Starting phenix.real_space_refine
on Tue Feb  3 19:40:17 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9lnb_63231/02_2026/9lnb_63231.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9lnb_63231/02_2026/9lnb_63231.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.15
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9lnb_63231/02_2026/9lnb_63231.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9lnb_63231/02_2026/9lnb_63231.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9lnb_63231/02_2026/9lnb_63231.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9lnb_63231/02_2026/9lnb_63231.cif"
  }
  resolution = 3.15
  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=   0.031
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: 4
    Type Number    sf(0)   Gaussians
     S      38      5.16       5
     C    4254      2.51       5
     N     980      2.21       5
     O    1170      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6442
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3083
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 404, 3083
          Classifications: {'peptide': 404}
          Link IDs: {'PTRANS': 15, 'TRANS': 388}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 138
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 138
          Unusual residues: {'LMN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Restraints were copied for chains:
    B
  Time building chain proxies: 2.23, per 1000 atoms: 0.35
  Number of scatterers: 6442
  At special positions: 0
  Unit cell: (90.95, 92.65, 69.7, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      38     16.00
     O    1170      8.00
     N     980      7.00
     C    4254      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: 0.73
  Conformation dependent library (CDL) restraints added in 241.2 milliseconds
  

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1452

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 0 sheets defined
      85.3% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.17
  Creating SS restraints...
    Processing helix  chain 'A' and resid 5 through 42
      removed outlier: 5.303A  pdb=" N   PHE A  31 " --> pdb=" O   ASN A  27 " (cutoff:3.500A)
      removed outlier: 5.574A  pdb=" N   SER A  32 " --> pdb=" O   ARG A  28 " (cutoff:3.500A)
      Proline residue:  A  36  - end of helix
    Processing helix  chain 'A' and resid 45 through 71
      removed outlier: 3.998A  pdb=" N   LEU A  49 " --> pdb=" O   ASP A  45 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   GLY A  50 " --> pdb=" O   LYS A  46 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 75 through 95
    Processing helix  chain 'A' and resid 99 through 115
      removed outlier: 3.539A  pdb=" N   PHE A 108 " --> pdb=" O   ALA A 104 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   LEU A 109 " --> pdb=" O   ALA A 105 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   GLY A 111 " --> pdb=" O   TRP A 107 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 117 through 129
      removed outlier: 3.950A  pdb=" N   CYS A 121 " --> pdb=" O   GLY A 117 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 130 through 134
      removed outlier: 4.167A  pdb=" N   PHE A 134 " --> pdb=" O   PRO A 131 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 135 through 161
      Proline residue:  A 153  - end of helix
    Processing helix  chain 'A' and resid 165 through 187
      removed outlier: 3.956A  pdb=" N   LEU A 169 " --> pdb=" O   TRP A 165 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   ALA A 170 " --> pdb=" O   ARG A 166 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 216 through 221
    Processing helix  chain 'A' and resid 223 through 254
      removed outlier: 4.258A  pdb=" N   TRP A 227 " --> pdb=" O   SER A 223 " (cutoff:3.500A)
      removed outlier: 5.395A  pdb=" N   GLN A 248 " --> pdb=" O   THR A 244 " (cutoff:3.500A)
      removed outlier: 5.205A  pdb=" N   PHE A 249 " --> pdb=" O   ASP A 245 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 260 through 291
    Processing helix  chain 'A' and resid 300 through 321
      removed outlier: 3.720A  pdb=" N   LEU A 304 " --> pdb=" O   ARG A 300 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 327 through 356
      Proline residue:  A 345  - end of helix
      removed outlier: 3.773A  pdb=" N   ASN A 354 " --> pdb=" O   GLY A 350 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 363 through 391
      removed outlier: 4.344A  pdb=" N   ILE A 368 " --> pdb=" O   THR A 364 " (cutoff:3.500A)
      removed outlier: 5.123A  pdb=" N   VAL A 369 " --> pdb=" O   SER A 365 " (cutoff:3.500A)
      Proline residue:  A 383  - end of helix
    Processing helix  chain 'A' and resid 392 through 414
      removed outlier: 3.525A  pdb=" N   ALA A 396 " --> pdb=" O   SER A 392 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 6 through 42
      removed outlier: 5.303A  pdb=" N   PHE B  31 " --> pdb=" O   ASN B  27 " (cutoff:3.500A)
      removed outlier: 5.574A  pdb=" N   SER B  32 " --> pdb=" O   ARG B  28 " (cutoff:3.500A)
      Proline residue:  B  36  - end of helix
    Processing helix  chain 'B' and resid 45 through 71
      removed outlier: 3.998A  pdb=" N   LEU B  49 " --> pdb=" O   ASP B  45 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   GLY B  50 " --> pdb=" O   LYS B  46 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 75 through 95
    Processing helix  chain 'B' and resid 99 through 115
      removed outlier: 3.539A  pdb=" N   PHE B 108 " --> pdb=" O   ALA B 104 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   LEU B 109 " --> pdb=" O   ALA B 105 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   GLY B 111 " --> pdb=" O   TRP B 107 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 117 through 129
      removed outlier: 3.950A  pdb=" N   CYS B 121 " --> pdb=" O   GLY B 117 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 130 through 134
      removed outlier: 4.168A  pdb=" N   PHE B 134 " --> pdb=" O   PRO B 131 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 135 through 161
      Proline residue:  B 153  - end of helix
    Processing helix  chain 'B' and resid 165 through 187
      removed outlier: 3.956A  pdb=" N   LEU B 169 " --> pdb=" O   TRP B 165 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   ALA B 170 " --> pdb=" O   ARG B 166 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 216 through 221
    Processing helix  chain 'B' and resid 223 through 254
      removed outlier: 4.258A  pdb=" N   TRP B 227 " --> pdb=" O   SER B 223 " (cutoff:3.500A)
      removed outlier: 5.395A  pdb=" N   GLN B 248 " --> pdb=" O   THR B 244 " (cutoff:3.500A)
      removed outlier: 5.205A  pdb=" N   PHE B 249 " --> pdb=" O   ASP B 245 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 260 through 291
    Processing helix  chain 'B' and resid 300 through 321
      removed outlier: 3.720A  pdb=" N   LEU B 304 " --> pdb=" O   ARG B 300 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 327 through 356
      Proline residue:  B 345  - end of helix
      removed outlier: 3.772A  pdb=" N   ASN B 354 " --> pdb=" O   GLY B 350 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 363 through 391
      removed outlier: 4.344A  pdb=" N   ILE B 368 " --> pdb=" O   THR B 364 " (cutoff:3.500A)
      removed outlier: 5.123A  pdb=" N   VAL B 369 " --> pdb=" O   SER B 365 " (cutoff:3.500A)
      Proline residue:  B 383  - end of helix
    Processing helix  chain 'B' and resid 392 through 414
      removed outlier: 3.525A  pdb=" N   ALA B 396 " --> pdb=" O   SER B 392 " (cutoff:3.500A)

