Starting phenix.real_space_refine
on Tue Feb 11 13:17:53 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wks_32568/02_2025/7wks_32568.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wks_32568/02_2025/7wks_32568.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wks_32568/02_2025/7wks_32568.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wks_32568/02_2025/7wks_32568.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wks_32568/02_2025/7wks_32568.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wks_32568/02_2025/7wks_32568.cif"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
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      42      5.16       5
     C    3902      2.51       5
     N     938      2.21       5
     O     992      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 5874
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "B"
      Number of atoms: 2937
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 377, 2937
          Classifications: {'peptide': 377}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 17, 'TRANS': 359}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 2937
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 377, 2937
          Classifications: {'peptide': 377}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 17, 'TRANS': 359}
          Chain breaks: 1
  Time building chain proxies: 4.07, per 1000 atoms: 0.69
  Number of scatterers: 5874
  At special positions: 0
  Unit cell: (79.143, 125.097, 69.782, 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      42     16.00
     O     992      8.00
     N     938      7.00
     C    3902      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.58
  Conformation dependent library (CDL) restraints added in 942.7 milliseconds
  

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1420

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 2 sheets defined
      79.0% alpha, 4.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.53
  Creating SS restraints...
    Processing helix  chain 'B' and resid 4 through 30
      Proline residue:  B  16  - end of helix
    Processing helix  chain 'B' and resid 35 through 62
      removed outlier: 4.757A  pdb=" N   VAL B  51 " --> pdb=" O   ALA B  47 " (cutoff:3.500A)
      Proline residue:  B  52  - end of helix
      removed outlier: 3.580A  pdb=" N   THR B  61 " --> pdb=" O   HIS B  57 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 68 through 92
      removed outlier: 3.611A  pdb=" N   LYS B  79 " --> pdb=" O   ASP B  75 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 97 through 110
    Processing helix  chain 'B' and resid 116 through 125
    Processing helix  chain 'B' and resid 126 through 143
      removed outlier: 3.533A  pdb=" N   GLY B 130 " --> pdb=" O   GLY B 126 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 143 through 165
    Processing helix  chain 'B' and resid 167 through 170
      removed outlier: 3.787A  pdb=" N   ALA B 170 " --> pdb=" O   GLU B 167 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 167 through 170'
    Processing helix  chain 'B' and resid 475 through 492
      removed outlier: 4.003A  pdb=" N   MET B 479 " --> pdb=" O   PRO B 475 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 494 through 514
      removed outlier: 3.561A  pdb=" N   TYR B 498 " --> pdb=" O   ASN B 494 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 518 through 530
      removed outlier: 4.177A  pdb=" N   LEU B 528 " --> pdb=" O   SER B 524 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 531 through 547
    Processing helix  chain 'B' and resid 554 through 581
      removed outlier: 4.278A  pdb=" N   GLY B 569 " --> pdb=" O   ARG B 565 " (cutoff:3.500A)
      Proline residue:  B 570  - end of helix
    Processing helix  chain 'B' and resid 584 through 595
    Processing helix  chain 'B' and resid 599 through 610
