Starting phenix.real_space_refine
on Tue Feb 11 05:19:19 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8cvn_27010/02_2025/8cvn_27010.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8cvn_27010/02_2025/8cvn_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_27010/02_2025/8cvn_27010.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8cvn_27010/02_2025/8cvn_27010.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8cvn_27010/02_2025/8cvn_27010.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8cvn_27010/02_2025/8cvn_27010.cif"
  }
  resolution = 2.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 5.57, per 1000 atoms: 1.37
  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: 1.03
  Conformation dependent library (CDL) restraints added in 500.6 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: 0.49
  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: 1.18

  Time building geometry restraints manager: 1.18 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: 0.01
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:             9.250
  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:          0.900
  Check model and map are aligned:         0.000
  Set scattering table:                    0.000
  Process input model:                     15.880
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.030
  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:12.350
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.540
-------------------------------------------------------------------------------
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= 1.124
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.60 (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
 TRP   0.013   0.002   TRP B 100 
 HIS   0.004   0.001   HIS A 156 
 PHE   0.035   0.003   PHE A  75 
 TYR   0.019   0.002   TYR A 121 
 ARG   0.002   0.000   ARG A  72 

*********************** 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  : 0.464 
Fit side-chains
  outliers start: 5
  outliers final: 0
  residues processed: 77
  average time/residue: 1.5874
  time to fit residues: 125.4591
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  : 0.465 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 42 optimal weight:    0.7980
   chunk 37 optimal weight:    0.8980
   chunk 21 optimal weight:    0.5980
   chunk 12 optimal weight:    0.7980
   chunk 25 optimal weight:    1.9990
   chunk 20 optimal weight:    0.0870
   chunk 39 optimal weight:    0.7980
   chunk 15 optimal weight:    0.9980
   chunk 23 optimal weight:    0.1980
   chunk 29 optimal weight:    0.7980
   chunk 45 optimal weight:    0.5980
   overall best weight:    0.4558

-------------------------------------------------------------------------------
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 = 0.3192 r_free = 0.3192 target = 0.095300 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3081 r_free = 0.3081 target = 0.087149 restraints weight = 5843.654|
|-----------------------------------------------------------------------------|
r_work (start): 0.3068 rms_B_bonded: 2.07
r_work: 0.2942 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.2818 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.2818
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2820
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2820 r_free = 0.2820    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2816 r_free = 0.2816    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.61   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2816
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8266
moved from start:          0.2474

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= 0.182
  Angle     :  0.492   5.937   5604  Z= 0.259
  Chirality :  0.042   0.126    634
  Planarity :  0.003   0.045    710
  Dihedral  :  9.406  85.034    686
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 2.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  : 21.50 %
    Favored  : 74.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.69 (0.39), residues: 508
  helix:  1.95 (0.35), residues: 260
  sheet:  0.71 (0.50), residues: 108
  loop : -0.02 (0.52), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 100 
 HIS   0.003   0.001   HIS A 252 
 PHE   0.008   0.001   PHE A  82 
 TYR   0.010   0.001   TYR B 151 
 ARG   0.005   0.001   ARG B  84 

*********************** 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: 15
    poor density    : 42
  time to evaluate  : 0.467 
Fit side-chains
REVERT: A    3 VAL cc_start: 0.8436 (p) cc_final: 0.8155 (t)
REVERT: B  197 GLU cc_start: 0.7330 (OUTLIER) cc_final: 0.7100 (tm-30)
  outliers start: 15
  outliers final: 3
  residues processed: 49
  average time/residue: 1.5150
  time to fit residues: 76.6298
Evaluate side-chains
  43 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 39
  time to evaluate  : 0.468 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue  248 SER
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 12 optimal weight:    1.9990
   chunk 14 optimal weight:    2.9990
   chunk 9 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   chunk 47 optimal weight:    0.5980
   chunk 18 optimal weight:    1.9990
   chunk 20 optimal weight:    0.5980
   chunk 16 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9980
   overall best weight:    1.2384