    509 hydrogen bonds defined for protein.
    1521 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: 0.99

  Time building geometry restraints manager: 0.92 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1840
        1.34 -     1.46: 1434
        1.46 -     1.58: 3264
        1.58 -     1.69: 28
        1.69 -     1.81: 62
  Bond restraints: 6628
  Sorted by residual:
  bond pdb=" C5  LMN A 501 "
       pdb=" O5  LMN A 501 "
    ideal  model  delta    sigma   weight residual
    1.413  1.546 -0.133 2.00e-02 2.50e+03 4.45e+01
  bond pdb=" C5  LMN B 501 "
       pdb=" O5  LMN B 501 "
    ideal  model  delta    sigma   weight residual
    1.413  1.546 -0.133 2.00e-02 2.50e+03 4.45e+01
  bond pdb=" C5  LMN A 502 "
       pdb=" O5  LMN A 502 "
    ideal  model  delta    sigma   weight residual
    1.413  1.545 -0.132 2.00e-02 2.50e+03 4.36e+01
  bond pdb=" C5  LMN B 502 "
       pdb=" O5  LMN B 502 "
    ideal  model  delta    sigma   weight residual
    1.413  1.545 -0.132 2.00e-02 2.50e+03 4.36e+01
  bond pdb=" CBQ LMN A 502 "
       pdb=" CCM LMN A 502 "
    ideal  model  delta    sigma   weight residual
    1.540  1.657 -0.117 2.00e-02 2.50e+03 3.41e+01
  ... (remaining 6623 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.20: 8725
        2.20 -     4.41: 251
        4.41 -     6.61: 34
        6.61 -     8.82: 6
        8.82 -    11.02: 6
  Bond angle restraints: 9022
  Sorted by residual:
  angle pdb=" N   HIS B 366 "
        pdb=" CA  HIS B 366 "
        pdb=" C   HIS B 366 "
      ideal   model   delta    sigma   weight residual
     114.56  109.89    4.67 1.27e+00 6.20e-01 1.35e+01
  angle pdb=" N   HIS A 366 "
        pdb=" CA  HIS A 366 "
        pdb=" C   HIS A 366 "
      ideal   model   delta    sigma   weight residual
     114.56  109.89    4.67 1.27e+00 6.20e-01 1.35e+01
  angle pdb=" CCQ LMN A 501 "
        pdb=" OCB LMN A 501 "
        pdb=" CCS LMN A 501 "
      ideal   model   delta    sigma   weight residual
     119.65  108.63   11.02 3.00e+00 1.11e-01 1.35e+01
  angle pdb=" CCQ LMN B 501 "
        pdb=" OCB LMN B 501 "
        pdb=" CCS LMN B 501 "
      ideal   model   delta    sigma   weight residual
     119.65  108.63   11.02 3.00e+00 1.11e-01 1.35e+01
  angle pdb=" CA  PHE A 134 "
        pdb=" CB  PHE A 134 "
        pdb=" CG  PHE A 134 "
      ideal   model   delta    sigma   weight residual
     113.80  117.34   -3.54 1.00e+00 1.00e+00 1.25e+01
  ... (remaining 9017 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.11: 3768
       34.11 -    68.23: 226
       68.23 -   102.34: 44
      102.34 -   136.45: 50
      136.45 -   170.56: 2
  Dihedral angle restraints: 4090
    sinusoidal: 1802
      harmonic: 2288
  Sorted by residual:
  dihedral pdb=" CBG LMN B 502 "
           pdb=" CBI LMN B 502 "
           pdb=" CBK LMN B 502 "
           pdb=" CBQ LMN B 502 "
      ideal   model   delta sinusoidal    sigma   weight residual
     181.33   10.77  170.56     1      3.00e+01 1.11e-03 2.12e+01
  dihedral pdb=" CBG LMN A 502 "
           pdb=" CBI LMN A 502 "
           pdb=" CBK LMN A 502 "
           pdb=" CBQ LMN A 502 "
      ideal   model   delta sinusoidal    sigma   weight residual
     181.33   10.83  170.50     1      3.00e+01 1.11e-03 2.12e+01
  dihedral pdb=" CCD LMN A 501 "
           pdb=" CCS LMN A 501 "
           pdb=" OBZ LMN A 501 "
           pdb=" OCB LMN A 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.96 -177.02 -122.02     1      3.00e+01 1.11e-03 1.63e+01
  ... (remaining 4087 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.038: 748
       0.038 -    0.076: 222
       0.076 -    0.114: 45
       0.114 -    0.152: 29
       0.152 -    0.191: 12
  Chirality restraints: 1056
  Sorted by residual:
  chirality pdb=" CCV LMN B 502 "
            pdb=" CCR LMN B 502 "
            pdb=" CCT LMN B 502 "
            pdb=" OAU LMN B 502 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.28    2.47   -0.19 2.00e-01 2.50e+01 9.08e-01
  chirality pdb=" CCV LMN A 502 "
            pdb=" CCR LMN A 502 "
            pdb=" CCT LMN A 502 "
            pdb=" OAU LMN A 502 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.28    2.47   -0.19 2.00e-01 2.50e+01 9.08e-01
  chirality pdb=" CA  MET B  17 "
            pdb=" N   MET B  17 "
            pdb=" C   MET B  17 "
            pdb=" CB  MET B  17 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.68   -0.17 2.00e-01 2.50e+01 7.44e-01
  ... (remaining 1053 not shown)