      removed outlier: 3.945A  pdb=" N   PHE B 603 " --> pdb=" O   GLY B 599 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 612 through 639
      removed outlier: 3.577A  pdb=" N   LEU B 616 " --> pdb=" O   HIS B 612 " (cutoff:3.500A)
      removed outlier: 5.012A  pdb=" N   LEU B 628 " --> pdb=" O   MET B 624 " (cutoff:3.500A)
      Proline residue:  B 629  - end of helix
    Processing helix  chain 'A' and resid 4 through 30
      Proline residue:  A  16  - end of helix
    Processing helix  chain 'A' and resid 35 through 62
      removed outlier: 4.760A  pdb=" N   VAL A  51 " --> pdb=" O   ALA A  47 " (cutoff:3.500A)
      Proline residue:  A  52  - end of helix
      removed outlier: 3.581A  pdb=" N   THR A  61 " --> pdb=" O   HIS A  57 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 68 through 92
      removed outlier: 3.612A  pdb=" N   LYS A  79 " --> pdb=" O   ASP A  75 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 97 through 110
    Processing helix  chain 'A' and resid 116 through 125
    Processing helix  chain 'A' and resid 126 through 143
      removed outlier: 3.535A  pdb=" N   GLY A 130 " --> pdb=" O   GLY A 126 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 143 through 165
    Processing helix  chain 'A' and resid 167 through 170
      removed outlier: 3.767A  pdb=" N   ALA A 170 " --> pdb=" O   GLU A 167 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 167 through 170'
    Processing helix  chain 'A' and resid 475 through 492
      removed outlier: 4.005A  pdb=" N   MET A 479 " --> pdb=" O   PRO A 475 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 494 through 514
      removed outlier: 3.560A  pdb=" N   TYR A 498 " --> pdb=" O   ASN A 494 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 518 through 530
      removed outlier: 4.179A  pdb=" N   LEU A 528 " --> pdb=" O   SER A 524 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 531 through 547
    Processing helix  chain 'A' and resid 554 through 581
      removed outlier: 4.253A  pdb=" N   GLY A 569 " --> pdb=" O   ARG A 565 " (cutoff:3.500A)
      Proline residue:  A 570  - end of helix
    Processing helix  chain 'A' and resid 584 through 595
    Processing helix  chain 'A' and resid 599 through 610
      removed outlier: 3.950A  pdb=" N   PHE A 603 " --> pdb=" O   GLY A 599 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 612 through 639
      removed outlier: 3.585A  pdb=" N   LEU A 616 " --> pdb=" O   HIS A 612 " (cutoff:3.500A)
      removed outlier: 5.023A  pdb=" N   LEU A 628 " --> pdb=" O   MET A 624 " (cutoff:3.500A)
      Proline residue:  A 629  - end of helix
    Processing sheet with id=AA1, first strand: chain 'B' and resid 172 through 177
      removed outlier: 4.581A  pdb=" N   ILE B 172 " --> pdb=" O   LEU B 202 " (cutoff:3.500A)
      removed outlier: 8.177A  pdb=" N   VAL B 204 " --> pdb=" O   ILE B 172 " (cutoff:3.500A)
      removed outlier: 6.281A  pdb=" N   SER B 174 " --> pdb=" O   VAL B 204 " (cutoff:3.500A)
      removed outlier: 7.629A  pdb=" N   VAL B 206 " --> pdb=" O   SER B 174 " (cutoff:3.500A)
      removed outlier: 6.248A  pdb=" N   LYS B 176 " --> pdb=" O   VAL B 206 " (cutoff:3.500A)
      removed outlier: 8.267A  pdb=" N   LYS B 208 " --> pdb=" O   LYS B 176 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 172 through 177
      removed outlier: 4.596A  pdb=" N   ILE A 172 " --> pdb=" O   LEU A 202 " (cutoff:3.500A)
      removed outlier: 8.176A  pdb=" N   VAL A 204 " --> pdb=" O   ILE A 172 " (cutoff:3.500A)
      removed outlier: 6.293A  pdb=" N   SER A 174 " --> pdb=" O   VAL A 204 " (cutoff:3.500A)
      removed outlier: 7.637A  pdb=" N   VAL A 206 " --> pdb=" O   SER A 174 " (cutoff:3.500A)
      removed outlier: 6.244A  pdb=" N   LYS A 176 " --> pdb=" O   VAL A 206 " (cutoff:3.500A)
      removed outlier: 8.310A  pdb=" N   LYS A 208 " --> pdb=" O   LYS A 176 " (cutoff:3.500A)

    434 hydrogen bonds defined for protein.
    1302 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.61

