Starting phenix.real_space_refine
on Wed Jul  1 23:37:57 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/8cvn_27010/07_2026/8cvn_27010.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8cvn_27010/07_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 {
    restraint_files = "/net/cci-nas-00/data/ceres_data/8cvn_27010/07_2026/8cvn_27010.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/8cvn_27010/07_2026/8cvn_27010.cif"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8cvn_27010/07_2026/8cvn_27010.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8cvn_27010/07_2026/8cvn_27010.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8cvn_27010/07_2026/8cvn_27010.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8cvn_27010/07_2026/8cvn_27010.map"
  }
  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-6108/lib/python3.11/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: 1.29, per 1000 atoms: 0.32
  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: 0.45
  Conformation dependent library (CDL) restraints added in 149.0 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: 0.12
  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: 0.59

  Time building geometry restraints manager: 0.49 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: 2033
       16.30 -    32.61: 270
       32.61 -    48.91: 80
       48.91 -    65.21: 33
       65.21 -    81.51: 12
  Dihedral angle restraints: 2428
    sinusoidal: 974
      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 2425 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:             16.200
  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:          0.150
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     6.000
  Find NCS groups from input model:        0.150
  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:6.430
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.970
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8671
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  : 18.045  81.509   1500
  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/Z
  covalent geometry    : bond        0.01752 /  0.99 ( 4128)
  covalent geometry    : angle       1.46720 /  0.91 ( 5604)
  hydrogen bonds       : bond        0.21904 / 14.63 (  223)
  hydrogen bonds       : angle       6.53955 /  4.62 (  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  : 0.113 
Fit side-chains
  outliers start: 5
  outliers final: 0
  residues processed: 77
  average time/residue: 0.7344
  time to fit residues: 57.9323
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  : 0.099 
-------------------------------------------------------------------------------
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...
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 = 0.3214 r_free = 0.3214 target = 0.096636 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.088361 restraints weight = 5883.196|
|-----------------------------------------------------------------------------|
r_work (start): 0.3083 rms_B_bonded: 2.11
r_work: 0.2958 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.2833 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.2833
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2835
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2835 r_free = 0.2835    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 = 0.2832 r_free = 0.2832    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.53   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 6 (12 function evaluations)
r_final: 0.2832
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8631
moved from start:          0.2476

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= 0.119
  Angle     :  0.483   5.936   5604  Z= 0.256
  Chirality :  0.041   0.126    634
  Planarity :  0.003   0.045    710
  Dihedral  :  6.002  59.179    586
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 2.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 21.50 %
    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:  1.72 (0.39), residues: 508
  helix:  1.97 (0.35), residues: 260
  sheet:  0.73 (0.50), residues: 108
  loop : -0.01 (0.52), 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   0.008   0.001   PHE A  82 
 TRP   0.005   0.001   TRP B 100 
 HIS   0.003   0.001   HIS A 252 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00261 /  0.12 ( 4128)
  covalent geometry    : angle       0.48310 /  0.26 ( 5604)
  hydrogen bonds       : bond        0.04522 /  3.03 (  223)
  hydrogen bonds       : angle       4.27529 /  3.04 (  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
  58 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 44
  time to evaluate  : 0.156 
Fit side-chains
REVERT: A    3 VAL cc_start: 0.8447 (p) cc_final: 0.8167 (t)
REVERT: B  197 GLU cc_start: 0.7336 (OUTLIER) cc_final: 0.7110 (tm-30)
  outliers start: 14
  outliers final: 2
  residues processed: 50
  average time/residue: 0.5914
  time to fit residues: 30.5348
Evaluate side-chains
  44 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 41
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
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:    0.0060
   chunk 48 optimal weight:    0.9990
   chunk 49 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 28 optimal weight:    0.7980
   chunk 45 optimal weight:    0.0010
   chunk 32 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9990
   chunk 4 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   overall best weight:    0.5606

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.089846 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3014 r_free = 0.3014 target = 0.082085 restraints weight = 6035.069|
|-----------------------------------------------------------------------------|
r_work (start): 0.2996 rms_B_bonded: 2.05
r_work: 0.2871 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.2748 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.2748
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2762
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2762 r_free = 0.2762    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.53   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2762 r_free = 0.2762    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.61   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 5 (11 function evaluations)
r_final: 0.2762
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8695
moved from start:          0.2977