  Planarity restraints: 1056
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE B  42 "    0.031 5.00e-02 4.00e+02   4.76e-02 3.63e+00
        pdb=" N   PRO B  43 "   -0.082 5.00e-02 4.00e+02
        pdb=" CA  PRO B  43 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO B  43 "    0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A  42 "   -0.031 5.00e-02 4.00e+02   4.76e-02 3.63e+00
        pdb=" N   PRO A  43 "    0.082 5.00e-02 4.00e+02
        pdb=" CA  PRO A  43 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO A  43 "   -0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A 130 "   -0.031 5.00e-02 4.00e+02   4.68e-02 3.50e+00
        pdb=" N   PRO A 131 "    0.081 5.00e-02 4.00e+02
        pdb=" CA  PRO A 131 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A 131 "   -0.026 5.00e-02 4.00e+02
  ... (remaining 1053 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.74: 489
        2.74 -     3.28: 6240
        3.28 -     3.82: 10920
        3.82 -     4.36: 11484
        4.36 -     4.90: 21257
  Nonbonded interactions: 50390
  Sorted by model distance:
  nonbonded pdb=" O6  LMN A 502 "
            pdb=" OAN LMN A 502 "
     model   vdw
     2.194 3.040
  nonbonded pdb=" O6  LMN B 502 "
            pdb=" OAN LMN B 502 "
     model   vdw
     2.194 3.040
  nonbonded pdb=" OE1 GLU B  41 "
            pdb=" NE1 TRP B 165 "
     model   vdw
     2.290 3.120
  nonbonded pdb=" OE1 GLU A  41 "
            pdb=" NE1 TRP A 165 "
     model   vdw
     2.290 3.120
  nonbonded pdb=" O2  LMN A 501 "
            pdb=" OAN LMN A 501 "
     model   vdw
     2.334 3.040
  ... (remaining 50385 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=1.00 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:             3.000
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     8.390
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.300
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.890
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8116
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      :  0.011   0.133   6628  Z= 0.550
  Angle     :  0.836  11.024   9022  Z= 0.410
  Chirality :  0.045   0.191   1056
  Planarity :  0.005   0.048   1056
  Dihedral  : 26.789 170.564   2638
  Min Nonbonded Distance : 2.194

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.25 %
    Favored  : 95.75 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  : 24.31 %
    Favored  : 75.38 %
  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:  2.79 (0.30), residues: 800
  helix:  2.64 (0.20), residues: 652
  sheet:  None (None), residues: 0
  loop : -2.02 (0.44), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 286 
 TYR   0.020   0.001   TYR A 265 
 PHE   0.015   0.002   PHE B 340 
 TRP   0.011   0.001   TRP B 165 
 HIS   0.004   0.001   HIS B 390 

Details of bonding type rmsd
  covalent geometry    : bond        0.01076 ( 6628)
  covalent geometry    : angle       0.83573 ( 9022)
  hydrogen bonds       : bond        0.08155 (  509)
  hydrogen bonds       : angle       4.00998 ( 1521)

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

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

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 84
  time to evaluate  : 0.232 
Fit side-chains
REVERT: A  266 MET cc_start: 0.7987 (tpp) cc_final: 0.7656 (mmm)
REVERT: B  266 MET cc_start: 0.7983 (tpp) cc_final: 0.7652 (mmm)
  outliers start: 2
  outliers final: 0
  residues processed: 86
  average time/residue: 0.0892
  time to fit residues: 10.2420
Evaluate side-chains
  76 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 76
  time to evaluate  : 0.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 49 optimal weight:    0.0170
   chunk 53 optimal weight:    0.7980
   chunk 5 optimal weight:    0.6980
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    0.8980
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    0.6980
   chunk 45 optimal weight:    0.7980
   chunk 74 optimal weight:    2.9990
   overall best weight:    0.5818

-------------------------------------------------------------------------------
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 = 0.3981 r_free = 0.3981 target = 0.172907 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.150704 restraints weight = 7290.651|
|-----------------------------------------------------------------------------|
r_work (start): 0.3749 rms_B_bonded: 1.54
r_work: 0.3635 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3512 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.3512
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8083
moved from start:          0.0734

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6628  Z= 0.152
  Angle     :  0.696   8.915   9022  Z= 0.318
  Chirality :  0.046   0.370   1056
  Planarity :  0.005   0.042   1056
  Dihedral  : 16.741 126.119   1362
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 4.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.50 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 23.38 %
    Favored  : 74.46 %
  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:  2.99 (0.30), residues: 800
  helix:  2.83 (0.20), residues: 648
  sheet:  None (None), residues: 0
  loop : -2.14 (0.42), residues: 152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 166 
 TYR   0.011   0.001   TYR B  24 
 PHE   0.015   0.002   PHE A 340 
 TRP   0.009   0.001   TRP B 138 
 HIS   0.003   0.001   HIS B 390 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 6628)
  covalent geometry    : angle       0.69645 ( 9022)
  hydrogen bonds       : bond        0.06122 (  509)
  hydrogen bonds       : angle       3.66817 ( 1521)

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

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

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 89
  time to evaluate  : 0.242 
Fit side-chains
REVERT: A  154 ILE cc_start: 0.8382 (OUTLIER) cc_final: 0.7686 (mp)
REVERT: A  266 MET cc_start: 0.7978 (tpp) cc_final: 0.7366 (mmm)
REVERT: B  154 ILE cc_start: 0.8385 (OUTLIER) cc_final: 0.7686 (mp)
REVERT: B  266 MET cc_start: 0.7980 (tpp) cc_final: 0.7368 (mmm)
  outliers start: 14
  outliers final: 8
  residues processed: 97
  average time/residue: 0.0839
  time to fit residues: 11.0340
Evaluate side-chains
  99 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 89
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 VAL
Chi-restraints excluded: chain A residue  127 LYS
Chi-restraints excluded: chain A residue  136 THR
Chi-restraints excluded: chain A residue  154 ILE
Chi-restraints excluded: chain A residue  323 THR
Chi-restraints excluded: chain B residue   69 VAL
Chi-restraints excluded: chain B residue  127 LYS
Chi-restraints excluded: chain B residue  136 THR
Chi-restraints excluded: chain B residue  154 ILE
Chi-restraints excluded: chain B residue  323 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 1 optimal weight:    2.9990
   chunk 11 optimal weight:    1.9990
   chunk 4 optimal weight:    0.5980
   chunk 19 optimal weight:    8.9990
   chunk 78 optimal weight:    2.9990
   chunk 71 optimal weight:    0.8980
   chunk 30 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9990
   chunk 42 optimal weight:    0.9980
   chunk 54 optimal weight:    0.5980
   chunk 17 optimal weight:    0.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
** A  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.168953 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.146756 restraints weight = 7284.292|
|-----------------------------------------------------------------------------|
r_work (start): 0.3695 rms_B_bonded: 1.49
r_work: 0.3583 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3464 rms_B_bonded: 4.28 restraints_weight: 0.2500
r_work (final): 0.3464
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8144
moved from start:          0.1020