  Time building geometry restraints manager: 1.71 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1770
        1.34 -     1.46: 1148
        1.46 -     1.58: 3022
        1.58 -     1.69: 0
        1.69 -     1.81: 78
  Bond restraints: 6018
  Sorted by residual:
  bond pdb=" C   ASN A 494 "
       pdb=" O   ASN A 494 "
    ideal  model  delta    sigma   weight residual
    1.238  1.249 -0.011 1.28e-02 6.10e+03 7.40e-01
  bond pdb=" C   GLN A 140 "
       pdb=" O   GLN A 140 "
    ideal  model  delta    sigma   weight residual
    1.237  1.227  0.010 1.17e-02 7.31e+03 6.72e-01
  bond pdb=" C   GLN B 140 "
       pdb=" O   GLN B 140 "
    ideal  model  delta    sigma   weight residual
    1.237  1.228  0.009 1.17e-02 7.31e+03 5.98e-01
  bond pdb=" CA  ASN B 112 "
       pdb=" C   ASN B 112 "
    ideal  model  delta    sigma   weight residual
    1.525  1.515  0.010 1.25e-02 6.40e+03 5.97e-01
  bond pdb=" C   ASN B 494 "
       pdb=" O   ASN B 494 "
    ideal  model  delta    sigma   weight residual
    1.238  1.248 -0.010 1.28e-02 6.10e+03 5.77e-01
  ... (remaining 6013 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.15: 7876
        1.15 -     2.30: 231
        2.30 -     3.45: 71
        3.45 -     4.60: 12
        4.60 -     5.75: 10
  Bond angle restraints: 8200
  Sorted by residual:
  angle pdb=" N   VAL A  14 "
        pdb=" CA  VAL A  14 "
        pdb=" C   VAL A  14 "
      ideal   model   delta    sigma   weight residual
     109.34  115.09   -5.75 2.08e+00 2.31e-01 7.65e+00
  angle pdb=" N   VAL B  14 "
        pdb=" CA  VAL B  14 "
        pdb=" C   VAL B  14 "
      ideal   model   delta    sigma   weight residual
     109.34  115.05   -5.71 2.08e+00 2.31e-01 7.55e+00
  angle pdb=" N   TYR B 125 "
        pdb=" CA  TYR B 125 "
        pdb=" C   TYR B 125 "
      ideal   model   delta    sigma   weight residual
     110.80  115.30   -4.50 2.13e+00 2.20e-01 4.46e+00
  angle pdb=" N   TYR A 125 "
        pdb=" CA  TYR A 125 "
        pdb=" C   TYR A 125 "
      ideal   model   delta    sigma   weight residual
     110.80  115.27   -4.47 2.13e+00 2.20e-01 4.41e+00
  angle pdb=" CB  ARG A 565 "
        pdb=" CG  ARG A 565 "
        pdb=" CD  ARG A 565 "
      ideal   model   delta    sigma   weight residual
     111.30  115.38   -4.08 2.30e+00 1.89e-01 3.15e+00
  ... (remaining 8195 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.96: 3240
       17.96 -    35.92: 251
       35.92 -    53.88: 35
       53.88 -    71.84: 8
       71.84 -    89.80: 4
  Dihedral angle restraints: 3538
    sinusoidal: 1346
      harmonic: 2192
  Sorted by residual:
  dihedral pdb=" CA  ASP B 199 "
           pdb=" CB  ASP B 199 "
           pdb=" CG  ASP B 199 "
           pdb=" OD1 ASP B 199 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -84.89   54.89     1      2.00e+01 2.50e-03 1.02e+01
  dihedral pdb=" CA  ASP A 199 "
           pdb=" CB  ASP A 199 "
           pdb=" CG  ASP A 199 "
           pdb=" OD1 ASP A 199 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -84.79   54.79     1      2.00e+01 2.50e-03 1.02e+01
  dihedral pdb=" CA  ASN B 112 "
           pdb=" CB  ASN B 112 "
           pdb=" CG  ASN B 112 "
           pdb=" OD1 ASN B 112 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00 -154.50   64.50     2      2.00e+01 2.50e-03 9.78e+00
  ... (remaining 3535 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 635
       0.030 -    0.061: 236
       0.061 -    0.091: 83
       0.091 -    0.121: 28
       0.121 -    0.152: 8
  Chirality restraints: 990
  Sorted by residual:
  chirality pdb=" CA  VAL B 206 "
            pdb=" N   VAL B 206 "
            pdb=" C   VAL B 206 "
            pdb=" CB  VAL B 206 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.15 2.00e-01 2.50e+01 5.75e-01
  chirality pdb=" CA  VAL A 206 "
            pdb=" N   VAL A 206 "
            pdb=" C   VAL A 206 "
            pdb=" CB  VAL A 206 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 4.70e-01
  chirality pdb=" CA  ASN B 112 "
            pdb=" N   ASN B 112 "
            pdb=" C   ASN B 112 "
            pdb=" CB  ASN B 112 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.64   -0.13 2.00e-01 2.50e+01 4.52e-01
  ... (remaining 987 not shown)