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= 0.130
  Angle     :  0.456   5.460   5604  Z= 0.245
  Chirality :  0.040   0.125    634
  Planarity :  0.004   0.043    710
  Dihedral  :  5.664  47.418    586
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 2.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 21.98 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.84 (0.40), residues: 508
  helix:  2.15 (0.36), residues: 260
  sheet:  0.54 (0.50), residues: 108
  loop :  0.10 (0.55), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B  84 
 TYR   0.008   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 A 252 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00296 /  0.13 ( 4128)
  covalent geometry    : angle       0.45560 /  0.25 ( 5604)
  hydrogen bonds       : bond        0.04829 /  3.24 (  223)
  hydrogen bonds       : angle       4.06405 /  2.89 (  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
  62 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 49
  time to evaluate  : 0.166 
Fit side-chains
REVERT: A    3 VAL cc_start: 0.8624 (p) cc_final: 0.8357 (t)
REVERT: A   84 ARG cc_start: 0.8452 (ptp90) cc_final: 0.7916 (ptt90)
REVERT: B    3 VAL cc_start: 0.8777 (p) cc_final: 0.8507 (t)
  outliers start: 13
  outliers final: 6
  residues processed: 56
  average time/residue: 0.5549
  time to fit residues: 32.1827
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  : 0.199 
-------------------------------------------------------------------------------
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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 7 optimal weight:    0.9980
   chunk 24 optimal weight:    0.0980
   chunk 21 optimal weight:    0.9980
   chunk 26 optimal weight:    1.9990
   chunk 22 optimal weight:    0.0970
   chunk 9 optimal weight:    0.0770
   chunk 37 optimal weight:    0.9980
   chunk 29 optimal weight:    0.5980
   chunk 8 optimal weight:    0.9990
   chunk 10 optimal weight:    0.7980
   chunk 14 optimal weight:    2.9990
   overall best weight:    0.3336

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.091778 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.083936 restraints weight = 5988.769|
|-----------------------------------------------------------------------------|
r_work (start): 0.3033 rms_B_bonded: 2.06
r_work: 0.2907 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.2785 rms_B_bonded: 4.28 restraints_weight: 0.2500
r_work (final): 0.2785
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2783
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2783 r_free = 0.2783    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.61   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2783 r_free = 0.2783    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.63   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2783
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8623
moved from start:          0.3189

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= 0.097
  Angle     :  0.411   5.261   5604  Z= 0.221
  Chirality :  0.039   0.125    634
  Planarity :  0.004   0.042    710
  Dihedral  :  5.831  57.464    586
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 2.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.98 %
    Favored  : 99.02 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 23.91 %
    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:  1.98 (0.40), residues: 508
  helix:  2.32 (0.36), residues: 260
  sheet:  0.52 (0.50), residues: 108
  loop :  0.12 (0.55), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   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 252 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00218 /  0.10 ( 4128)
  covalent geometry    : angle       0.41116 /  0.22 ( 5604)
  hydrogen bonds       : bond        0.03836 /  2.57 (  223)
  hydrogen bonds       : angle       3.82176 /  2.72 (  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
  54 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 48
  time to evaluate  : 0.156 
Fit side-chains
REVERT: A    3 VAL cc_start: 0.8673 (p) cc_final: 0.8378 (t)
REVERT: A   84 ARG cc_start: 0.8387 (ptp90) cc_final: 0.7848 (ptt90)
REVERT: B    3 VAL cc_start: 0.8766 (p) cc_final: 0.8485 (t)
REVERT: B   84 ARG cc_start: 0.8366 (ptp90) cc_final: 0.7725 (ptt90)
REVERT: B  255 ASP cc_start: 0.8455 (t70) cc_final: 0.8230 (t70)
  outliers start: 6
  outliers final: 3
  residues processed: 50
  average time/residue: 0.5855
  time to fit residues: 30.2857
Evaluate side-chains
  49 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 46
  time to evaluate  : 0.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain B residue   58 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 46 optimal weight:    0.0980
   chunk 47 optimal weight:    0.7980
   chunk 29 optimal weight:    1.9990
   chunk 11 optimal weight:    0.5980
   chunk 23 optimal weight:    1.9990
   chunk 10 optimal weight:    0.0970
   chunk 4 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 39 optimal weight:    0.0980
   chunk 5 optimal weight:    0.4980
   overall best weight:    0.2778

