Starting phenix.real_space_refine
on Sun Apr  5 04:57:52 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9if5_52841/04_2026/9if5_52841.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9if5_52841/04_2026/9if5_52841.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9if5_52841/04_2026/9if5_52841.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9if5_52841/04_2026/9if5_52841.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9if5_52841/04_2026/9if5_52841.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9if5_52841/04_2026/9if5_52841.map"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     Zn      2      6.06       5
     P     106      5.49       5
     S      24      5.16       5
     C    4790      2.51       5
     N    1491      2.21       5
     O    1738      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8151
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "E"
      Number of atoms: 1085
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 1085
          Classifications: {'DNA': 53}
          Modifications used: {'p5*END': 1}
          Link IDs: {'rna3p': 52}
    Chain: "F"
      Number of atoms: 1090
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 1090
          Classifications: {'DNA': 53}
          Modifications used: {'p5*END': 1}
          Link IDs: {'rna3p': 52}
    Chain: "A"
      Number of atoms: 2987
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 381, 2987
          Classifications: {'peptide': 381}
          Link IDs: {'PTRANS': 26, 'TRANS': 354}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2987
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 381, 2987
          Classifications: {'peptide': 381}
          Link IDs: {'PTRANS': 26, 'TRANS': 354}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   3953  SG  CYS A 366      79.402  36.391  40.342  1.00 90.00           S
  ATOM   3968  SG  CYS A 368      76.980  35.552  42.970  1.00 97.35           S
  ATOM   4113  SG  CYS A 387      80.721  34.283  43.379  1.00 93.39           S
  ATOM   6940  SG  CYS B 366      38.431  52.450 114.143  1.00150.68           S
  ATOM   6955  SG  CYS B 368      39.624  50.251 111.398  1.00142.28           S
  ATOM   7100  SG  CYS B 387      36.011  51.920 111.252  1.00148.63           S

  Time building chain proxies: 1.90, per 1000 atoms: 0.23
  Number of scatterers: 8151
  At special positions: 0
  Unit cell: (120.613, 93.68, 149.888, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      2     29.99
     S      24     16.00
     P     106     15.00
     O    1738      8.00
     N    1491      7.00
     C    4790      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: 0.51
  Conformation dependent library (CDL) restraints added in 253.5 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 601 "
        pdb="ZN    ZN A 601 " - pdb=" NE2 HIS A 401 "
        pdb="ZN    ZN A 601 " - pdb=" SG  CYS A 366 "
        pdb="ZN    ZN A 601 " - pdb=" SG  CYS A 368 "
        pdb="ZN    ZN A 601 " - pdb=" SG  CYS A 387 "
      pdb="  ZN B 601 "
        pdb="ZN    ZN B 601 " - pdb=" NE2 HIS B 401 "
        pdb="ZN    ZN B 601 " - pdb=" SG  CYS B 366 "
        pdb="ZN    ZN B 601 " - pdb=" SG  CYS B 368 "
        pdb="ZN    ZN B 601 " - pdb=" SG  CYS B 387 "
      Number of angles added : 6


  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1392

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 9 sheets defined
      40.4% alpha, 14.0% beta
      51 base pairs and 85 stacking pairs defined.
    Time for finding SS restraints: 1.31
  Creating SS restraints...
    Processing helix  chain 'A' and resid 140 through 163
    Processing helix  chain 'A' and resid 211 through 227
      removed outlier: 3.529A  pdb=" N   VAL A 215 " --> pdb=" O   PHE A 211 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   ILE A 216 " --> pdb=" O   GLU A 212 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 243 through 254
    Processing helix  chain 'A' and resid 258 through 263
    Processing helix  chain 'A' and resid 273 through 283
    Processing helix  chain 'A' and resid 284 through 288
    Processing helix  chain 'A' and resid 331 through 346
    Processing helix  chain 'A' and resid 379 through 382
    Processing helix  chain 'A' and resid 409 through 426
      removed outlier: 3.524A  pdb=" N   ILE A 424 " --> pdb=" O   ILE A 420 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 430 through 448
    Processing helix  chain 'A' and resid 522 through 527
    Processing helix  chain 'A' and resid 546 through 557
      removed outlier: 3.749A  pdb=" N   PHE A 557 " --> pdb=" O   PHE A 553 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 575 through 578
    Processing helix  chain 'B' and resid 141 through 163
      removed outlier: 3.641A  pdb=" N   LEU B 159 " --> pdb=" O   ASP B 155 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 211 through 227
      removed outlier: 3.588A  pdb=" N   VAL B 215 " --> pdb=" O   PHE B 211 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   ILE B 216 " --> pdb=" O   GLU B 212 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 243 through 254
    Processing helix  chain 'B' and resid 258 through 263
    Processing helix  chain 'B' and resid 273 through 283
    Processing helix  chain 'B' and resid 284 through 288
    Processing helix  chain 'B' and resid 331 through 345
    Processing helix  chain 'B' and resid 409 through 426
    Processing helix  chain 'B' and resid 430 through 448
    Processing helix  chain 'B' and resid 522 through 527
    Processing helix  chain 'B' and resid 540 through 545
    Processing helix  chain 'B' and resid 546 through 557
      removed outlier: 4.045A  pdb=" N   PHE B 557 " --> pdb=" O   PHE B 553 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 575 through 578
    Processing sheet with id=AA1, first strand: chain 'A' and resid 175 through 186
    Processing sheet with id=AA2, first strand: chain 'A' and resid 291 through 297
      removed outlier: 5.463A  pdb=" N   LYS A 296 " --> pdb=" O   ILE A 307 " (cutoff:3.500A)
      removed outlier: 6.735A  pdb=" N   ILE A 307 " --> pdb=" O   LYS A 296 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 364 through 366
    Processing sheet with id=AA4, first strand: chain 'A' and resid 371 through 372
      removed outlier: 4.290A  pdb=" N   VAL A 371 " --> pdb=" O   ARG A 388 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 384 through 385
    Processing sheet with id=AA6, first strand: chain 'B' and resid 175 through 186
    Processing sheet with id=AA7, first strand: chain 'B' and resid 291 through 297
      removed outlier: 5.519A  pdb=" N   LYS B 296 " --> pdb=" O   ILE B 307 " (cutoff:3.500A)
      removed outlier: 6.934A  pdb=" N   ILE B 307 " --> pdb=" O   LYS B 296 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 364 through 366
    Processing sheet with id=AA9, first strand: chain 'B' and resid 372 through 374
      removed outlier: 3.623A  pdb=" N   VAL B 407 " --> pdb=" O   TYR B 385 " (cutoff:3.500A)

    251 hydrogen bonds defined for protein.
    723 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      142 hydrogen bonds
      284 hydrogen bond angles
      0 basepair planarities
      51 basepair parallelities
      85 stacking parallelities
  Total time for adding SS restraints: 1.59