  Planarity restraints: 990
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 474 "   -0.029 5.00e-02 4.00e+02   4.45e-02 3.17e+00
        pdb=" N   PRO A 475 "    0.077 5.00e-02 4.00e+02
        pdb=" CA  PRO A 475 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO A 475 "   -0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO B 474 "    0.029 5.00e-02 4.00e+02   4.44e-02 3.15e+00
        pdb=" N   PRO B 475 "   -0.077 5.00e-02 4.00e+02
        pdb=" CA  PRO B 475 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO B 475 "    0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL B 564 "    0.009 2.00e-02 2.50e+03   1.73e-02 2.99e+00
        pdb=" C   VAL B 564 "   -0.030 2.00e-02 2.50e+03
        pdb=" O   VAL B 564 "    0.011 2.00e-02 2.50e+03
        pdb=" N   ARG B 565 "    0.010 2.00e-02 2.50e+03
  ... (remaining 987 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 95
        2.71 -     3.26: 5969
        3.26 -     3.80: 9380
        3.80 -     4.35: 11271
        4.35 -     4.90: 19488
  Nonbonded interactions: 46203
  Sorted by model distance:
  nonbonded pdb=" O   PHE B 105 "
            pdb=" OG1 THR B 109 "
     model   vdw
     2.162 3.040
  nonbonded pdb=" O   PHE A 105 "
            pdb=" OG1 THR A 109 "
     model   vdw
     2.163 3.040
  nonbonded pdb=" O   ILE A 492 "
            pdb=" OH  TYR A 498 "
     model   vdw
     2.193 3.040
  nonbonded pdb=" O   ILE B 492 "
            pdb=" OH  TYR B 498 "
     model   vdw
     2.193 3.040
  nonbonded pdb=" OE1 GLN B 547 "
            pdb=" OG  SER B 617 "
     model   vdw
     2.234 3.040
  ... (remaining 46198 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: 0.03
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:             1.220
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.230
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     17.210
  Find NCS groups from input model:        0.100
  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:12.750
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.620
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7913
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      :  0.002   0.023   6018  Z= 0.155
  Angle     :  0.543   5.752   8200  Z= 0.290
  Chirality :  0.038   0.152    990
  Planarity :  0.005   0.044    990
  Dihedral  : 13.066  89.799   2118
  Min Nonbonded Distance : 2.162

Molprobity Statistics.
  All-atom Clashscore : 7.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.07 %
    Favored  : 98.93 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.77 (0.31), residues: 746
  helix:  1.67 (0.22), residues: 558
  sheet:  2.09 (0.86), residues: 42
  loop : -0.97 (0.53), residues: 146

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 506 
 HIS   0.001   0.000   HIS B 514 
 PHE   0.010   0.001   PHE A 566 
 TYR   0.006   0.001   TYR A 635 
 ARG   0.008   0.000   ARG B 207 

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

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

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 113
  time to evaluate  : 0.633 
Fit side-chains
REVERT: B  610 ASN cc_start: 0.8317 (t0) cc_final: 0.7890 (t0)
REVERT: A  160 LEU cc_start: 0.6733 (tt) cc_final: 0.6162 (mt)
REVERT: A  610 ASN cc_start: 0.8314 (t0) cc_final: 0.7890 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 113
  average time/residue: 1.2387
  time to fit residues: 146.2979
Evaluate side-chains
  97 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.660 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 62 optimal weight:    0.0050
   chunk 56 optimal weight:    5.9990
   chunk 31 optimal weight:    1.9990
   chunk 19 optimal weight:    7.9990
   chunk 37 optimal weight:    4.9990
   chunk 29 optimal weight:    1.9990
   chunk 58 optimal weight:    0.7980
   chunk 22 optimal weight:    2.9990
   chunk 35 optimal weight:    1.9990
   chunk 43 optimal weight:    6.9990
   chunk 67 optimal weight:    6.9990
   overall best weight:    1.3600