-------------------------------------------------------------------------------
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 = 0.3043 r_free = 0.3043 target = 0.085694 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2937 r_free = 0.2937 target = 0.078064 restraints weight = 6098.944|
|-----------------------------------------------------------------------------|
r_work (start): 0.2932 rms_B_bonded: 2.01
r_work: 0.2803 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.2682 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.2682
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2684
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2684 r_free = 0.2684    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.61   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2684 r_free = 0.2684    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.66   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2684
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8356
moved from start:          0.3051

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.049   4128  Z= 0.368
  Angle     :  0.546   5.568   5604  Z= 0.288
  Chirality :  0.043   0.128    634
  Planarity :  0.004   0.045    710
  Dihedral  :  9.434  84.971    686
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 3.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 22.22 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.53 (0.40), residues: 508
  helix:  1.84 (0.35), residues: 260
  sheet:  0.34 (0.50), residues: 108
  loop :  0.16 (0.55), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 100 
 HIS   0.003   0.001   HIS A 156 
 PHE   0.006   0.001   PHE A  82 
 TYR   0.011   0.001   TYR B 216 
 ARG   0.003   0.000   ARG B  84 

*********************** 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
  60 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 46
  time to evaluate  : 0.445 
Fit side-chains
REVERT: A    3 VAL cc_start: 0.8631 (p) cc_final: 0.8363 (t)
REVERT: B    3 VAL cc_start: 0.8744 (p) cc_final: 0.8472 (t)
REVERT: B   84 ARG cc_start: 0.8380 (ptp90) cc_final: 0.7603 (ptt90)
  outliers start: 14
  outliers final: 7
  residues processed: 53
  average time/residue: 1.3018
  time to fit residues: 71.3801
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  : 0.420 
-------------------------------------------------------------------------------
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  207 LYS
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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 18 optimal weight:    1.9990
   chunk 24 optimal weight:    0.8980
   chunk 27 optimal weight:    0.2980
   chunk 38 optimal weight:    2.9990
   chunk 20 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9990
   chunk 39 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9990
   chunk 41 optimal weight:    0.9980
   chunk 36 optimal weight:    0.5980
   chunk 23 optimal weight:    0.9990
   overall best weight:    0.7582

-------------------------------------------------------------------------------
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 = 0.3082 r_free = 0.3082 target = 0.087024 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2973 r_free = 0.2973 target = 0.079565 restraints weight = 6119.025|
|-----------------------------------------------------------------------------|
r_work (start): 0.2972 rms_B_bonded: 2.02
r_work: 0.2844 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.2723 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.2723
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2730
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2730 r_free = 0.2730    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.66   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2730 r_free = 0.2730    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.61   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2730
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8398
moved from start:          0.3202

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   4128  Z= 0.240
  Angle     :  0.467   5.221   5604  Z= 0.249
  Chirality :  0.041   0.123    634
  Planarity :  0.004   0.045    710
  Dihedral  :  9.292  87.678    686
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 2.98
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.61 (0.40), residues: 508
  helix:  1.98 (0.35), residues: 260
  sheet:  0.21 (0.49), residues: 108
  loop :  0.16 (0.56), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 100 
 HIS   0.003   0.001   HIS A 156 
 PHE   0.006   0.001   PHE A  82 
 TYR   0.008   0.001   TYR B 216 
 ARG   0.005   0.001   ARG A  84 