  Time building geometry restraints manager: 0.73 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2061
        1.33 -     1.45: 2193
        1.45 -     1.58: 4054
        1.58 -     1.70: 210
        1.70 -     1.82: 36
  Bond restraints: 8554
  Sorted by residual:
  bond pdb=" CA  MET A 361 "
       pdb=" C   MET A 361 "
    ideal  model  delta    sigma   weight residual
    1.523  1.496  0.027 1.41e-02 5.03e+03 3.61e+00
  bond pdb=" CG  ARG B 320 "
       pdb=" CD  ARG B 320 "
    ideal  model  delta    sigma   weight residual
    1.520  1.466  0.054 3.00e-02 1.11e+03 3.22e+00
  bond pdb=" CB  TRP A 219 "
       pdb=" CG  TRP A 219 "
    ideal  model  delta    sigma   weight residual
    1.498  1.449  0.049 3.10e-02 1.04e+03 2.53e+00
  bond pdb=" C3'  DC E   2 "
       pdb=" O3'  DC E   2 "
    ideal  model  delta    sigma   weight residual
    1.422  1.458 -0.036 3.00e-02 1.11e+03 1.46e+00
  bond pdb=" CB  ASP A 362 "
       pdb=" CG  ASP A 362 "
    ideal  model  delta    sigma   weight residual
    1.516  1.546 -0.030 2.50e-02 1.60e+03 1.46e+00
  ... (remaining 8549 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.17: 11992
        3.17 -     6.34: 32
        6.34 -     9.50: 3
        9.50 -    12.67: 3
       12.67 -    15.84: 1
  Bond angle restraints: 12031
  Sorted by residual:
  angle pdb=" CA  LEU A 319 "
        pdb=" CB  LEU A 319 "
        pdb=" CG  LEU A 319 "
      ideal   model   delta    sigma   weight residual
     116.30  132.14  -15.84 3.50e+00 8.16e-02 2.05e+01
  angle pdb=" CB  MET A 190 "
        pdb=" CG  MET A 190 "
        pdb=" SD  MET A 190 "
      ideal   model   delta    sigma   weight residual
     112.70  122.98  -10.28 3.00e+00 1.11e-01 1.17e+01
  angle pdb=" CB  ARG B 320 "
        pdb=" CG  ARG B 320 "
        pdb=" CD  ARG B 320 "
      ideal   model   delta    sigma   weight residual
     111.30  118.93   -7.63 2.30e+00 1.89e-01 1.10e+01
  angle pdb=" CA  ARG B 320 "
        pdb=" CB  ARG B 320 "
        pdb=" CG  ARG B 320 "
      ideal   model   delta    sigma   weight residual
     114.10  120.68   -6.58 2.00e+00 2.50e-01 1.08e+01
  angle pdb=" N   ARG B 320 "
        pdb=" CA  ARG B 320 "
        pdb=" CB  ARG B 320 "
      ideal   model   delta    sigma   weight residual
     110.03  113.89   -3.86 1.21e+00 6.83e-01 1.02e+01
  ... (remaining 12026 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.93: 4273
       35.93 -    71.86: 529
       71.86 -   107.79: 8
      107.79 -   143.72: 0
      143.72 -   179.65: 2
  Dihedral angle restraints: 4812
    sinusoidal: 2648
      harmonic: 2164
  Sorted by residual:
  dihedral pdb=" C4'  DC E   2 "
           pdb=" C3'  DC E   2 "
           pdb=" O3'  DC E   2 "
           pdb=" P    DG E   3 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   40.35  179.65     1      3.50e+01 8.16e-04 1.57e+01
  dihedral pdb=" C4'  DC E  36 "
           pdb=" C3'  DC E  36 "
           pdb=" O3'  DC E  36 "
           pdb=" P    DC E  37 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00   34.82 -174.82     1      3.50e+01 8.16e-04 1.56e+01
  dihedral pdb=" CA  THR B 318 "
           pdb=" C   THR B 318 "
           pdb=" N   LEU B 319 "
           pdb=" CA  LEU B 319 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.46   17.54     0      5.00e+00 4.00e-02 1.23e+01
  ... (remaining 4809 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 930
       0.036 -    0.071: 280
       0.071 -    0.107: 76
       0.107 -    0.143: 25
       0.143 -    0.178: 1
  Chirality restraints: 1312
  Sorted by residual:
  chirality pdb=" CA  LEU A 319 "
            pdb=" N   LEU A 319 "
            pdb=" C   LEU A 319 "
            pdb=" CB  LEU A 319 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 7.94e-01
  chirality pdb=" CA  PRO B 316 "
            pdb=" N   PRO B 316 "
            pdb=" C   PRO B 316 "
            pdb=" CB  PRO B 316 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.59    0.13 2.00e-01 2.50e+01 4.40e-01
  chirality pdb=" C1'  DA F  31 "
            pdb=" O4'  DA F  31 "
            pdb=" C2'  DA F  31 "
            pdb=" N9   DA F  31 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.42    2.29    0.13 2.00e-01 2.50e+01 4.27e-01
  ... (remaining 1309 not shown)

  Planarity restraints: 1172
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 320 "   -0.213 9.50e-02 1.11e+02   9.58e-02 5.72e+00
        pdb=" NE  ARG B 320 "    0.014 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 320 "   -0.003 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 320 "    0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 320 "   -0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU B 212 "    0.032 5.00e-02 4.00e+02   4.76e-02 3.63e+00
        pdb=" N   PRO B 213 "   -0.082 5.00e-02 4.00e+02
        pdb=" CA  PRO B 213 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO B 213 "    0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DT E  23 "    0.025 2.00e-02 2.50e+03   1.17e-02 3.43e+00
        pdb=" N1   DT E  23 "   -0.025 2.00e-02 2.50e+03
        pdb=" C2   DT E  23 "   -0.004 2.00e-02 2.50e+03
        pdb=" O2   DT E  23 "   -0.003 2.00e-02 2.50e+03
        pdb=" N3   DT E  23 "    0.003 2.00e-02 2.50e+03
        pdb=" C4   DT E  23 "    0.003 2.00e-02 2.50e+03
        pdb=" O4   DT E  23 "    0.008 2.00e-02 2.50e+03
        pdb=" C5   DT E  23 "    0.000 2.00e-02 2.50e+03
        pdb=" C7   DT E  23 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6   DT E  23 "   -0.006 2.00e-02 2.50e+03
  ... (remaining 1169 not shown)