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.092587 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.084723 restraints weight = 6010.567|
|-----------------------------------------------------------------------------|
r_work (start): 0.3048 rms_B_bonded: 2.06
r_work: 0.2927 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.2808 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.2808
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2799
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2799 r_free = 0.2799    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.63   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2799 r_free = 0.2799    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.63   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2799
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8595
moved from start:          0.3327

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   4128  Z= 0.088
  Angle     :  0.389   5.260   5604  Z= 0.209
  Chirality :  0.039   0.123    634
  Planarity :  0.004   0.041    710
  Dihedral  :  5.489  51.701    586
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 3.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 22.95 %
    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:  2.04 (0.40), residues: 508
  helix:  2.45 (0.36), residues: 260
  sheet:  0.50 (0.50), residues: 108
  loop :  0.01 (0.54), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  84 
 TYR   0.006   0.001   TYR B 151 
 PHE   0.006   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/Z
  covalent geometry    : bond        0.00198 /  0.09 ( 4128)
  covalent geometry    : angle       0.38910 /  0.21 ( 5604)
  hydrogen bonds       : bond        0.03502 /  2.34 (  223)
  hydrogen bonds       : angle       3.69150 /  2.63 (  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
  57 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 47
  time to evaluate  : 0.157 
Fit side-chains
REVERT: A    3 VAL cc_start: 0.8689 (p) cc_final: 0.8385 (t)
REVERT: A   84 ARG cc_start: 0.8384 (ptp90) cc_final: 0.7841 (ptt90)
REVERT: B    3 VAL cc_start: 0.8779 (p) cc_final: 0.8480 (t)
REVERT: B  198 GLU cc_start: 0.7583 (mp0) cc_final: 0.7359 (pm20)
  outliers start: 10
  outliers final: 4
  residues processed: 50
  average time/residue: 0.5740
  time to fit residues: 29.6509
Evaluate side-chains
  52 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 48
  time to evaluate  : 0.092 
-------------------------------------------------------------------------------
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   58 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 42 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9990
   chunk 23 optimal weight:    0.4980
   chunk 47 optimal weight:    0.8980
   chunk 10 optimal weight:    1.9990
   chunk 45 optimal weight:    0.2980
   chunk 33 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 41 optimal weight:    0.8980
   overall best weight:    0.7182

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.087485 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2976 r_free = 0.2976 target = 0.079822 restraints weight = 6217.107|
|-----------------------------------------------------------------------------|
r_work (start): 0.2969 rms_B_bonded: 2.05
r_work: 0.2841 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.2719 rms_B_bonded: 4.29 restraints_weight: 0.2500
r_work (final): 0.2719
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2713
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2713 r_free = 0.2713    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.63   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2713 r_free = 0.2713    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.64   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (10 function evaluations)
r_final: 0.2713
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8676
moved from start:          0.3288

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= 0.149
  Angle     :  0.449   5.340   5604  Z= 0.238
  Chirality :  0.040   0.124    634
  Planarity :  0.004   0.041    710
  Dihedral  :  5.263  43.066    586
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 3.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 23.67 %
    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:  1.82 (0.40), residues: 508
  helix:  2.27 (0.35), residues: 260
  sheet:  0.35 (0.50), residues: 108
  loop : -0.05 (0.54), residues: 140