*********************** 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
  55 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 45
  time to evaluate  : 0.445 
Fit side-chains
REVERT: A    3 VAL cc_start: 0.8731 (p) cc_final: 0.8429 (t)
REVERT: A   84 ARG cc_start: 0.8412 (ptp90) cc_final: 0.7883 (ptt90)
REVERT: B    3 VAL cc_start: 0.8820 (p) cc_final: 0.8517 (t)
REVERT: B   84 ARG cc_start: 0.8415 (ptp90) cc_final: 0.7893 (ptt90)
  outliers start: 10
  outliers final: 7
  residues processed: 51
  average time/residue: 1.2786
  time to fit residues: 67.5168
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  : 0.518 
-------------------------------------------------------------------------------
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  207 LYS
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
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 7 optimal weight:    1.9990
   chunk 13 optimal weight:    2.9990
   chunk 5 optimal weight:    0.8980
   chunk 48 optimal weight:    0.9980
   chunk 43 optimal weight:    2.9990
   chunk 49 optimal weight:    1.9990
   chunk 34 optimal weight:    0.1980
   chunk 27 optimal weight:    0.4980
   chunk 39 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9980
   chunk 18 optimal weight:    0.9990
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.3075 r_free = 0.3075 target = 0.086745 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2967 r_free = 0.2967 target = 0.079199 restraints weight = 6214.356|
|-----------------------------------------------------------------------------|
r_work (start): 0.2948 rms_B_bonded: 2.03
r_work: 0.2818 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.2696 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.2696
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2725
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2725 r_free = 0.2725    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.61   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2725 r_free = 0.2725    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.60   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2725
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8385
moved from start:          0.3306

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= 0.229
  Angle     :  0.450   5.156   5604  Z= 0.239
  Chirality :  0.040   0.124    634
  Planarity :  0.004   0.045    710
  Dihedral  :  8.862  78.747    686
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 2.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.18 %
    Favored  : 98.82 %
  Rotamer:
    Outliers :  4.11 %
    Allowed  : 21.26 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.66 (0.40), residues: 508
  helix:  2.07 (0.35), residues: 260
  sheet:  0.17 (0.49), residues: 108
  loop :  0.14 (0.56), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 100 
 HIS   0.003   0.001   HIS A 156 
 PHE   0.005   0.001   PHE A  82 
 TYR   0.007   0.001   TYR B 151 
 ARG   0.004   0.000   ARG A  84 

*********************** 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
  63 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 46
  time to evaluate  : 0.430 
Fit side-chains
REVERT: A    3 VAL cc_start: 0.8739 (p) cc_final: 0.8428 (t)
REVERT: A   84 ARG cc_start: 0.8434 (ptp90) cc_final: 0.7890 (ptt90)
REVERT: B    3 VAL cc_start: 0.8830 (p) cc_final: 0.8514 (t)
REVERT: B   84 ARG cc_start: 0.8411 (ptp90) cc_final: 0.7563 (ptm160)
  outliers start: 17
  outliers final: 7
  residues processed: 56
  average time/residue: 1.2420
  time to fit residues: 72.0886
Evaluate side-chains
  50 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 43
  time to evaluate  : 0.461 
-------------------------------------------------------------------------------
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  207 LYS
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 0 optimal weight:    2.9990
   chunk 18 optimal weight:    2.9990
   chunk 17 optimal weight:    0.5980
   chunk 32 optimal weight:    0.9980
   chunk 12 optimal weight:    0.9990
   chunk 6 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9980
   chunk 49 optimal weight:    0.5980
   chunk 14 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9980
   overall best weight:    0.8380

-------------------------------------------------------------------------------
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 = 0.3068 r_free = 0.3068 target = 0.086162 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2962 r_free = 0.2962 target = 0.078815 restraints weight = 6119.059|
|-----------------------------------------------------------------------------|
r_work (start): 0.2959 rms_B_bonded: 1.98
r_work: 0.2831 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.2712 rms_B_bonded: 4.13 restraints_weight: 0.2500
r_work (final): 0.2712
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2717
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2717 r_free = 0.2717    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.60   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2717 r_free = 0.2717    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.61   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2717
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8435
moved from start:          0.3329

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   4128  Z= 0.259
  Angle     :  0.458   5.157   5604  Z= 0.243
  Chirality :  0.041   0.128    634
  Planarity :  0.004   0.044    710
  Dihedral  :  8.647  73.983    686
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 2.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  : 21.50 %
    Favored  : 74.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.59 (0.40), residues: 508
  helix:  2.05 (0.35), residues: 260
  sheet:  0.06 (0.48), residues: 108
  loop :  0.11 (0.56), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 100 
 HIS   0.003   0.001   HIS A 156 
 PHE   0.005   0.001   PHE A  82 
 TYR   0.007   0.001   TYR B 151 
 ARG   0.004   0.000   ARG A  84 