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6628  Z= 0.166
  Angle     :  0.655   6.837   9022  Z= 0.315
  Chirality :  0.044   0.299   1056
  Planarity :  0.005   0.042   1056
  Dihedral  : 14.529 111.669   1362
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 4.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.50 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 24.31 %
    Favored  : 73.85 %
  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:  2.92 (0.31), residues: 800
  helix:  2.76 (0.20), residues: 654
  sheet:  None (None), residues: 0
  loop : -2.25 (0.43), residues: 146

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 415 
 TYR   0.012   0.001   TYR B  24 
 PHE   0.015   0.002   PHE B 340 
 TRP   0.010   0.002   TRP B 107 
 HIS   0.004   0.001   HIS B 390 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 6628)
  covalent geometry    : angle       0.65543 ( 9022)
  hydrogen bonds       : bond        0.06939 (  509)
  hydrogen bonds       : angle       3.74413 ( 1521)

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

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

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 80
  time to evaluate  : 0.222 
Fit side-chains
REVERT: A  154 ILE cc_start: 0.8385 (OUTLIER) cc_final: 0.7687 (mp)
REVERT: A  266 MET cc_start: 0.8027 (tpp) cc_final: 0.7425 (mmm)
REVERT: B  154 ILE cc_start: 0.8385 (OUTLIER) cc_final: 0.7691 (mp)
REVERT: B  266 MET cc_start: 0.8021 (tpp) cc_final: 0.7418 (mmm)
  outliers start: 12
  outliers final: 8
  residues processed: 86
  average time/residue: 0.0671
  time to fit residues: 8.3282
Evaluate side-chains
  88 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 78
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  127 LYS
Chi-restraints excluded: chain A residue  136 THR
Chi-restraints excluded: chain A residue  144 SER
Chi-restraints excluded: chain A residue  154 ILE
Chi-restraints excluded: chain A residue  323 THR
Chi-restraints excluded: chain B residue  127 LYS
Chi-restraints excluded: chain B residue  136 THR
Chi-restraints excluded: chain B residue  144 SER
Chi-restraints excluded: chain B residue  154 ILE
Chi-restraints excluded: chain B residue  323 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 55 optimal weight:    1.9990
   chunk 76 optimal weight:    1.9990
   chunk 62 optimal weight:    0.5980
   chunk 4 optimal weight:    0.7980
   chunk 52 optimal weight:    0.9990
   chunk 1 optimal weight:    2.9990
   chunk 47 optimal weight:    0.5980
   chunk 11 optimal weight:    0.4980
   chunk 58 optimal weight:    2.9990
   chunk 36 optimal weight:    0.5980
   chunk 24 optimal weight:    4.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** A  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.172200 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.150225 restraints weight = 7360.397|
|-----------------------------------------------------------------------------|
r_work (start): 0.3738 rms_B_bonded: 1.51
r_work: 0.3627 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3505 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.3505
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8096
moved from start:          0.1052

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6628  Z= 0.143
  Angle     :  0.599   6.556   9022  Z= 0.292
  Chirality :  0.040   0.297   1056
  Planarity :  0.005   0.042   1056
  Dihedral  : 13.293 107.046   1362
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 4.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 22.46 %
    Favored  : 74.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.97 (0.31), residues: 800
  helix:  2.78 (0.20), residues: 654
  sheet:  None (None), residues: 0
  loop : -2.15 (0.44), residues: 146

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 300 
 TYR   0.011   0.001   TYR A  24 
 PHE   0.016   0.001   PHE A 340 
 TRP   0.009   0.001   TRP B 227 
 HIS   0.003   0.001   HIS B 390 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 6628)
  covalent geometry    : angle       0.59893 ( 9022)
  hydrogen bonds       : bond        0.06064 (  509)
  hydrogen bonds       : angle       3.62841 ( 1521)

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

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

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 87
  time to evaluate  : 0.212 
Fit side-chains
REVERT: A   74 MET cc_start: 0.6025 (tpt) cc_final: 0.5812 (mmm)
REVERT: A  154 ILE cc_start: 0.8313 (OUTLIER) cc_final: 0.7624 (mp)
REVERT: A  266 MET cc_start: 0.7923 (tpp) cc_final: 0.7333 (tpp)
REVERT: B   74 MET cc_start: 0.5987 (tpt) cc_final: 0.5784 (mmm)
REVERT: B  154 ILE cc_start: 0.8320 (OUTLIER) cc_final: 0.7632 (mp)
REVERT: B  266 MET cc_start: 0.7919 (tpp) cc_final: 0.7328 (tpp)
  outliers start: 23
  outliers final: 12
  residues processed: 104
  average time/residue: 0.0571
  time to fit residues: 8.3783
Evaluate side-chains
  101 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 87
  time to evaluate  : 0.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 VAL
Chi-restraints excluded: chain A residue  127 LYS
Chi-restraints excluded: chain A residue  136 THR
Chi-restraints excluded: chain A residue  144 SER
Chi-restraints excluded: chain A residue  154 ILE
Chi-restraints excluded: chain A residue  323 THR
Chi-restraints excluded: chain A residue  364 THR
Chi-restraints excluded: chain B residue   69 VAL
Chi-restraints excluded: chain B residue  127 LYS
Chi-restraints excluded: chain B residue  136 THR
Chi-restraints excluded: chain B residue  144 SER
Chi-restraints excluded: chain B residue  154 ILE
Chi-restraints excluded: chain B residue  323 THR
Chi-restraints excluded: chain B residue  364 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 50 optimal weight:    0.7980
   chunk 52 optimal weight:    2.9990
   chunk 2 optimal weight:    1.9990
   chunk 74 optimal weight:    2.9990
   chunk 14 optimal weight:    2.9990
   chunk 68 optimal weight:    0.6980
   chunk 9 optimal weight:    0.5980
   chunk 65 optimal weight:    0.9980
   chunk 32 optimal weight:    0.0670
   chunk 35 optimal weight:    0.6980
   chunk 3 optimal weight:    0.8980
   overall best weight:    0.5718