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



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00351 /  0.15 ( 4128)
  covalent geometry    : angle       0.44910 /  0.24 ( 5604)
  hydrogen bonds       : bond        0.04974 /  3.33 (  223)
  hydrogen bonds       : angle       3.94305 /  2.81 (  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
  56 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 46
  time to evaluate  : 0.161 
Fit side-chains
REVERT: A    3 VAL cc_start: 0.8703 (p) cc_final: 0.8395 (t)
REVERT: B    3 VAL cc_start: 0.8786 (p) cc_final: 0.8483 (t)
REVERT: B   84 ARG cc_start: 0.8351 (ptp90) cc_final: 0.7519 (ptm160)
REVERT: B  255 ASP cc_start: 0.8442 (t70) cc_final: 0.8193 (t70)
  outliers start: 10
  outliers final: 5
  residues processed: 50
  average time/residue: 0.5734
  time to fit residues: 29.7169
Evaluate side-chains
  50 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 45
  time to evaluate  : 0.156 
-------------------------------------------------------------------------------
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
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:    1.9990
   chunk 25 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   chunk 30 optimal weight:    0.7980
   chunk 0 optimal weight:    2.9990
   chunk 17 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 11 optimal weight:    0.5980
   overall best weight:    1.0784

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.085554 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2948 r_free = 0.2948 target = 0.078133 restraints weight = 6311.833|
|-----------------------------------------------------------------------------|
r_work (start): 0.2943 rms_B_bonded: 2.03
r_work: 0.2815 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.2693 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.2693
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2671
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2671 r_free = 0.2671    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.64   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2671 r_free = 0.2671    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.65   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2671
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8778
moved from start:          0.3323

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   4128  Z= 0.209
  Angle     :  0.500   5.343   5604  Z= 0.263
  Chirality :  0.042   0.126    634
  Planarity :  0.004   0.043    710
  Dihedral  :  5.314  39.931    586
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 3.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 24.15 %
    Favored  : 73.19 %
  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:  1.64 (0.40), residues: 508
  helix:  2.12 (0.35), residues: 260
  sheet:  0.20 (0.50), residues: 108
  loop : -0.05 (0.55), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  84 
 TYR   0.009   0.001   TYR B 216 
 PHE   0.006   0.001   PHE B  60 
 TRP   0.006   0.001   TRP A 100 
 HIS   0.003   0.001   HIS B 156 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00500 /  0.21 ( 4128)
  covalent geometry    : angle       0.49970 /  0.26 ( 5604)
  hydrogen bonds       : bond        0.05859 /  3.93 (  223)
  hydrogen bonds       : angle       4.19891 /  3.00 (  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
  55 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 44
  time to evaluate  : 0.160 
Fit side-chains
REVERT: A    3 VAL cc_start: 0.8778 (p) cc_final: 0.8465 (t)
REVERT: B    3 VAL cc_start: 0.8848 (p) cc_final: 0.8534 (t)
REVERT: B   84 ARG cc_start: 0.8408 (ptp90) cc_final: 0.7607 (ptm160)
REVERT: B  255 ASP cc_start: 0.8498 (t70) cc_final: 0.8285 (t70)
  outliers start: 11
  outliers final: 7
  residues processed: 48
  average time/residue: 0.5131
  time to fit residues: 25.5886
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  : 0.152 
-------------------------------------------------------------------------------
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
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:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 31 optimal weight:    0.0670
   chunk 10 optimal weight:    0.5980
   chunk 12 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 7 optimal weight:    0.5980
   chunk 42 optimal weight:    3.9990
   chunk 48 optimal weight:    0.7980
   chunk 11 optimal weight:    0.5980
   overall best weight:    0.5318

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.088185 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2984 r_free = 0.2984 target = 0.080604 restraints weight = 6086.706|
|-----------------------------------------------------------------------------|
r_work (start): 0.2978 rms_B_bonded: 2.03
r_work: 0.2852 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.2730 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.2730
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2729
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2729 r_free = 0.2729    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.65   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2729 r_free = 0.2729    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.67   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (10 function evaluations)
r_final: 0.2729
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8653
moved from start:          0.3401