*********************** 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
  57 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 42
  time to evaluate  : 0.457 
Fit side-chains
REVERT: A    3 VAL cc_start: 0.8783 (p) cc_final: 0.8465 (t)
REVERT: A   84 ARG cc_start: 0.8446 (ptp90) cc_final: 0.7925 (ptt90)
REVERT: B    3 VAL cc_start: 0.8855 (p) cc_final: 0.8529 (t)
REVERT: B   84 ARG cc_start: 0.8419 (ptp90) cc_final: 0.7616 (ptm160)
  outliers start: 15
  outliers final: 8
  residues processed: 51
  average time/residue: 1.2319
  time to fit residues: 65.2330
Evaluate side-chains
  49 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 41
  time to evaluate  : 0.502 
-------------------------------------------------------------------------------
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  207 LYS
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 8 optimal weight:    0.1980
   chunk 21 optimal weight:    0.9980
   chunk 23 optimal weight:    0.8980
   chunk 30 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9990
   chunk 49 optimal weight:    1.9990
   chunk 35 optimal weight:    0.6980
   chunk 28 optimal weight:    0.8980
   chunk 25 optimal weight:    0.5980
   chunk 3 optimal weight:    0.9980
   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 = 0.3083 r_free = 0.3083 target = 0.087136 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2978 r_free = 0.2978 target = 0.079729 restraints weight = 6161.662|
|-----------------------------------------------------------------------------|
r_work (start): 0.2953 rms_B_bonded: 1.98
r_work: 0.2827 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.2706 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.2706
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2734
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2734 r_free = 0.2734    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.61   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2734 r_free = 0.2734    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.61   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2734
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8376
moved from start:          0.3378

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= 0.212
  Angle     :  0.433   5.099   5604  Z= 0.231
  Chirality :  0.040   0.124    634
  Planarity :  0.004   0.044    710
  Dihedral  :  8.408  67.755    686
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 3.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 21.50 %
    Favored  : 75.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.68 (0.40), residues: 508
  helix:  2.16 (0.35), residues: 260
  sheet:  0.14 (0.48), residues: 108
  loop :  0.04 (0.55), residues: 140

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

*********************** 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
  54 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 41
  time to evaluate  : 0.446 
Fit side-chains
REVERT: A    3 VAL cc_start: 0.8752 (p) cc_final: 0.8432 (t)
REVERT: B    3 VAL cc_start: 0.8832 (p) cc_final: 0.8501 (t)
REVERT: B   84 ARG cc_start: 0.8394 (ptp90) cc_final: 0.7573 (ptm160)
  outliers start: 13
  outliers final: 7
  residues processed: 49
  average time/residue: 1.2510
  time to fit residues: 63.6893
Evaluate side-chains
  46 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 39
  time to evaluate  : 0.454 
-------------------------------------------------------------------------------
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  207 LYS
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 9 optimal weight:    2.9990
   chunk 43 optimal weight:    2.9990
   chunk 28 optimal weight:    0.6980
   chunk 31 optimal weight:    0.9990
   chunk 44 optimal weight:    0.8980
   chunk 15 optimal weight:    1.9990
   chunk 23 optimal weight:    0.0470
   chunk 12 optimal weight:    1.9990
   chunk 25 optimal weight:    2.9990
   chunk 19 optimal weight:    2.9990
   chunk 7 optimal weight:    0.7980
   overall best weight:    0.6880

-------------------------------------------------------------------------------
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 = 0.3081 r_free = 0.3081 target = 0.086852 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2975 r_free = 0.2975 target = 0.079480 restraints weight = 6093.874|
|-----------------------------------------------------------------------------|
r_work (start): 0.2953 rms_B_bonded: 1.96
r_work: 0.2826 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.2704 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.2704
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2731
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2731 r_free = 0.2731    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.61   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2731 r_free = 0.2731    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.60   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2731
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8357
moved from start:          0.3406

