG cc_start: 0.8373 (ptp90) cc_final: 0.7560 (ptm160)
REVERT: B  198 GLU cc_start: 0.7523 (mp0) cc_final: 0.7315 (pm20)
REVERT: B  255 ASP cc_start: 0.8498 (t70) cc_final: 0.8141 (t70)
  outliers start: 10
  outliers final: 8
  residues processed: 51
  average time/residue: 0.5948
  time to fit residues: 31.4423
Evaluate side-chains
  52 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 44
  time to evaluate  : 0.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   63 CYS
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  248 SER
Chi-restraints excluded: chain B residue   58 THR
Chi-restraints excluded: chain B residue  213 MET
Chi-restraints excluded: chain B residue  219 ILE
Chi-restraints excluded: chain B residue  248 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 35 optimal weight:    0.2980
   chunk 16 optimal weight:    0.8980
   chunk 32 optimal weight:    0.8980
   chunk 38 optimal weight:    2.9990
   chunk 24 optimal weight:    0.4980
   chunk 39 optimal weight:    0.0980
   chunk 9 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9990
   chunk 31 optimal weight:    0.7980
   chunk 21 optimal weight:    0.9990
   chunk 37 optimal weight:    0.7980
   overall best weight:    0.4980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.088853 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.081249 restraints weight = 6149.029|
|-----------------------------------------------------------------------------|
r_work (start): 0.2980 rms_B_bonded: 2.04
r_work: 0.2858 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.2737 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.2737
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2735
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2735 r_free = 0.2735    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.62   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2735 r_free = 0.2735    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.66   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2735
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8317
moved from start:          0.3444

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   4128  Z= 0.114
  Angle     :  0.412   5.123   5604  Z= 0.220
  Chirality :  0.039   0.122    634
  Planarity :  0.004   0.043    710
  Dihedral  :  7.861  57.968    686
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 3.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 23.67 %
    Favored  : 74.15 %
  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:  1.89 (0.40), residues: 508
  helix:  2.37 (0.35), residues: 260
  sheet:  0.32 (0.50), residues: 108
  loop : -0.06 (0.54), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  84 
 TYR   0.006   0.001   TYR B 151 
 PHE   0.005   0.001   PHE A  82 
 TRP   0.006   0.001   TRP B 100 
 HIS   0.003   0.001   HIS A 252 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 4128)
  covalent geometry    : angle       0.41214 ( 5604)
  hydrogen bonds       : bond        0.04255 (  223)
  hydrogen bonds       : angle       3.83865 (  625)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1956.98 seconds
wall clock time: 33 minutes 56.35 seconds (2036.35 seconds total)