  Histogram of nonbonded interaction distances:
        2.51 -     2.98: 3897
        2.98 -     3.46: 8431
        3.46 -     3.94: 15685
        3.94 -     4.42: 17495
        4.42 -     4.90: 24696
  Nonbonded interactions: 70204
  Sorted by model distance:
  nonbonded pdb=" O5'  DC E  50 "
            pdb=" O4'  DC E  50 "
     model   vdw
     2.505 2.432
  nonbonded pdb=" O   MET A 361 "
            pdb=" OD1 ASP A 362 "
     model   vdw
     2.512 3.040
  nonbonded pdb=" O5'  DG E  40 "
            pdb=" O4'  DG E  40 "
     model   vdw
     2.522 2.432
  nonbonded pdb=" O   TRP A 526 "
            pdb=" CA  PHE A 527 "
     model   vdw
     2.532 2.776
  nonbonded pdb=" O5'  DA E  47 "
            pdb=" O4'  DA E  47 "
     model   vdw
     2.545 2.432
  ... (remaining 70199 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=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:             2.990
  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:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     11.480
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.020
  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:1.450
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.200
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6516
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      :  0.005   0.054   8562  Z= 0.216
  Angle     :  0.667  15.841  12037  Z= 0.372
  Chirality :  0.039   0.178   1312
  Planarity :  0.005   0.096   1172
  Dihedral  : 23.486 179.648   3420
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 9.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  0.32 %
    Allowed  : 15.03 %
    Favored  : 84.65 %
  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:  0.73 (0.30), residues: 754
  helix:  1.17 (0.30), residues: 293
  sheet: -0.34 (0.54), residues: 77
  loop :  0.26 (0.32), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 425 
 TYR   0.009   0.001   TYR B 385 
 PHE   0.009   0.001   PHE A 553 
 TRP   0.014   0.001   TRP B 219 
 HIS   0.002   0.001   HIS B 226 

Details of bonding type rmsd
  covalent geometry    : bond        0.00465 ( 8554)
  covalent geometry    : angle       0.65736 (12031)
  hydrogen bonds       : bond        0.14287 (  393)
  hydrogen bonds       : angle       5.25636 ( 1007)
  metal coordination   : bond        0.01499 (    8)
  metal coordination   : angle       5.13012 (    6)

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

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

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 106
  time to evaluate  : 0.235 
Fit side-chains
   revert: symmetry clash
REVERT: A  152 LYS cc_start: 0.6455 (mttt) cc_final: 0.5796 (mmmt)
REVERT: A  159 LEU cc_start: 0.7023 (tp) cc_final: 0.6781 (tp)
REVERT: A  197 LYS cc_start: 0.8204 (mmtp) cc_final: 0.7689 (mmtt)
REVERT: A  224 LYS cc_start: 0.7761 (tttt) cc_final: 0.7521 (ttpt)
REVERT: A  267 THR cc_start: 0.7412 (p) cc_final: 0.7109 (p)
REVERT: A  292 GLU cc_start: 0.8257 (mt-10) cc_final: 0.7799 (tt0)
REVERT: A  296 LYS cc_start: 0.7400 (tttt) cc_final: 0.7104 (ttmt)
REVERT: A  347 ARG cc_start: 0.6837 (mtt180) cc_final: 0.6616 (ttm170)
REVERT: A  351 LEU cc_start: 0.7036 (tp) cc_final: 0.6245 (mt)
REVERT: A  362 ASP cc_start: 0.7569 (p0) cc_final: 0.6877 (m-30)
REVERT: A  367 GLU cc_start: 0.7518 (pt0) cc_final: 0.7269 (pt0)
REVERT: A  390 ARG cc_start: 0.6636 (ppt170) cc_final: 0.6067 (tpm170)
REVERT: A  414 LYS cc_start: 0.7440 (tttt) cc_final: 0.6971 (ttpp)
REVERT: A  544 ARG cc_start: 0.6412 (mtt180) cc_final: 0.6135 (mtm110)
REVERT: A  559 ASP cc_start: 0.8200 (m-30) cc_final: 0.7781 (m-30)
REVERT: A  578 LYS cc_start: 0.7622 (mttt) cc_final: 0.7361 (mtmt)
REVERT: A  583 THR cc_start: 0.8138 (m) cc_final: 0.7906 (p)
REVERT: B  176 GLU cc_start: 0.6520 (pt0) cc_final: 0.6275 (tp30)
REVERT: B  190 MET cc_start: 0.4454 (ppp) cc_final: 0.3856 (ttp)
REVERT: B  296 LYS cc_start: 0.7197 (ttmt) cc_final: 0.6589 (mtpp)
REVERT: B  297 LYS cc_start: 0.6983 (mmtp) cc_final: 0.6695 (ttmm)
REVERT: B  306 LYS cc_start: 0.7053 (tttm) cc_final: 0.5757 (mmtt)
REVERT: B  313 GLN cc_start: 0.7045 (mt0) cc_final: 0.6733 (mt0)
REVERT: B  323 GLU cc_start: 0.6728 (mt-10) cc_final: 0.6393 (mm-30)
REVERT: B  349 LYS cc_start: 0.5835 (mttt) cc_final: 0.5632 (ptpt)
REVERT: B  395 PRO cc_start: 0.5518 (Cg_endo) cc_final: 0.5262 (Cg_exo)
REVERT: B  579 ARG cc_start: 0.5915 (mtp180) cc_final: 0.5498 (mtp180)
  outliers start: 2
  outliers final: 1
  residues processed: 108
  average time/residue: 0.1313
  time to fit residues: 17.6537
Evaluate side-chains
  79 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 78
  time to evaluate  : 0.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  407 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 49 optimal weight:    0.6980
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    0.0170
   chunk 51 optimal weight:    4.9990
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.6980
   chunk 45 optimal weight:    0.5980
   chunk 74 optimal weight:    4.9990
   overall best weight:    0.6018

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

Flipped N/Q/H residues before XYZ refinement:
A 160 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4282 r_free = 0.4282 target = 0.203181 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.169868 restraints weight = 9696.775|
|-----------------------------------------------------------------------------|
r_work (start): 0.3931 rms_B_bonded: 1.68
r_work: 0.3528 rms_B_bonded: 4.14 restraints_weight: 0.5000
r_work (final): 0.3528
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7617
moved from start:          0.1449

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   8562  Z= 0.178
  Angle     :  0.591  12.136  12037  Z= 0.319
  Chirality :  0.040   0.153   1312
  Planarity :  0.005   0.040   1172
  Dihedral  : 27.177 179.180   1929
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 8.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 13.92 %
    Favored  : 84.02 %
  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:  0.93 (0.30), residues: 754
  helix:  1.51 (0.30), residues: 295
  sheet: -0.72 (0.52), residues: 92
  loop :  0.38 (0.33), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 544 
 TYR   0.008   0.001   TYR B 385 
 PHE   0.008   0.001   PHE A 553 
 TRP   0.011   0.001   TRP A 220 
 HIS   0.002   0.000   HIS B 226 

Details of bonding type rmsd
  covalent geometry    : bond        0.00402 ( 8554)
  covalent geometry    : angle       0.58221 (12031)
  hydrogen bonds       : bond        0.03505 (  393)
  hydrogen bonds       : angle       3.76292 ( 1007)
  metal coordination   : bond        0.01049 (    8)
  metal coordination   : angle       4.52625 (    6)