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= 0.121
  Angle     :  0.420   5.148   5604  Z= 0.225
  Chirality :  0.040   0.121    634
  Planarity :  0.004   0.043    710
  Dihedral  :  4.957  40.388    586
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 3.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 24.88 %
    Favored  : 72.71 %
  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:  2.31 (0.35), residues: 260
  sheet:  0.23 (0.50), residues: 108
  loop : -0.03 (0.55), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  84 
 TYR   0.007   0.001   TYR B 151 
 PHE   0.004   0.001   PHE A  82 
 TRP   0.005   0.001   TRP B 100 
 HIS   0.002   0.001   HIS A 252 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00282 /  0.12 ( 4128)
  covalent geometry    : angle       0.42020 /  0.22 ( 5604)
  hydrogen bonds       : bond        0.04380 /  2.94 (  223)
  hydrogen bonds       : angle       3.91707 /  2.79 (  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
  55 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 45
  time to evaluate  : 0.159 
Fit side-chains
REVERT: A    3 VAL cc_start: 0.8698 (p) cc_final: 0.8376 (t)
REVERT: B    3 VAL cc_start: 0.8812 (p) cc_final: 0.8497 (t)
REVERT: B   84 ARG cc_start: 0.8331 (ptp90) cc_final: 0.7497 (ptm160)
REVERT: B  198 GLU cc_start: 0.7556 (mp0) cc_final: 0.7330 (pm20)
REVERT: B  255 ASP cc_start: 0.8454 (t70) cc_final: 0.8240 (t70)
  outliers start: 10
  outliers final: 7
  residues processed: 50
  average time/residue: 0.4770
  time to fit residues: 24.8222
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  : 0.157 
-------------------------------------------------------------------------------
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 32 optimal weight:    0.7980
   chunk 13 optimal weight:    1.9990
   chunk 47 optimal weight:    1.9990
   chunk 19 optimal weight:    2.9990
   chunk 14 optimal weight:    2.9990
   chunk 31 optimal weight:    0.0570
   chunk 38 optimal weight:    2.9990
   chunk 49 optimal weight:    0.7980
   chunk 42 optimal weight:    0.9980
   chunk 46 optimal weight:    0.9990
   chunk 6 optimal weight:    0.6980
   overall best weight:    0.6698

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3073 r_free = 0.3073 target = 0.086925 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2965 r_free = 0.2965 target = 0.079351 restraints weight = 6249.203|
|-----------------------------------------------------------------------------|
r_work (start): 0.2953 rms_B_bonded: 2.05
r_work: 0.2824 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.2702 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.2702
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2699
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2699 r_free = 0.2699    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.67   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2699 r_free = 0.2699    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.66   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (10 function evaluations)
r_final: 0.2699
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8689
moved from start:          0.3390

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= 0.140
  Angle     :  0.438   5.192   5604  Z= 0.232
  Chirality :  0.040   0.123    634
  Planarity :  0.004   0.043    710
  Dihedral  :  5.002  40.151    586
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 3.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.18 %
    Favored  : 98.82 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 24.64 %
    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:  1.77 (0.40), residues: 508
  helix:  2.27 (0.35), residues: 260
  sheet:  0.22 (0.50), residues: 108
  loop : -0.06 (0.55), residues: 140

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



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00332 /  0.14 ( 4128)
  covalent geometry    : angle       0.43800 /  0.23 ( 5604)
  hydrogen bonds       : bond        0.04783 /  3.20 (  223)
  hydrogen bonds       : angle       3.94959 /  2.82 (  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
  50 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 44
  time to evaluate  : 0.199 
Fit side-chains
REVERT: A    3 VAL cc_start: 0.8726 (p) cc_final: 0.8405 (t)
REVERT: A   84 ARG cc_start: 0.8346 (ptp90) cc_final: 0.7768 (ptt90)
REVERT: B    3 VAL cc_start: 0.8824 (p) cc_final: 0.8503 (t)
REVERT: B   84 ARG cc_start: 0.8352 (ptp90) cc_final: 0.7534 (ptm160)
REVERT: B  198 GLU cc_start: 0.7566 (mp0) cc_final: 0.7301 (pm20)
REVERT: B  255 ASP cc_start: 0.8489 (t70) cc_final: 0.8281 (t70)
  outliers start: 6
  outliers final: 6
  residues processed: 47
  average time/residue: 0.5497
  time to fit residues: 26.8294
Evaluate side-chains
  50 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 44
  time to evaluate  : 0.162 
-------------------------------------------------------------------------------
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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 45 optimal weight:    0.9980
   chunk 46 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 35 optimal weight:    0.0670
   chunk 1 optimal weight:    1.9990
   chunk 39 optimal weight:    0.7980
   chunk 11 optimal weight:    0.5980
   chunk 3 optimal weight:    0.2980
   chunk 22 optimal weight:    0.0370
   chunk 34 optimal weight:    0.7980
   chunk 21 optimal weight:    0.9990
   overall best weight:    0.3596