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= 0.220
  Angle     :  0.437   5.108   5604  Z= 0.232
  Chirality :  0.040   0.125    634
  Planarity :  0.004   0.044    710
  Dihedral  :  8.407  64.457    686
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 3.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 21.74 %
    Favored  : 75.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.69 (0.40), residues: 508
  helix:  2.19 (0.35), residues: 260
  sheet:  0.07 (0.48), residues: 108
  loop :  0.04 (0.55), residues: 140

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

*********************** 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
  54 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 42
  time to evaluate  : 0.428 
Fit side-chains
REVERT: A    3 VAL cc_start: 0.8741 (p) cc_final: 0.8421 (t)
REVERT: A   84 ARG cc_start: 0.8423 (ptp90) cc_final: 0.7858 (ptt90)
REVERT: B    3 VAL cc_start: 0.8813 (p) cc_final: 0.8481 (t)
REVERT: B   84 ARG cc_start: 0.8379 (ptp90) cc_final: 0.7561 (ptm160)
  outliers start: 12
  outliers final: 8
  residues processed: 49
  average time/residue: 1.1531
  time to fit residues: 58.7601
Evaluate side-chains
  50 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 42
  time to evaluate  : 0.455 
-------------------------------------------------------------------------------
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  207 LYS
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 27 optimal weight:    0.6980
   chunk 39 optimal weight:    0.0050
   chunk 1 optimal weight:    1.9990
   chunk 5 optimal weight:    0.8980
   chunk 12 optimal weight:    0.8980
   chunk 45 optimal weight:    1.9990
   chunk 48 optimal weight:    0.1980
   chunk 8 optimal weight:    0.9990
   chunk 49 optimal weight:    0.2980
   chunk 7 optimal weight:    0.8980
   chunk 0 optimal weight:    0.5980
   overall best weight:    0.3594

-------------------------------------------------------------------------------
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 = 0.3126 r_free = 0.3126 target = 0.089799 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.082272 restraints weight = 6073.151|
|-----------------------------------------------------------------------------|
r_work (start): 0.3001 rms_B_bonded: 2.00
r_work: 0.2877 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.2756 rms_B_bonded: 4.21 restraints_weight: 0.2500
r_work (final): 0.2756
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2778
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2778 r_free = 0.2778    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.60   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2778 r_free = 0.2778    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.60   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2778
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8289
moved from start:          0.3487

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   4128  Z= 0.141
  Angle     :  0.392   5.041   5604  Z= 0.211
  Chirality :  0.039   0.125    634
  Planarity :  0.004   0.044    710
  Dihedral  :  7.816  57.460    686
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 3.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.18 %
    Favored  : 98.82 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 21.98 %
    Favored  : 75.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.91 (0.40), residues: 508
  helix:  2.37 (0.35), residues: 260
  sheet:  0.10 (0.48), residues: 112
  loop :  0.22 (0.56), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 100 
 HIS   0.003   0.001   HIS A 252 
 PHE   0.004   0.001   PHE B  82 
 TYR   0.006   0.001   TYR A 151 
 ARG   0.003   0.000   ARG A  84 