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

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

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 81
  time to evaluate  : 0.180 
Fit side-chains
REVERT: A  152 LYS cc_start: 0.7743 (mttt) cc_final: 0.7156 (mmmt)
REVERT: A  320 ARG cc_start: 0.7351 (mmm-85) cc_final: 0.7002 (mmm160)
REVERT: A  351 LEU cc_start: 0.8110 (tp) cc_final: 0.7682 (mt)
REVERT: A  362 ASP cc_start: 0.7308 (OUTLIER) cc_final: 0.6992 (m-30)
REVERT: A  414 LYS cc_start: 0.8386 (tttt) cc_final: 0.8156 (ttpp)
REVERT: B  190 MET cc_start: 0.4523 (ppp) cc_final: 0.4282 (ttm)
  outliers start: 13
  outliers final: 3
  residues processed: 90
  average time/residue: 0.1234
  time to fit residues: 13.9172
Evaluate side-chains
  74 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 70
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  362 ASP
Chi-restraints excluded: chain A residue  552 VAL
Chi-restraints excluded: chain B residue  358 LEU
Chi-restraints excluded: chain B residue  407 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 58 optimal weight:    1.9990
   chunk 14 optimal weight:    0.7980
   chunk 68 optimal weight:    0.7980
   chunk 62 optimal weight:    0.6980
   chunk 41 optimal weight:    0.5980
   chunk 23 optimal weight:    0.7980
   chunk 39 optimal weight:    3.9990
   chunk 64 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 0 optimal weight:    5.9990
   chunk 26 optimal weight:    0.8980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.4256 r_free = 0.4256 target = 0.200684 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.167340 restraints weight = 9567.026|
|-----------------------------------------------------------------------------|
r_work (start): 0.3910 rms_B_bonded: 1.67
r_work: 0.3502 rms_B_bonded: 4.19 restraints_weight: 0.5000
r_work (final): 0.3502
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7662
moved from start:          0.2189

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   8562  Z= 0.196
  Angle     :  0.589  10.792  12037  Z= 0.320
  Chirality :  0.040   0.160   1312
  Planarity :  0.004   0.035   1172
  Dihedral  : 27.211 177.091   1929
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 9.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 15.03 %
    Favored  : 82.75 %
  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:  0.99 (0.30), residues: 754
  helix:  1.50 (0.30), residues: 295
  sheet: -0.30 (0.51), residues: 82
  loop :  0.33 (0.33), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 285 
 TYR   0.008   0.001   TYR B 385 
 PHE   0.009   0.002   PHE A 553 
 TRP   0.010   0.001   TRP A 220 
 HIS   0.002   0.001   HIS A 401 

Details of bonding type rmsd
  covalent geometry    : bond        0.00446 ( 8554)
  covalent geometry    : angle       0.58155 (12031)
  hydrogen bonds       : bond        0.03639 (  393)
  hydrogen bonds       : angle       3.57435 ( 1007)
  metal coordination   : bond        0.01330 (    8)
  metal coordination   : angle       4.23190 (    6)

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

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

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 74
  time to evaluate  : 0.182 
Fit side-chains
REVERT: A  152 LYS cc_start: 0.7839 (mttt) cc_final: 0.7217 (mmmt)
REVERT: A  320 ARG cc_start: 0.7428 (mmm-85) cc_final: 0.7081 (mmm160)
REVERT: A  351 LEU cc_start: 0.8104 (tp) cc_final: 0.7693 (mt)
REVERT: A  362 ASP cc_start: 0.7406 (OUTLIER) cc_final: 0.7175 (m-30)
REVERT: A  414 LYS cc_start: 0.8387 (tttt) cc_final: 0.8133 (ttpp)
REVERT: A  423 LYS cc_start: 0.7087 (mmtt) cc_final: 0.6840 (tmtt)
REVERT: B  306 LYS cc_start: 0.8012 (tttm) cc_final: 0.7765 (mmtt)
REVERT: B  371 VAL cc_start: 0.8405 (OUTLIER) cc_final: 0.8177 (m)
  outliers start: 14
  outliers final: 9
  residues processed: 83
  average time/residue: 0.1038
  time to fit residues: 11.2215
Evaluate side-chains
  78 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 67
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  263 ILE
Chi-restraints excluded: chain A residue  362 ASP
Chi-restraints excluded: chain A residue  540 SER
Chi-restraints excluded: chain A residue  552 VAL
Chi-restraints excluded: chain A residue  583 THR
Chi-restraints excluded: chain B residue  358 LEU
Chi-restraints excluded: chain B residue  371 VAL
Chi-restraints excluded: chain B residue  380 SER
Chi-restraints excluded: chain B residue  381 ILE
Chi-restraints excluded: chain B residue  392 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 52 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 65 optimal weight:    0.5980
   chunk 11 optimal weight:    0.9990
   chunk 73 optimal weight:    0.0010
   chunk 22 optimal weight:    0.0770
   chunk 25 optimal weight:    0.7980
   chunk 23 optimal weight:    0.7980
   chunk 80 optimal weight:    5.9990
   chunk 31 optimal weight:    0.0870
   chunk 75 optimal weight:    0.9980
   overall best weight:    0.3122

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

Flipped N/Q/H residues before XYZ refinement:
** B 401 HIS ** 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 = 0.4303 r_free = 0.4303 target = 0.205747 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.174384 restraints weight = 9709.109|
|-----------------------------------------------------------------------------|
r_work (start): 0.3974 rms_B_bonded: 1.47
r_work: 0.3577 rms_B_bonded: 4.30 restraints_weight: 0.5000
r_work (final): 0.3577
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7590
moved from start:          0.2516

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8562  Z= 0.139
  Angle     :  0.544  10.019  12037  Z= 0.295
  Chirality :  0.038   0.146   1312
  Planarity :  0.004   0.034   1172
  Dihedral  : 27.050 175.118   1928
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 8.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 12.50 %
    Favored  : 84.65 %
  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:  1.13 (0.30), residues: 754
  helix:  1.72 (0.30), residues: 302
  sheet: -0.26 (0.51), residues: 82
  loop :  0.29 (0.33), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 285 
 TYR   0.006   0.001   TYR A 385 
 PHE   0.013   0.001   PHE A 557 
 TRP   0.009   0.001   TRP B 584 
 HIS   0.001   0.000   HIS B 226 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 8554)
  covalent geometry    : angle       0.53835 (12031)
  hydrogen bonds       : bond        0.03038 (  393)
  hydrogen bonds       : angle       3.39690 ( 1007)
  metal coordination   : bond        0.00835 (    8)
  metal coordination   : angle       3.52174 (    6)