-------------------------------------------------------------------------------
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 = 0.3853 r_free = 0.3853 target = 0.159734 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.125912 restraints weight = 7092.210|
|-----------------------------------------------------------------------------|
r_work (start): 0.3472 rms_B_bonded: 1.63
r_work: 0.3362 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.3248 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.3248
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8186
moved from start:          0.0947

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6018  Z= 0.204
  Angle     :  0.552   6.266   8200  Z= 0.286
  Chirality :  0.039   0.154    990
  Planarity :  0.005   0.040    990
  Dihedral  :  4.181  15.268    800
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 6.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.54 %
    Favored  : 99.46 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  :  9.87 %
    Favored  : 88.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.87 (0.31), residues: 746
  helix:  1.73 (0.22), residues: 564
  sheet:  1.74 (0.80), residues: 42
  loop : -0.86 (0.57), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 506 
 HIS   0.001   0.000   HIS A 187 
 PHE   0.012   0.001   PHE B  92 
 TYR   0.006   0.001   TYR A 635 
 ARG   0.001   0.000   ARG B 493 

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

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

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 110
  time to evaluate  : 0.610 
Fit side-chains
REVERT: B  160 LEU cc_start: 0.6979 (tm) cc_final: 0.5929 (mt)
REVERT: B  176 LYS cc_start: 0.7177 (mmtt) cc_final: 0.6265 (ttpp)
REVERT: B  610 ASN cc_start: 0.8513 (t0) cc_final: 0.8134 (t0)
REVERT: A  176 LYS cc_start: 0.7212 (mmtt) cc_final: 0.6297 (ttpp)
REVERT: A  585 ASP cc_start: 0.7596 (m-30) cc_final: 0.7367 (m-30)
REVERT: A  610 ASN cc_start: 0.8507 (t0) cc_final: 0.8130 (t0)
  outliers start: 10
  outliers final: 5
  residues processed: 116
  average time/residue: 1.1711
  time to fit residues: 142.2806
Evaluate side-chains
  101 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 96
  time to evaluate  : 0.630 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  159 MET
Chi-restraints excluded: chain B residue  568 THR
Chi-restraints excluded: chain A residue  159 MET
Chi-restraints excluded: chain A residue  201 LYS
Chi-restraints excluded: chain A residue  568 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 50 optimal weight:    4.9990
   chunk 28 optimal weight:    3.9990
   chunk 48 optimal weight:    3.9990
   chunk 33 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9980
   chunk 29 optimal weight:    0.9980
   chunk 18 optimal weight:    7.9990
   chunk 69 optimal weight:    0.9990
   chunk 43 optimal weight:    5.9990
   chunk 47 optimal weight:    4.9990
   chunk 21 optimal weight:    0.0270
   overall best weight:    1.0042

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

Flipped N/Q/H residues before XYZ refinement:
B 112 ASN
B 472 ASN
A 112 ASN
A 472 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.158477 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.124739 restraints weight = 7194.017|
|-----------------------------------------------------------------------------|
r_work (start): 0.3480 rms_B_bonded: 1.64
r_work: 0.3371 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.3251 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.3251
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8166
moved from start:          0.1251

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6018  Z= 0.172
  Angle     :  0.525   7.207   8200  Z= 0.270
  Chirality :  0.038   0.138    990
  Planarity :  0.004   0.039    990
  Dihedral  :  4.107  15.329    800
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 5.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.07 %
    Favored  : 98.93 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 13.32 %
    Favored  : 85.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.00 (0.31), residues: 746
  helix:  1.81 (0.22), residues: 564
  sheet:  1.90 (0.78), residues: 42
  loop : -0.80 (0.58), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 506 
 HIS   0.001   0.000   HIS A 187 
 PHE   0.010   0.001   PHE B  92 
 TYR   0.007   0.001   TYR B 635 
 ARG   0.001   0.000   ARG A 512 