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

Flipped N/Q/H residues before XYZ refinement:
A  27 ASN
A  91 ASN
B  27 ASN
B  91 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.157572 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.133417 restraints weight = 7527.691|
|-----------------------------------------------------------------------------|
r_work (start): 0.3428 rms_B_bonded: 1.65
r_work: 0.3344 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.3213 rms_B_bonded: 4.09 restraints_weight: 0.2500
r_work (final): 0.3213
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7592
moved from start:          0.1232

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6628  Z= 0.139
  Angle     :  0.581   6.500   9022  Z= 0.286
  Chirality :  0.039   0.290   1056
  Planarity :  0.005   0.042   1056
  Dihedral  : 12.906 107.042   1362
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 4.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.50 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 22.31 %
    Favored  : 74.31 %
  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:  3.00 (0.30), residues: 800
  helix:  2.79 (0.20), residues: 654
  sheet:  None (None), residues: 0
  loop : -2.08 (0.45), residues: 146

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 415 
 TYR   0.012   0.001   TYR A  24 
 PHE   0.016   0.001   PHE B 340 
 TRP   0.011   0.001   TRP B 107 
 HIS   0.003   0.001   HIS A 390 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 6628)
  covalent geometry    : angle       0.58103 ( 9022)
  hydrogen bonds       : bond        0.06048 (  509)
  hydrogen bonds       : angle       3.59620 ( 1521)

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

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

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 88
  time to evaluate  : 0.194 
Fit side-chains
REVERT: A    6 TYR cc_start: 0.5827 (OUTLIER) cc_final: 0.5374 (m-80)
REVERT: A   74 MET cc_start: 0.5765 (tpt) cc_final: 0.5537 (mmm)
REVERT: A  154 ILE cc_start: 0.7544 (OUTLIER) cc_final: 0.6999 (mp)
REVERT: A  266 MET cc_start: 0.7350 (tpp) cc_final: 0.6716 (tpp)
REVERT: A  360 ASN cc_start: 0.7359 (m-40) cc_final: 0.6726 (p0)
REVERT: B   74 MET cc_start: 0.5737 (tpt) cc_final: 0.5507 (mmm)
REVERT: B  154 ILE cc_start: 0.7540 (OUTLIER) cc_final: 0.6998 (mp)
REVERT: B  266 MET cc_start: 0.7334 (tpp) cc_final: 0.6699 (tpp)
REVERT: B  360 ASN cc_start: 0.7350 (m-40) cc_final: 0.6726 (p0)
  outliers start: 22
  outliers final: 14
  residues processed: 104
  average time/residue: 0.0502
  time to fit residues: 7.6085
Evaluate side-chains
  105 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 88
  time to evaluate  : 0.213 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 TYR
Chi-restraints excluded: chain A residue   69 VAL
Chi-restraints excluded: chain A residue  127 LYS
Chi-restraints excluded: chain A residue  136 THR
Chi-restraints excluded: chain A residue  144 SER
Chi-restraints excluded: chain A residue  154 ILE
Chi-restraints excluded: chain A residue  274 LEU
Chi-restraints excluded: chain A residue  323 THR
Chi-restraints excluded: chain A residue  364 THR
Chi-restraints excluded: chain B residue   69 VAL
Chi-restraints excluded: chain B residue  127 LYS
Chi-restraints excluded: chain B residue  136 THR
Chi-restraints excluded: chain B residue  144 SER
Chi-restraints excluded: chain B residue  154 ILE
Chi-restraints excluded: chain B residue  274 LEU
Chi-restraints excluded: chain B residue  323 THR
Chi-restraints excluded: chain B residue  364 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 53 optimal weight:    1.9990
   chunk 60 optimal weight:    1.9990
   chunk 67 optimal weight:    4.9990
   chunk 12 optimal weight:    2.9990
   chunk 32 optimal weight:    0.0670
   chunk 36 optimal weight:    0.7980
   chunk 34 optimal weight:    1.9990
   chunk 51 optimal weight:    0.7980
   chunk 33 optimal weight:    0.5980
   chunk 9 optimal weight:    0.5980
   chunk 54 optimal weight:    0.9990
   overall best weight:    0.5718

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

Flipped N/Q/H residues before XYZ refinement:
A  91 ASN
B  91 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.157863 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.133872 restraints weight = 7500.940|
|-----------------------------------------------------------------------------|
r_work (start): 0.3434 rms_B_bonded: 1.64
r_work: 0.3351 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.3220 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.3220
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7584
moved from start:          0.1299

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   6628  Z= 0.138
  Angle     :  0.580   7.204   9022  Z= 0.285
  Chirality :  0.039   0.284   1056
  Planarity :  0.005   0.041   1056
  Dihedral  : 12.649 105.455   1362
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 5.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.25 %
    Favored  : 95.75 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 21.23 %
    Favored  : 75.23 %
  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:  3.05 (0.30), residues: 800
  helix:  2.81 (0.20), residues: 654
  sheet:  None (None), residues: 0
  loop : -1.98 (0.45), residues: 146

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 415 
 TYR   0.012   0.001   TYR B  24 
 PHE   0.016   0.001   PHE A 340 
 TRP   0.008   0.001   TRP B 138 
 HIS   0.003   0.001   HIS B 390 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 6628)
  covalent geometry    : angle       0.58012 ( 9022)
  hydrogen bonds       : bond        0.05977 (  509)
  hydrogen bonds       : angle       3.57290 ( 1521)