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

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

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 75
  time to evaluate  : 0.252 
Fit side-chains
REVERT: A  152 LYS cc_start: 0.7708 (mttt) cc_final: 0.7051 (mmmt)
REVERT: A  320 ARG cc_start: 0.7289 (mmm-85) cc_final: 0.6987 (mmm160)
REVERT: A  351 LEU cc_start: 0.8118 (tp) cc_final: 0.7724 (mt)
REVERT: A  414 LYS cc_start: 0.8310 (tttt) cc_final: 0.8087 (ttpp)
REVERT: A  423 LYS cc_start: 0.6917 (mmtt) cc_final: 0.6693 (tmtt)
REVERT: B  152 LYS cc_start: 0.6601 (OUTLIER) cc_final: 0.6273 (ptmt)
REVERT: B  400 GLN cc_start: 0.6447 (pp30) cc_final: 0.5799 (tt0)
REVERT: B  409 MET cc_start: 0.7324 (mtp) cc_final: 0.6964 (mtp)
REVERT: B  539 LYS cc_start: 0.5808 (OUTLIER) cc_final: 0.5049 (pptt)
REVERT: B  560 LYS cc_start: 0.8090 (OUTLIER) cc_final: 0.7847 (tppt)
  outliers start: 18
  outliers final: 12
  residues processed: 88
  average time/residue: 0.1175
  time to fit residues: 13.1403
Evaluate side-chains
  81 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 66
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  163 LEU
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  358 LEU
Chi-restraints excluded: chain A residue  387 CYS
Chi-restraints excluded: chain A residue  402 GLU
Chi-restraints excluded: chain A residue  540 SER
Chi-restraints excluded: chain A residue  583 THR
Chi-restraints excluded: chain B residue  152 LYS
Chi-restraints excluded: chain B residue  358 LEU
Chi-restraints excluded: chain B residue  380 SER
Chi-restraints excluded: chain B residue  381 ILE
Chi-restraints excluded: chain B residue  392 VAL
Chi-restraints excluded: chain B residue  405 CYS
Chi-restraints excluded: chain B residue  539 LYS
Chi-restraints excluded: chain B residue  560 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 12 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 50 optimal weight:    4.9990
   chunk 73 optimal weight:    3.9990
   chunk 55 optimal weight:    0.8980
   chunk 83 optimal weight:    3.9990
   chunk 14 optimal weight:    2.9990
   chunk 4 optimal weight:    2.9990
   chunk 26 optimal weight:    0.6980
   chunk 75 optimal weight:    0.8980
   chunk 63 optimal weight:    1.9990
   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 160 GLN
** B 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4215 r_free = 0.4215 target = 0.196655 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.162538 restraints weight = 9722.194|
|-----------------------------------------------------------------------------|
r_work (start): 0.3845 rms_B_bonded: 1.70
r_work: 0.3458 rms_B_bonded: 4.06 restraints_weight: 0.5000
r_work (final): 0.3458
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7744
moved from start:          0.2940

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.069   8562  Z= 0.279
  Angle     :  0.638   9.658  12037  Z= 0.347
  Chirality :  0.042   0.153   1312
  Planarity :  0.005   0.034   1172
  Dihedral  : 27.294 177.504   1928
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 9.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 15.35 %
    Favored  : 82.12 %
  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:  0.69 (0.30), residues: 754
  helix:  1.22 (0.30), residues: 295
  sheet: -0.29 (0.51), residues: 82
  loop :  0.13 (0.33), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 250 
 TYR   0.010   0.002   TYR B 385 
 PHE   0.017   0.002   PHE A 557 
 TRP   0.012   0.002   TRP A 542 
 HIS   0.004   0.001   HIS A 401 

Details of bonding type rmsd
  covalent geometry    : bond        0.00643 ( 8554)
  covalent geometry    : angle       0.62929 (12031)
  hydrogen bonds       : bond        0.03989 (  393)
  hydrogen bonds       : angle       3.65518 ( 1007)
  metal coordination   : bond        0.01611 (    8)
  metal coordination   : angle       4.85668 (    6)

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

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

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 69
  time to evaluate  : 0.228 
Fit side-chains
REVERT: A  152 LYS cc_start: 0.7764 (mttt) cc_final: 0.7183 (mmmt)
REVERT: A  320 ARG cc_start: 0.7484 (mmm-85) cc_final: 0.7174 (mmm160)
REVERT: A  351 LEU cc_start: 0.8150 (tp) cc_final: 0.7808 (mt)
REVERT: A  414 LYS cc_start: 0.8434 (tttt) cc_final: 0.8145 (ttpp)
REVERT: A  423 LYS cc_start: 0.7063 (mmtt) cc_final: 0.6842 (tmtt)
REVERT: A  557 PHE cc_start: 0.8161 (m-80) cc_final: 0.7954 (m-10)
REVERT: B  152 LYS cc_start: 0.6531 (OUTLIER) cc_final: 0.6120 (tttm)
REVERT: B  345 ARG cc_start: 0.8123 (OUTLIER) cc_final: 0.4224 (mtp-110)
REVERT: B  367 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.7149 (pm20)
REVERT: B  405 CYS cc_start: 0.8593 (OUTLIER) cc_final: 0.8371 (p)
REVERT: B  409 MET cc_start: 0.7297 (mtp) cc_final: 0.6907 (mtp)
REVERT: B  539 LYS cc_start: 0.6056 (OUTLIER) cc_final: 0.5038 (pptt)
REVERT: B  560 LYS cc_start: 0.8171 (OUTLIER) cc_final: 0.7811 (tppt)
  outliers start: 16
  outliers final: 8
  residues processed: 82
  average time/residue: 0.1270
  time to fit residues: 13.2112
Evaluate side-chains
  77 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 63
  time to evaluate  : 0.178 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  163 LEU
Chi-restraints excluded: chain A residue  263 ILE
Chi-restraints excluded: chain A residue  540 SER
Chi-restraints excluded: chain A residue  552 VAL
Chi-restraints excluded: chain A residue  583 THR
Chi-restraints excluded: chain B residue  152 LYS
Chi-restraints excluded: chain B residue  345 ARG
Chi-restraints excluded: chain B residue  358 LEU
Chi-restraints excluded: chain B residue  367 GLU
Chi-restraints excluded: chain B residue  381 ILE
Chi-restraints excluded: chain B residue  392 VAL
Chi-restraints excluded: chain B residue  405 CYS
Chi-restraints excluded: chain B residue  539 LYS
Chi-restraints excluded: chain B residue  560 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 76 optimal weight:    6.9990
   chunk 13 optimal weight:    0.0070
   chunk 36 optimal weight:    0.0270
   chunk 65 optimal weight:    0.5980
   chunk 23 optimal weight:    0.5980
   chunk 85 optimal weight:    1.9990
   chunk 15 optimal weight:    6.9990
   chunk 8 optimal weight:    0.9990
   chunk 10 optimal weight:    7.9990
   chunk 24 optimal weight:    0.6980
   chunk 31 optimal weight:    0.8980
   overall best weight:    0.3856