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

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

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 99
  time to evaluate  : 0.646 
Fit side-chains
REVERT: B  160 LEU cc_start: 0.6968 (tm) cc_final: 0.5834 (mt)
REVERT: B  176 LYS cc_start: 0.7239 (mmtt) cc_final: 0.6374 (ttpp)
REVERT: B  610 ASN cc_start: 0.8450 (t0) cc_final: 0.8091 (t0)
REVERT: A  160 LEU cc_start: 0.6943 (tm) cc_final: 0.5836 (mt)
REVERT: A  176 LYS cc_start: 0.7257 (mmtt) cc_final: 0.6381 (ttpp)
REVERT: A  544 MET cc_start: 0.8624 (ttt) cc_final: 0.8359 (ttp)
REVERT: A  610 ASN cc_start: 0.8435 (t0) cc_final: 0.8086 (t0)
  outliers start: 9
  outliers final: 3
  residues processed: 105
  average time/residue: 1.1481
  time to fit residues: 126.8679
Evaluate side-chains
  93 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 90
  time to evaluate  : 0.759 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  201 LYS
Chi-restraints excluded: chain B residue  568 THR
Chi-restraints excluded: chain A residue  568 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 6 optimal weight:    0.7980
   chunk 12 optimal weight:    5.9990
   chunk 41 optimal weight:    3.9990
   chunk 50 optimal weight:    4.9990
   chunk 2 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   chunk 70 optimal weight:    1.9990
   chunk 54 optimal weight:    9.9990
   chunk 53 optimal weight:    6.9990
   chunk 40 optimal weight:    0.9990
   chunk 0 optimal weight:    6.9990
   overall best weight:    1.7588

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

Flipped N/Q/H residues before XYZ refinement:
B  68 ASN
A  68 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.158057 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.124677 restraints weight = 7287.813|
|-----------------------------------------------------------------------------|
r_work (start): 0.3426 rms_B_bonded: 1.70
r_work: 0.3310 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3192 rms_B_bonded: 4.10 restraints_weight: 0.2500
r_work (final): 0.3192
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8195
moved from start:          0.1575

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   6018  Z= 0.250
  Angle     :  0.567   5.703   8200  Z= 0.297
  Chirality :  0.040   0.154    990
  Planarity :  0.004   0.041    990
  Dihedral  :  4.223  15.902    800
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 5.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.07 %
    Favored  : 98.93 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 15.05 %
    Favored  : 82.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.66 (0.31), residues: 746
  helix:  1.60 (0.21), residues: 560
  sheet:  1.87 (0.78), residues: 42
  loop : -1.06 (0.55), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 506 
 HIS   0.002   0.001   HIS B 187 
 PHE   0.013   0.002   PHE B 603 
 TYR   0.008   0.001   TYR B 635 
 ARG   0.001   0.000   ARG A  70 

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

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

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 102
  time to evaluate  : 0.669 
Fit side-chains
REVERT: B  160 LEU cc_start: 0.6968 (tm) cc_final: 0.5817 (mt)
REVERT: B  176 LYS cc_start: 0.7272 (mmtt) cc_final: 0.6370 (ttpp)
REVERT: B  472 ASN cc_start: 0.5161 (t0) cc_final: 0.4637 (t0)
REVERT: B  610 ASN cc_start: 0.8423 (t0) cc_final: 0.8041 (t0)
REVERT: A  176 LYS cc_start: 0.7351 (mmtt) cc_final: 0.6470 (ttpp)
REVERT: A  472 ASN cc_start: 0.5154 (t0) cc_final: 0.4637 (t0)
REVERT: A  610 ASN cc_start: 0.8421 (t0) cc_final: 0.8019 (t0)
  outliers start: 13
  outliers final: 4
  residues processed: 113
  average time/residue: 1.1276
  time to fit residues: 134.2544
Evaluate side-chains
  99 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 95
  time to evaluate  : 0.605 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  527 ILE
Chi-restraints excluded: chain B residue  568 THR
Chi-restraints excluded: chain A residue  527 ILE
Chi-restraints excluded: chain A residue  568 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 3 optimal weight:    0.7980
   chunk 10 optimal weight:    5.9990
   chunk 11 optimal weight:    0.6980
   chunk 31 optimal weight:    7.9990
   chunk 23 optimal weight:    0.8980
   chunk 24 optimal weight:    0.9990
   chunk 37 optimal weight:    4.9990
   chunk 16 optimal weight:    4.9990
   chunk 68 optimal weight:    6.9990
   chunk 57 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
B  68 ASN
A  68 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.157897 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.124322 restraints weight = 7127.499|
|-----------------------------------------------------------------------------|
r_work (start): 0.3454 rms_B_bonded: 1.69
r_work: 0.3340 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3221 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.3221
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8169
moved from start:          0.1651