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

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

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 88
  time to evaluate  : 0.214 
Fit side-chains
REVERT: A    6 TYR cc_start: 0.5836 (OUTLIER) cc_final: 0.5383 (m-80)
REVERT: A   74 MET cc_start: 0.5794 (tpt) cc_final: 0.5557 (mmm)
REVERT: A  154 ILE cc_start: 0.7507 (OUTLIER) cc_final: 0.6963 (mp)
REVERT: A  266 MET cc_start: 0.7320 (tpp) cc_final: 0.6703 (tpp)
REVERT: A  360 ASN cc_start: 0.7415 (m-40) cc_final: 0.6764 (p0)
REVERT: B   74 MET cc_start: 0.5733 (tpt) cc_final: 0.5510 (mmm)
REVERT: B  154 ILE cc_start: 0.7506 (OUTLIER) cc_final: 0.6966 (mp)
REVERT: B  266 MET cc_start: 0.7312 (tpp) cc_final: 0.6690 (tpp)
REVERT: B  360 ASN cc_start: 0.7407 (m-40) cc_final: 0.6761 (p0)
  outliers start: 23
  outliers final: 16
  residues processed: 105
  average time/residue: 0.0482
  time to fit residues: 7.5156
Evaluate side-chains
  107 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 88
  time to evaluate  : 0.157 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 TYR
Chi-restraints excluded: chain A residue   69 VAL
Chi-restraints excluded: chain A residue   91 ASN
Chi-restraints excluded: chain A residue  127 LYS
Chi-restraints excluded: chain A residue  136 THR
Chi-restraints excluded: chain A residue  144 SER
Chi-restraints excluded: chain A residue  154 ILE
Chi-restraints excluded: chain A residue  274 LEU
Chi-restraints excluded: chain A residue  323 THR
Chi-restraints excluded: chain A residue  364 THR
Chi-restraints excluded: chain B residue   69 VAL
Chi-restraints excluded: chain B residue   91 ASN
Chi-restraints excluded: chain B residue  127 LYS
Chi-restraints excluded: chain B residue  136 THR
Chi-restraints excluded: chain B residue  144 SER
Chi-restraints excluded: chain B residue  154 ILE
Chi-restraints excluded: chain B residue  274 LEU
Chi-restraints excluded: chain B residue  323 THR
Chi-restraints excluded: chain B residue  364 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 45 optimal weight:    4.9990
   chunk 25 optimal weight:    0.9980
   chunk 17 optimal weight:    0.9990
   chunk 18 optimal weight:    3.9990
   chunk 67 optimal weight:    0.6980
   chunk 74 optimal weight:    0.0270
   chunk 72 optimal weight:    0.0980
   chunk 55 optimal weight:    1.9990
   chunk 48 optimal weight:    2.9990
   chunk 42 optimal weight:    0.6980
   chunk 19 optimal weight:    8.9990
   overall best weight:    0.5038

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

Flipped N/Q/H residues before XYZ refinement:
A  91 ASN
B  91 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.158641 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.134633 restraints weight = 7433.918|
|-----------------------------------------------------------------------------|
r_work (start): 0.3436 rms_B_bonded: 1.64
r_work: 0.3351 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.3221 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.3221
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7566
moved from start:          0.1354

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   6628  Z= 0.133
  Angle     :  0.568   6.819   9022  Z= 0.280
  Chirality :  0.038   0.282   1056
  Planarity :  0.005   0.041   1056
  Dihedral  : 12.541 104.908   1362
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 5.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 21.54 %
    Favored  : 75.54 %
  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:  3.08 (0.30), residues: 800
  helix:  2.82 (0.20), residues: 654
  sheet:  None (None), residues: 0
  loop : -1.91 (0.45), residues: 146

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 415 
 TYR   0.011   0.001   TYR A  24 
 PHE   0.016   0.001   PHE A 340 
 TRP   0.012   0.001   TRP A 107 
 HIS   0.003   0.001   HIS A 390 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 ( 6628)
  covalent geometry    : angle       0.56834 ( 9022)
  hydrogen bonds       : bond        0.05825 (  509)
  hydrogen bonds       : angle       3.54818 ( 1521)

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

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

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 88
  time to evaluate  : 0.132 
Fit side-chains
REVERT: A    6 TYR cc_start: 0.5802 (OUTLIER) cc_final: 0.5354 (m-80)
REVERT: A   74 MET cc_start: 0.5775 (tpt) cc_final: 0.5540 (mmm)
REVERT: A  154 ILE cc_start: 0.7483 (OUTLIER) cc_final: 0.6936 (mp)
REVERT: A  266 MET cc_start: 0.7267 (tpp) cc_final: 0.6653 (tpp)
REVERT: A  360 ASN cc_start: 0.7419 (m-40) cc_final: 0.6736 (p0)
REVERT: B   74 MET cc_start: 0.5745 (tpt) cc_final: 0.5511 (mmm)
REVERT: B  154 ILE cc_start: 0.7489 (OUTLIER) cc_final: 0.6946 (mp)
REVERT: B  266 MET cc_start: 0.7255 (tpp) cc_final: 0.6638 (tpp)
REVERT: B  360 ASN cc_start: 0.7410 (m-40) cc_final: 0.6734 (p0)
  outliers start: 19
  outliers final: 16
  residues processed: 101
  average time/residue: 0.0501
  time to fit residues: 7.3219
Evaluate side-chains
  107 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 88
  time to evaluate  : 0.205 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 TYR
Chi-restraints excluded: chain A residue   69 VAL
Chi-restraints excluded: chain A residue   91 ASN
Chi-restraints excluded: chain A residue  127 LYS
Chi-restraints excluded: chain A residue  136 THR
Chi-restraints excluded: chain A residue  144 SER
Chi-restraints excluded: chain A residue  154 ILE
Chi-restraints excluded: chain A residue  274 LEU
Chi-restraints excluded: chain A residue  323 THR
Chi-restraints excluded: chain A residue  364 THR
Chi-restraints excluded: chain B residue   69 VAL
Chi-restraints excluded: chain B residue   91 ASN
Chi-restraints excluded: chain B residue  127 LYS
Chi-restraints excluded: chain B residue  136 THR
Chi-restraints excluded: chain B residue  144 SER
Chi-restraints excluded: chain B residue  154 ILE
Chi-restraints excluded: chain B residue  274 LEU
Chi-restraints excluded: chain B residue  323 THR
Chi-restraints excluded: chain B residue  364 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 34 optimal weight:    3.9990
   chunk 41 optimal weight:    2.9990
   chunk 12 optimal weight:    2.9990
   chunk 14 optimal weight:    2.9990
   chunk 43 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 9 optimal weight:    0.7980
   chunk 68 optimal weight:    0.9980
   chunk 2 optimal weight:    0.6980
   chunk 79 optimal weight:    2.9990
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
A  91 ASN
B  91 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.149082 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.124670 restraints weight = 7560.371|
|-----------------------------------------------------------------------------|
r_work (start): 0.3325 rms_B_bonded: 1.63
r_work: 0.3236 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.3102 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.3102
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7734
moved from start:          0.1637