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

Flipped N/Q/H residues before XYZ refinement:
A 160 GLN
** B 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4274 r_free = 0.4274 target = 0.202855 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.170958 restraints weight = 9588.822|
|-----------------------------------------------------------------------------|
r_work (start): 0.3947 rms_B_bonded: 1.56
r_work: 0.3565 rms_B_bonded: 4.07 restraints_weight: 0.5000
r_work (final): 0.3565
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7615
moved from start:          0.3023

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8562  Z= 0.146
  Angle     :  0.544   9.468  12037  Z= 0.297
  Chirality :  0.038   0.139   1312
  Planarity :  0.004   0.035   1172
  Dihedral  : 27.084 173.841   1928
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 9.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 15.98 %
    Favored  : 81.80 %
  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:  1.05 (0.31), residues: 754
  helix:  1.63 (0.30), residues: 296
  sheet: -0.23 (0.50), residues: 92
  loop :  0.29 (0.33), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 221 
 TYR   0.008   0.001   TYR A 385 
 PHE   0.012   0.001   PHE A 557 
 TRP   0.010   0.001   TRP A 584 
 HIS   0.001   0.000   HIS B 226 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 8554)
  covalent geometry    : angle       0.53757 (12031)
  hydrogen bonds       : bond        0.03178 (  393)
  hydrogen bonds       : angle       3.44825 ( 1007)
  metal coordination   : bond        0.01049 (    8)
  metal coordination   : angle       3.88543 (    6)

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

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

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 68
  time to evaluate  : 0.406 
Fit side-chains
REVERT: A  152 LYS cc_start: 0.7771 (mttt) cc_final: 0.7210 (mmmt)
REVERT: A  320 ARG cc_start: 0.7366 (mmm-85) cc_final: 0.7137 (mmm160)
REVERT: A  351 LEU cc_start: 0.8150 (tp) cc_final: 0.7820 (mt)
REVERT: A  414 LYS cc_start: 0.8322 (tttt) cc_final: 0.8075 (ttpp)
REVERT: B  152 LYS cc_start: 0.6625 (OUTLIER) cc_final: 0.6228 (tttm)
REVERT: B  539 LYS cc_start: 0.5992 (OUTLIER) cc_final: 0.4969 (pptt)
REVERT: B  560 LYS cc_start: 0.8135 (OUTLIER) cc_final: 0.7886 (tppt)
  outliers start: 14
  outliers final: 10
  residues processed: 78
  average time/residue: 0.1187
  time to fit residues: 12.1084
Evaluate side-chains
  80 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 67
  time to evaluate  : 0.196 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  163 LEU
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  263 ILE
Chi-restraints excluded: chain A residue  358 LEU
Chi-restraints excluded: chain A residue  387 CYS
Chi-restraints excluded: chain A residue  583 THR
Chi-restraints excluded: chain B residue  152 LYS
Chi-restraints excluded: chain B residue  358 LEU
Chi-restraints excluded: chain B residue  380 SER
Chi-restraints excluded: chain B residue  381 ILE
Chi-restraints excluded: chain B residue  392 VAL
Chi-restraints excluded: chain B residue  539 LYS
Chi-restraints excluded: chain B residue  560 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 78 optimal weight:    1.9990
   chunk 84 optimal weight:    3.9990
   chunk 11 optimal weight:    0.9980
   chunk 38 optimal weight:    0.5980
   chunk 82 optimal weight:    0.9990
   chunk 40 optimal weight:    3.9990
   chunk 13 optimal weight:    0.7980
   chunk 1 optimal weight:    1.9990
   chunk 17 optimal weight:    0.3980
   chunk 74 optimal weight:    0.6980
   chunk 47 optimal weight:    1.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 406 ASN
** B 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4246 r_free = 0.4246 target = 0.199898 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.166492 restraints weight = 9703.047|
|-----------------------------------------------------------------------------|
r_work (start): 0.3899 rms_B_bonded: 1.63
r_work: 0.3522 rms_B_bonded: 4.11 restraints_weight: 0.5000
r_work (final): 0.3522
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7669
moved from start:          0.3185

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   8562  Z= 0.186
  Angle     :  0.572   8.906  12037  Z= 0.309
  Chirality :  0.039   0.205   1312
  Planarity :  0.004   0.033   1172
  Dihedral  : 27.089 176.279   1928
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 10.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 16.14 %
    Favored  : 81.17 %
  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:  0.95 (0.30), residues: 754
  helix:  1.59 (0.30), residues: 295
  sheet: -0.26 (0.52), residues: 82
  loop :  0.18 (0.33), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 221 
 TYR   0.006   0.001   TYR A 385 
 PHE   0.011   0.001   PHE A 553 
 TRP   0.009   0.001   TRP B 584 
 HIS   0.002   0.001   HIS A 401 

Details of bonding type rmsd
  covalent geometry    : bond        0.00424 ( 8554)
  covalent geometry    : angle       0.56193 (12031)
  hydrogen bonds       : bond        0.03400 (  393)
  hydrogen bonds       : angle       3.49479 ( 1007)
  metal coordination   : bond        0.01277 (    8)
  metal coordination   : angle       4.72905 (    6)

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

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

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 70
  time to evaluate  : 0.234 
Fit side-chains
REVERT: A  152 LYS cc_start: 0.7830 (mttt) cc_final: 0.7274 (mmmt)
REVERT: A  320 ARG cc_start: 0.7423 (mmm-85) cc_final: 0.7125 (mmm160)
REVERT: A  351 LEU cc_start: 0.8175 (tp) cc_final: 0.7841 (mt)
REVERT: A  414 LYS cc_start: 0.8265 (tttt) cc_final: 0.8023 (ttpp)
REVERT: B  152 LYS cc_start: 0.6569 (OUTLIER) cc_final: 0.6202 (tttm)
REVERT: B  345 ARG cc_start: 0.8091 (OUTLIER) cc_final: 0.4430 (mtp-110)
REVERT: B  400 GLN cc_start: 0.5885 (pp30) cc_final: 0.5382 (tt0)
REVERT: B  539 LYS cc_start: 0.6048 (OUTLIER) cc_final: 0.4961 (pptt)
REVERT: B  560 LYS cc_start: 0.8184 (OUTLIER) cc_final: 0.7894 (tppt)
  outliers start: 17
  outliers final: 12
  residues processed: 81
  average time/residue: 0.1245
  time to fit residues: 12.7694
Evaluate side-chains
  82 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 66
  time to evaluate  : 0.171 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  163 LEU
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  263 ILE
Chi-restraints excluded: chain A residue  358 LEU
Chi-restraints excluded: chain A residue  387 CYS
Chi-restraints excluded: chain A residue  540 SER
Chi-restraints excluded: chain A residue  552 VAL
Chi-restraints excluded: chain A residue  583 THR
Chi-restraints excluded: chain B residue  152 LYS
Chi-restraints excluded: chain B residue  345 ARG
Chi-restraints excluded: chain B residue  358 LEU
Chi-restraints excluded: chain B residue  380 SER
Chi-restraints excluded: chain B residue  381 ILE
Chi-restraints excluded: chain B residue  392 VAL
Chi-restraints excluded: chain B residue  539 LYS
Chi-restraints excluded: chain B residue  560 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 41 optimal weight:    0.6980
   chunk 6 optimal weight:    1.9990
   chunk 54 optimal weight:    2.9990
   chunk 15 optimal weight:    0.7980
   chunk 48 optimal weight:    9.9990
   chunk 67 optimal weight:    0.9990
   chunk 80 optimal weight:    8.9990
   chunk 37 optimal weight:    0.9990
   chunk 26 optimal weight:    0.8980
   chunk 28 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9980
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
A 160 GLN
** B 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4237 r_free = 0.4237 target = 0.198744 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.166679 restraints weight = 9598.528|
|-----------------------------------------------------------------------------|
r_work (start): 0.3902 rms_B_bonded: 1.45
r_work: 0.3528 rms_B_bonded: 3.88 restraints_weight: 0.5000
r_work (final): 0.3528
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7679
moved from start:          0.3459