*********************** 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
  54 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 43
  time to evaluate  : 0.487 
Fit side-chains
REVERT: A    3 VAL cc_start: 0.8713 (p) cc_final: 0.8382 (t)
REVERT: B    3 VAL cc_start: 0.8822 (p) cc_final: 0.8484 (t)
REVERT: B   84 ARG cc_start: 0.8343 (ptp90) cc_final: 0.7581 (ptm160)
REVERT: B  255 ASP cc_start: 0.8501 (t70) cc_final: 0.8134 (t70)
  outliers start: 11
  outliers final: 6
  residues processed: 50
  average time/residue: 1.1703
  time to fit residues: 60.8446
Evaluate side-chains
  47 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 41
  time to evaluate  : 0.468 
-------------------------------------------------------------------------------
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 B residue   56 GLN
Chi-restraints excluded: chain B residue   58 THR
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 28 optimal weight:    0.8980
   chunk 49 optimal weight:    1.9990
   chunk 10 optimal weight:    0.8980
   chunk 47 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9980
   chunk 36 optimal weight:    0.5980
   chunk 34 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 40 optimal weight:    0.5980
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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 = 0.3070 r_free = 0.3070 target = 0.086377 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2965 r_free = 0.2965 target = 0.079048 restraints weight = 6125.291|
|-----------------------------------------------------------------------------|
r_work (start): 0.2941 rms_B_bonded: 1.97
r_work: 0.2815 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.2695 rms_B_bonded: 4.14 restraints_weight: 0.2500
r_work (final): 0.2695
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2723
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2723 r_free = 0.2723    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.60   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2723 r_free = 0.2723    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.61   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2723
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8407
moved from start:          0.3423

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   4128  Z= 0.250
  Angle     :  0.448   5.164   5604  Z= 0.237
  Chirality :  0.041   0.127    634
  Planarity :  0.004   0.044    710
  Dihedral  :  8.326  62.690    686
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 3.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.18 %
    Favored  : 98.82 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 22.95 %
    Favored  : 74.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.72 (0.40), residues: 508
  helix:  2.22 (0.35), residues: 260
  sheet:  0.10 (0.48), residues: 108
  loop :  0.04 (0.55), residues: 140

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

********************** 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
  51 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 42
  time to evaluate  : 0.453 
Fit side-chains
REVERT: A    3 VAL cc_start: 0.8762 (p) cc_final: 0.8441 (t)
REVERT: A   84 ARG cc_start: 0.8446 (ptp90) cc_final: 0.7881 (ptt90)
REVERT: B   84 ARG cc_start: 0.8395 (ptp90) cc_final: 0.7617 (ptm160)
  outliers start: 9
  outliers final: 7
  residues processed: 48
  average time/residue: 1.2163
  time to fit residues: 60.7674
Evaluate side-chains
  49 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 42
  time to evaluate  : 0.468 
-------------------------------------------------------------------------------
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 B residue   56 GLN
Chi-restraints excluded: chain B residue   58 THR
Chi-restraints excluded: chain B residue  113 SER
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 1 optimal weight:    1.9990
   chunk 15 optimal weight:    2.9990
   chunk 23 optimal weight:    0.0770
   chunk 18 optimal weight:    0.7980
   chunk 4 optimal weight:    0.5980
   chunk 2 optimal weight:    0.7980
   chunk 11 optimal weight:    0.9980
   chunk 43 optimal weight:    2.9990
   chunk 22 optimal weight:    0.4980
   chunk 35 optimal weight:    0.7980
   chunk 36 optimal weight:    0.9990
   overall best weight:    0.5538

-------------------------------------------------------------------------------
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 = 0.087733 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.080412 restraints weight = 6110.664|
|-----------------------------------------------------------------------------|
r_work (start): 0.2985 rms_B_bonded: 1.99
r_work: 0.2861 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.2740 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.2740
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2740
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2740 r_free = 0.2740    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.61   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2741 r_free = 0.2741    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.63   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2741
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8409
moved from start:          0.3507

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= 0.186
  Angle     :  0.418   5.068   5604  Z= 0.223
  Chirality :  0.040   0.123    634
  Planarity :  0.004   0.044    710
  Dihedral  :  8.060  60.176    686
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 3.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 23.19 %
    Favored  : 74.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.83 (0.40), residues: 508
  helix:  2.31 (0.35), residues: 260
  sheet:  0.04 (0.48), residues: 112
  loop :  0.20 (0.56), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 100 
 HIS   0.003   0.001   HIS A 252 
 PHE   0.005   0.001   PHE B  82 
 TYR   0.007   0.001   TYR A 151 
 ARG   0.003   0.000   ARG A  84 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3618.39 seconds
wall clock time: 64 minutes 51.41 seconds (3891.41 seconds total)