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   6628  Z= 0.204
  Angle     :  0.675   7.774   9022  Z= 0.334
  Chirality :  0.043   0.285   1056
  Planarity :  0.005   0.044   1056
  Dihedral  : 12.983 108.527   1362
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 4.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.75 %
    Favored  : 95.25 %
  Rotamer:
    Outliers :  4.15 %
    Allowed  : 20.92 %
    Favored  : 74.92 %
  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:  2.76 (0.30), residues: 800
  helix:  2.61 (0.20), residues: 658
  sheet:  None (None), residues: 0
  loop : -2.22 (0.43), residues: 142

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 415 
 TYR   0.013   0.002   TYR A  24 
 PHE   0.017   0.002   PHE A  94 
 TRP   0.013   0.002   TRP A 107 
 HIS   0.004   0.001   HIS A 390 

Details of bonding type rmsd
  covalent geometry    : bond        0.00456 ( 6628)
  covalent geometry    : angle       0.67477 ( 9022)
  hydrogen bonds       : bond        0.08134 (  509)
  hydrogen bonds       : angle       3.87788 ( 1521)

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

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

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 78
  time to evaluate  : 0.177 
Fit side-chains
REVERT: A  154 ILE cc_start: 0.7564 (OUTLIER) cc_final: 0.7021 (mp)
REVERT: B  154 ILE cc_start: 0.7578 (OUTLIER) cc_final: 0.7035 (mp)
  outliers start: 27
  outliers final: 23
  residues processed: 101
  average time/residue: 0.0616
  time to fit residues: 8.9888
Evaluate side-chains
  103 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 78
  time to evaluate  : 0.202 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 TYR
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue   69 VAL
Chi-restraints excluded: chain A residue   91 ASN
Chi-restraints excluded: chain A residue  127 LYS
Chi-restraints excluded: chain A residue  136 THR
Chi-restraints excluded: chain A residue  144 SER
Chi-restraints excluded: chain A residue  154 ILE
Chi-restraints excluded: chain A residue  223 SER
Chi-restraints excluded: chain A residue  274 LEU
Chi-restraints excluded: chain A residue  323 THR
Chi-restraints excluded: chain A residue  364 THR
Chi-restraints excluded: chain A residue  394 SER
Chi-restraints excluded: chain B residue   38 LEU
Chi-restraints excluded: chain B residue   69 VAL
Chi-restraints excluded: chain B residue   91 ASN
Chi-restraints excluded: chain B residue  127 LYS
Chi-restraints excluded: chain B residue  136 THR
Chi-restraints excluded: chain B residue  144 SER
Chi-restraints excluded: chain B residue  154 ILE
Chi-restraints excluded: chain B residue  223 SER
Chi-restraints excluded: chain B residue  274 LEU
Chi-restraints excluded: chain B residue  323 THR
Chi-restraints excluded: chain B residue  364 THR
Chi-restraints excluded: chain B residue  394 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 37 optimal weight:    1.9990
   chunk 34 optimal weight:    2.9990
   chunk 27 optimal weight:    4.9990
   chunk 30 optimal weight:    0.5980
   chunk 22 optimal weight:    0.6980
   chunk 75 optimal weight:    0.8980
   chunk 49 optimal weight:    0.8980
   chunk 42 optimal weight:    0.9990
   chunk 69 optimal weight:    0.9980
   chunk 5 optimal weight:    1.9990
   chunk 17 optimal weight:    0.7980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A  91 ASN
B  91 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.154123 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.129874 restraints weight = 7629.803|
|-----------------------------------------------------------------------------|
r_work (start): 0.3397 rms_B_bonded: 1.64
r_work: 0.3310 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3177 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.3177
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7706
moved from start:          0.1493

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6628  Z= 0.156
  Angle     :  0.612   7.094   9022  Z= 0.304
  Chirality :  0.040   0.289   1056
  Planarity :  0.005   0.043   1056
  Dihedral  : 12.713 108.088   1362
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 5.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  4.15 %
    Allowed  : 21.08 %
    Favored  : 74.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.89 (0.30), residues: 800
  helix:  2.70 (0.20), residues: 654
  sheet:  None (None), residues: 0
  loop : -2.04 (0.44), residues: 146

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 415 
 TYR   0.012   0.001   TYR A  24 
 PHE   0.016   0.002   PHE A 340 
 TRP   0.011   0.001   TRP A 227 
 HIS   0.004   0.001   HIS B 390 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 6628)
  covalent geometry    : angle       0.61245 ( 9022)
  hydrogen bonds       : bond        0.06806 (  509)
  hydrogen bonds       : angle       3.71672 ( 1521)

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

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

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 80
  time to evaluate  : 0.152 
Fit side-chains
REVERT: A   74 MET cc_start: 0.5818 (tpt) cc_final: 0.5578 (mmm)
REVERT: A  154 ILE cc_start: 0.7651 (OUTLIER) cc_final: 0.7094 (mp)
REVERT: A  266 MET cc_start: 0.7449 (tpp) cc_final: 0.6868 (tpp)
REVERT: B   74 MET cc_start: 0.5813 (tpt) cc_final: 0.5575 (mmm)
REVERT: B  154 ILE cc_start: 0.7655 (OUTLIER) cc_final: 0.7099 (mp)
REVERT: B  266 MET cc_start: 0.7435 (tpp) cc_final: 0.6847 (tpp)
  outliers start: 27
  outliers final: 21
  residues processed: 101
  average time/residue: 0.0531
  time to fit residues: 7.8313
Evaluate side-chains
  103 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 80
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue   69 VAL
Chi-restraints excluded: chain A residue   91 ASN
Chi-restraints excluded: chain A residue  127 LYS
Chi-restraints excluded: chain A residue  136 THR
Chi-restraints excluded: chain A residue  141 LEU
Chi-restraints excluded: chain A residue  144 SER
Chi-restraints excluded: chain A residue  154 ILE
Chi-restraints excluded: chain A residue  274 LEU
Chi-restraints excluded: chain A residue  323 THR
Chi-restraints excluded: chain A residue  364 THR
Chi-restraints excluded: chain A residue  394 SER
Chi-restraints excluded: chain B residue   38 LEU
Chi-restraints excluded: chain B residue   69 VAL
Chi-restraints excluded: chain B residue   91 ASN
Chi-restraints excluded: chain B residue  127 LYS
Chi-restraints excluded: chain B residue  136 THR
Chi-restraints excluded: chain B residue  144 SER
Chi-restraints excluded: chain B residue  154 ILE
Chi-restraints excluded: chain B residue  274 LEU
Chi-restraints excluded: chain B residue  323 THR
Chi-restraints excluded: chain B residue  364 THR
Chi-restraints excluded: chain B residue  394 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 13 optimal weight:    0.9980
   chunk 30 optimal weight:    0.4980
   chunk 73 optimal weight:    0.7980
   chunk 53 optimal weight:    0.9980
   chunk 24 optimal weight:    5.9990
   chunk 54 optimal weight:    0.6980
   chunk 17 optimal weight:    0.9980
   chunk 48 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9990
   chunk 74 optimal weight:    0.0030
   chunk 58 optimal weight:    2.9990
   overall best weight:    0.5990