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.057   8562  Z= 0.215
  Angle     :  0.596   8.583  12037  Z= 0.322
  Chirality :  0.040   0.166   1312
  Planarity :  0.004   0.032   1172
  Dihedral  : 27.141 176.233   1928
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 10.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 16.30 %
    Favored  : 81.33 %
  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:  0.80 (0.31), residues: 754
  helix:  1.43 (0.30), residues: 294
  sheet: -0.39 (0.52), residues: 92
  loop :  0.15 (0.33), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 221 
 TYR   0.005   0.001   TYR A 385 
 PHE   0.012   0.002   PHE A 553 
 TRP   0.011   0.002   TRP A 542 
 HIS   0.003   0.001   HIS A 401 

Details of bonding type rmsd
  covalent geometry    : bond        0.00492 ( 8554)
  covalent geometry    : angle       0.58583 (12031)
  hydrogen bonds       : bond        0.03681 (  393)
  hydrogen bonds       : angle       3.62802 ( 1007)
  metal coordination   : bond        0.01318 (    8)
  metal coordination   : angle       4.86368 (    6)

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

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

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 66
  time to evaluate  : 0.228 
Fit side-chains
REVERT: A  152 LYS cc_start: 0.7826 (mttt) cc_final: 0.7320 (mmmt)
REVERT: A  320 ARG cc_start: 0.7451 (mmm-85) cc_final: 0.7134 (mmm160)
REVERT: A  351 LEU cc_start: 0.8157 (tp) cc_final: 0.7854 (mt)
REVERT: B  152 LYS cc_start: 0.6565 (OUTLIER) cc_final: 0.6222 (tttm)
REVERT: B  345 ARG cc_start: 0.8173 (OUTLIER) cc_final: 0.4458 (mtp-110)
REVERT: B  539 LYS cc_start: 0.6045 (OUTLIER) cc_final: 0.4816 (pptt)
REVERT: B  560 LYS cc_start: 0.8165 (OUTLIER) cc_final: 0.7904 (tppt)
  outliers start: 15
  outliers final: 10
  residues processed: 76
  average time/residue: 0.1181
  time to fit residues: 11.2874
Evaluate side-chains
  78 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 64
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  163 LEU
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  263 ILE
Chi-restraints excluded: chain A residue  358 LEU
Chi-restraints excluded: chain A residue  540 SER
Chi-restraints excluded: chain A residue  552 VAL
Chi-restraints excluded: chain A residue  583 THR
Chi-restraints excluded: chain B residue  152 LYS
Chi-restraints excluded: chain B residue  345 ARG
Chi-restraints excluded: chain B residue  358 LEU
Chi-restraints excluded: chain B residue  381 ILE
Chi-restraints excluded: chain B residue  392 VAL
Chi-restraints excluded: chain B residue  539 LYS
Chi-restraints excluded: chain B residue  560 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 25 optimal weight:    0.9980
   chunk 47 optimal weight:    0.9990
   chunk 67 optimal weight:    0.5980
   chunk 8 optimal weight:    0.9990
   chunk 82 optimal weight:    0.7980
   chunk 48 optimal weight:    9.9990
   chunk 21 optimal weight:    0.1980
   chunk 23 optimal weight:    0.7980
   chunk 49 optimal weight:    0.9980
   chunk 1 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 160 GLN
** B 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4254 r_free = 0.4254 target = 0.200470 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.166615 restraints weight = 9638.862|
|-----------------------------------------------------------------------------|
r_work (start): 0.3882 rms_B_bonded: 1.66
r_work: 0.3551 rms_B_bonded: 3.73 restraints_weight: 0.5000
r_work (final): 0.3551
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7640
moved from start:          0.3557

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   8562  Z= 0.184
  Angle     :  0.583   8.461  12037  Z= 0.315
  Chirality :  0.039   0.142   1312
  Planarity :  0.004   0.034   1172
  Dihedral  : 27.061 175.697   1928
  Min Nonbonded Distance : 2.319

Molprobity Statistics.
  All-atom Clashscore : 10.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 16.14 %
    Favored  : 81.33 %
  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:  0.86 (0.31), residues: 754
  helix:  1.52 (0.30), residues: 294
  sheet: -0.37 (0.52), residues: 92
  loop :  0.16 (0.33), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 221 
 TYR   0.008   0.001   TYR A 385 
 PHE   0.012   0.001   PHE A 553 
 TRP   0.009   0.001   TRP A 526 
 HIS   0.002   0.001   HIS A 401 

Details of bonding type rmsd
  covalent geometry    : bond        0.00417 ( 8554)
  covalent geometry    : angle       0.57338 (12031)
  hydrogen bonds       : bond        0.03432 (  393)
  hydrogen bonds       : angle       3.57148 ( 1007)
  metal coordination   : bond        0.01315 (    8)
  metal coordination   : angle       4.63364 (    6)