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.089951 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 23)----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.082233 restraints weight = 6082.908|
|-----------------------------------------------------------------------------|
r_work (start): 0.3006 rms_B_bonded: 2.03
r_work: 0.2884 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.2764 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.2764
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2781
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2781 r_free = 0.2781    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.66   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2781 r_free = 0.2781    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.66   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (10 function evaluations)
r_final: 0.2781
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8635
moved from start:          0.3482

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   4128  Z= 0.096
  Angle     :  0.394   5.103   5604  Z= 0.211
  Chirality :  0.039   0.124    634
  Planarity :  0.004   0.043    710
  Dihedral  :  4.756  40.484    586
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 3.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.98 %
    Favored  : 99.02 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 24.40 %
    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:  1.98 (0.40), residues: 508
  helix:  2.45 (0.35), residues: 260
  sheet:  0.21 (0.50), residues: 112
  loop :  0.13 (0.55), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  84 
 TYR   0.006   0.001   TYR B 151 
 PHE   0.004   0.001   PHE B  82 
 TRP   0.005   0.001   TRP B 100 
 HIS   0.003   0.001   HIS A 252 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00222 /  0.10 ( 4128)
  covalent geometry    : angle       0.39416 /  0.21 ( 5604)
  hydrogen bonds       : bond        0.03747 /  2.51 (  223)
  hydrogen bonds       : angle       3.75265 /  2.68 (  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
  49 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 42
  time to evaluate  : 0.153 
Fit side-chains
REVERT: A    3 VAL cc_start: 0.8736 (p) cc_final: 0.8411 (t)
REVERT: B    3 VAL cc_start: 0.8831 (p) cc_final: 0.8504 (t)
REVERT: B   84 ARG cc_start: 0.8320 (ptp90) cc_final: 0.7582 (ptm160)
  outliers start: 7
  outliers final: 7
  residues processed: 46
  average time/residue: 0.5340
  time to fit residues: 25.5102
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  : 0.141 
-------------------------------------------------------------------------------
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 35 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9990
   chunk 32 optimal weight:    0.7980
   chunk 38 optimal weight:    2.9990
   chunk 24 optimal weight:    0.5980
   chunk 39 optimal weight:    0.7980
   chunk 9 optimal weight:    0.0020
   chunk 29 optimal weight:    0.9980
   chunk 31 optimal weight:    0.7980
   chunk 21 optimal weight:    0.9990
   chunk 37 optimal weight:    0.6980
   overall best weight:    0.5788

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.088130 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2991 r_free = 0.2991 target = 0.080578 restraints weight = 6139.744|
|-----------------------------------------------------------------------------|
r_work (start): 0.2968 rms_B_bonded: 2.03
r_work: 0.2841 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.2719 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.2719
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2716
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2716 r_free = 0.2716    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 = 0.2716 r_free = 0.2716    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.64   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2716
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8709
moved from start:          0.3405

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= 0.126
  Angle     :  0.419   5.154   5604  Z= 0.223
  Chirality :  0.040   0.124    634
  Planarity :  0.004   0.043    710
  Dihedral  :  4.895  40.152    586
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 3.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  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:  1.88 (0.40), residues: 508
  helix:  2.37 (0.35), residues: 260
  sheet:  0.30 (0.51), residues: 108
  loop : -0.06 (0.54), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  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/Z
  covalent geometry    : bond        0.00296 /  0.13 ( 4128)
  covalent geometry    : angle       0.41870 /  0.22 ( 5604)
  hydrogen bonds       : bond        0.04483 /  3.00 (  223)
  hydrogen bonds       : angle       3.83204 /  2.74 (  625)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1876.23 seconds
wall clock time: 32 minutes 49.22 seconds (1969.22 seconds total)