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

Flipped N/Q/H residues before XYZ refinement:
A  91 ASN
B  91 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.154630 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.130510 restraints weight = 7509.116|
|-----------------------------------------------------------------------------|
r_work (start): 0.3424 rms_B_bonded: 1.63
r_work: 0.3339 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.3209 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.3209
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7654
moved from start:          0.1448

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6628  Z= 0.144
  Angle     :  0.599   6.890   9022  Z= 0.298
  Chirality :  0.039   0.287   1056
  Planarity :  0.005   0.043   1056
  Dihedral  : 12.459 107.081   1362
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 5.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.75 %
    Favored  : 95.25 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 21.38 %
    Favored  : 74.92 %
  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:  2.94 (0.30), residues: 800
  helix:  2.73 (0.20), residues: 654
  sheet:  None (None), residues: 0
  loop : -1.99 (0.45), residues: 146

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 415 
 TYR   0.012   0.001   TYR A  24 
 PHE   0.016   0.001   PHE A  18 
 TRP   0.009   0.001   TRP A 227 
 HIS   0.003   0.001   HIS A 390 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 6628)
  covalent geometry    : angle       0.59939 ( 9022)
  hydrogen bonds       : bond        0.06323 (  509)
  hydrogen bonds       : angle       3.66105 ( 1521)

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

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

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 86
  time to evaluate  : 0.136 
Fit side-chains
REVERT: A   74 MET cc_start: 0.5805 (tpt) cc_final: 0.5565 (mmm)
REVERT: A  154 ILE cc_start: 0.7612 (OUTLIER) cc_final: 0.7059 (mp)
REVERT: A  266 MET cc_start: 0.7370 (tpp) cc_final: 0.6786 (tpp)
REVERT: A  360 ASN cc_start: 0.7467 (m-40) cc_final: 0.6899 (p0)
REVERT: B   74 MET cc_start: 0.5788 (tpt) cc_final: 0.5549 (mmm)
REVERT: B  154 ILE cc_start: 0.7627 (OUTLIER) cc_final: 0.7075 (mp)
REVERT: B  266 MET cc_start: 0.7351 (tpp) cc_final: 0.6759 (tpp)
REVERT: B  360 ASN cc_start: 0.7463 (m-40) cc_final: 0.6904 (p0)
  outliers start: 24
  outliers final: 22
  residues processed: 106
  average time/residue: 0.0648
  time to fit residues: 9.6056
Evaluate side-chains
  108 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 84
  time to evaluate  : 0.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 TYR
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue   69 VAL
Chi-restraints excluded: chain A residue   91 ASN
Chi-restraints excluded: chain A residue  127 LYS
Chi-restraints excluded: chain A residue  136 THR
Chi-restraints excluded: chain A residue  141 LEU
Chi-restraints excluded: chain A residue  144 SER
Chi-restraints excluded: chain A residue  154 ILE
Chi-restraints excluded: chain A residue  274 LEU
Chi-restraints excluded: chain A residue  323 THR
Chi-restraints excluded: chain A residue  364 THR
Chi-restraints excluded: chain A residue  394 SER
Chi-restraints excluded: chain B residue   38 LEU
Chi-restraints excluded: chain B residue   69 VAL
Chi-restraints excluded: chain B residue   91 ASN
Chi-restraints excluded: chain B residue  127 LYS
Chi-restraints excluded: chain B residue  136 THR
Chi-restraints excluded: chain B residue  144 SER
Chi-restraints excluded: chain B residue  154 ILE
Chi-restraints excluded: chain B residue  274 LEU
Chi-restraints excluded: chain B residue  323 THR
Chi-restraints excluded: chain B residue  364 THR
Chi-restraints excluded: chain B residue  394 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 73 optimal weight:    3.9990
   chunk 20 optimal weight:    3.9990
   chunk 64 optimal weight:    5.9990
   chunk 38 optimal weight:    2.9990
   chunk 60 optimal weight:    3.9990
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    4.9990
   chunk 7 optimal weight:    0.6980
   chunk 77 optimal weight:    2.9990
   chunk 68 optimal weight:    0.6980
   chunk 41 optimal weight:    2.9990
   overall best weight:    1.6784

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

Flipped N/Q/H residues before XYZ refinement:
A  91 ASN
B  91 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.146876 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.122150 restraints weight = 7630.038|
|-----------------------------------------------------------------------------|
r_work (start): 0.3291 rms_B_bonded: 1.64
r_work: 0.3201 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.3070 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.3070
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7742
moved from start:          0.1903

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.043   6628  Z= 0.242
  Angle     :  0.743   8.135   9022  Z= 0.369
  Chirality :  0.045   0.292   1056
  Planarity :  0.006   0.045   1056
  Dihedral  : 13.309 111.696   1362
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 4.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.75 %
    Favored  : 95.25 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 21.38 %
    Favored  : 74.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.45 (0.30), residues: 800
  helix:  2.39 (0.20), residues: 658
  sheet:  None (None), residues: 0
  loop : -2.29 (0.43), residues: 142

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 415 
 TYR   0.014   0.002   TYR B  24 
 PHE   0.018   0.002   PHE B  94 
 TRP   0.012   0.002   TRP A 107 
 HIS   0.007   0.002   HIS B 390 

Details of bonding type rmsd
  covalent geometry    : bond        0.00559 ( 6628)
  covalent geometry    : angle       0.74261 ( 9022)
  hydrogen bonds       : bond        0.09181 (  509)
  hydrogen bonds       : angle       4.06542 ( 1521)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1481.55 seconds
wall clock time: 26 minutes 8.89 seconds (1568.89 seconds total)