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

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

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 68
  time to evaluate  : 0.211 
Fit side-chains
REVERT: A  152 LYS cc_start: 0.7683 (mttt) cc_final: 0.7198 (mmmt)
REVERT: A  320 ARG cc_start: 0.7453 (mmm-85) cc_final: 0.7070 (mmm160)
REVERT: A  351 LEU cc_start: 0.8150 (tp) cc_final: 0.7837 (mt)
REVERT: B  152 LYS cc_start: 0.6711 (OUTLIER) cc_final: 0.6372 (tttm)
REVERT: B  345 ARG cc_start: 0.8088 (OUTLIER) cc_final: 0.4515 (mtp-110)
REVERT: B  539 LYS cc_start: 0.6102 (OUTLIER) cc_final: 0.4823 (pptt)
REVERT: B  560 LYS cc_start: 0.8152 (OUTLIER) cc_final: 0.7863 (tppt)
  outliers start: 16
  outliers final: 11
  residues processed: 78
  average time/residue: 0.1230
  time to fit residues: 12.1478
Evaluate side-chains
  81 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 66
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  163 LEU
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  263 ILE
Chi-restraints excluded: chain A residue  358 LEU
Chi-restraints excluded: chain A residue  387 CYS
Chi-restraints excluded: chain A residue  540 SER
Chi-restraints excluded: chain A residue  552 VAL
Chi-restraints excluded: chain A residue  583 THR
Chi-restraints excluded: chain B residue  152 LYS
Chi-restraints excluded: chain B residue  345 ARG
Chi-restraints excluded: chain B residue  358 LEU
Chi-restraints excluded: chain B residue  381 ILE
Chi-restraints excluded: chain B residue  392 VAL
Chi-restraints excluded: chain B residue  539 LYS
Chi-restraints excluded: chain B residue  560 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 24 optimal weight:    0.6980
   chunk 15 optimal weight:    0.7980
   chunk 19 optimal weight:    1.9990
   chunk 17 optimal weight:    0.4980
   chunk 11 optimal weight:    0.5980
   chunk 46 optimal weight:    4.9990
   chunk 71 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   chunk 36 optimal weight:    0.0970
   chunk 7 optimal weight:    1.9990
   chunk 41 optimal weight:    0.7980
   overall best weight:    0.5378

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

Flipped N/Q/H residues before XYZ refinement:
** B 401 HIS ** 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 = 0.4266 r_free = 0.4266 target = 0.201714 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.170327 restraints weight = 9607.596|
|-----------------------------------------------------------------------------|
r_work (start): 0.3942 rms_B_bonded: 1.54
r_work: 0.3588 rms_B_bonded: 3.84 restraints_weight: 0.5000
r_work (final): 0.3588
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7612
moved from start:          0.3638

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   8562  Z= 0.163
  Angle     :  0.554   8.538  12037  Z= 0.300
  Chirality :  0.038   0.142   1312
  Planarity :  0.004   0.034   1172
  Dihedral  : 26.968 175.130   1928
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 9.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 16.46 %
    Favored  : 81.17 %
  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:  0.90 (0.31), residues: 754
  helix:  1.54 (0.30), residues: 294
  sheet: -0.37 (0.56), residues: 82
  loop :  0.18 (0.32), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 221 
 TYR   0.007   0.001   TYR A 385 
 PHE   0.009   0.001   PHE A 553 
 TRP   0.010   0.001   TRP A 526 
 HIS   0.002   0.000   HIS A 426 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 ( 8554)
  covalent geometry    : angle       0.54581 (12031)
  hydrogen bonds       : bond        0.03333 (  393)
  hydrogen bonds       : angle       3.55382 ( 1007)
  metal coordination   : bond        0.01119 (    8)
  metal coordination   : angle       4.30902 (    6)

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

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

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 71
  time to evaluate  : 0.229 
Fit side-chains
REVERT: A  152 LYS cc_start: 0.7792 (mttt) cc_final: 0.7203 (mmmt)
REVERT: A  320 ARG cc_start: 0.7280 (mmm-85) cc_final: 0.6985 (mmm160)
REVERT: A  351 LEU cc_start: 0.8186 (tp) cc_final: 0.7875 (mt)
REVERT: B  152 LYS cc_start: 0.6666 (OUTLIER) cc_final: 0.6303 (tttm)
REVERT: B  345 ARG cc_start: 0.8058 (OUTLIER) cc_final: 0.4501 (mtp-110)
REVERT: B  539 LYS cc_start: 0.6058 (OUTLIER) cc_final: 0.4752 (pptt)
REVERT: B  560 LYS cc_start: 0.8125 (OUTLIER) cc_final: 0.7886 (tppt)
  outliers start: 15
  outliers final: 11
  residues processed: 81
  average time/residue: 0.1283
  time to fit residues: 13.1927
Evaluate side-chains
  84 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 69
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  163 LEU
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  263 ILE
Chi-restraints excluded: chain A residue  358 LEU
Chi-restraints excluded: chain A residue  387 CYS
Chi-restraints excluded: chain A residue  540 SER
Chi-restraints excluded: chain A residue  552 VAL
Chi-restraints excluded: chain A residue  583 THR
Chi-restraints excluded: chain B residue  152 LYS
Chi-restraints excluded: chain B residue  345 ARG
Chi-restraints excluded: chain B residue  358 LEU
Chi-restraints excluded: chain B residue  381 ILE
Chi-restraints excluded: chain B residue  392 VAL
Chi-restraints excluded: chain B residue  539 LYS
Chi-restraints excluded: chain B residue  560 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 6 optimal weight:    1.9990
   chunk 56 optimal weight:    0.6980
   chunk 51 optimal weight:    0.6980
   chunk 17 optimal weight:    0.5980
   chunk 16 optimal weight:    0.0980
   chunk 62 optimal weight:    0.4980
   chunk 8 optimal weight:    1.9990
   chunk 60 optimal weight:    1.9990
   chunk 20 optimal weight:    0.7980
   chunk 46 optimal weight:    4.9990
   chunk 81 optimal weight:    6.9990
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
** B 401 HIS ** 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 = 0.4272 r_free = 0.4272 target = 0.202296 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.172061 restraints weight = 9705.643|
|-----------------------------------------------------------------------------|
r_work (start): 0.3947 rms_B_bonded: 1.37
r_work: 0.3593 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.3593
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7594
moved from start:          0.3756

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   8562  Z= 0.161
  Angle     :  0.556   8.523  12037  Z= 0.301
  Chirality :  0.038   0.153   1312
  Planarity :  0.004   0.034   1172
  Dihedral  : 26.830 175.035   1928
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 9.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 16.61 %
    Favored  : 81.01 %
  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:  0.95 (0.31), residues: 754
  helix:  1.58 (0.30), residues: 294
  sheet: -0.35 (0.56), residues: 82
  loop :  0.22 (0.32), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 221 
 TYR   0.008   0.001   TYR A 385 
 PHE   0.009   0.001   PHE A 553 
 TRP   0.009   0.001   TRP A 526 
 HIS   0.002   0.000   HIS A 426 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 ( 8554)
  covalent geometry    : angle       0.54829 (12031)
  hydrogen bonds       : bond        0.03281 (  393)
  hydrogen bonds       : angle       3.55527 ( 1007)
  metal coordination   : bond        0.00990 (    8)
  metal coordination   : angle       4.13310 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1952.79 seconds
wall clock time: 34 minutes 5.56 seconds (2045.56 seconds total)