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6018  Z= 0.184
  Angle     :  0.529   7.050   8200  Z= 0.278
  Chirality :  0.038   0.138    990
  Planarity :  0.004   0.039    990
  Dihedral  :  4.161  15.657    800
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 6.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.21 %
    Favored  : 98.79 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 16.93 %
    Favored  : 81.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.83 (0.31), residues: 746
  helix:  1.74 (0.22), residues: 560
  sheet:  1.72 (0.78), residues: 42
  loop : -1.02 (0.56), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 506 
 HIS   0.001   0.000   HIS A 203 
 PHE   0.014   0.001   PHE B 603 
 TYR   0.006   0.001   TYR A   8 
 ARG   0.001   0.000   ARG B 512 

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

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

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 103
  time to evaluate  : 0.623 
Fit side-chains
REVERT: B  160 LEU cc_start: 0.6981 (tm) cc_final: 0.5827 (mt)
REVERT: B  176 LYS cc_start: 0.7261 (mmtt) cc_final: 0.6374 (ttpp)
REVERT: B  472 ASN cc_start: 0.5158 (t0) cc_final: 0.4576 (t0)
REVERT: B  610 ASN cc_start: 0.8423 (t0) cc_final: 0.8013 (t0)
REVERT: A  160 LEU cc_start: 0.6996 (tm) cc_final: 0.5869 (mt)
REVERT: A  176 LYS cc_start: 0.7249 (mmtt) cc_final: 0.6359 (ttpp)
REVERT: A  472 ASN cc_start: 0.5149 (t0) cc_final: 0.4576 (t0)
REVERT: A  610 ASN cc_start: 0.8437 (t0) cc_final: 0.8038 (t0)
  outliers start: 9
  outliers final: 3
  residues processed: 109
  average time/residue: 0.9778
  time to fit residues: 112.6946
Evaluate side-chains
  100 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 97
  time to evaluate  : 0.583 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  568 THR
Chi-restraints excluded: chain A residue  159 MET
Chi-restraints excluded: chain A residue  568 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 14 optimal weight:    3.9990
   chunk 57 optimal weight:    0.0770
   chunk 63 optimal weight:    5.9990
   chunk 4 optimal weight:    1.9990
   chunk 10 optimal weight:    4.9990
   chunk 8 optimal weight:   10.0000
   chunk 73 optimal weight:    0.6980
   chunk 26 optimal weight:    0.7980
   chunk 19 optimal weight:    0.6980
   chunk 52 optimal weight:    6.9990
   chunk 22 optimal weight:    0.8980
   overall best weight:    0.6338

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

Flipped N/Q/H residues before XYZ refinement:
B  68 ASN
A  68 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.162769 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.129909 restraints weight = 7108.229|
|-----------------------------------------------------------------------------|
r_work (start): 0.3475 rms_B_bonded: 1.61
r_work: 0.3366 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.3246 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.3246
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8170
moved from start:          0.1686

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041   6018  Z= 0.156
  Angle     :  0.515   6.561   8200  Z= 0.269
  Chirality :  0.037   0.125    990
  Planarity :  0.004   0.038    990
  Dihedral  :  4.104  15.571    800
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.80 %
    Favored  : 99.20 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 17.40 %
    Favored  : 81.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.94 (0.31), residues: 746
  helix:  1.82 (0.22), residues: 560
  sheet:  1.76 (0.76), residues: 42
  loop : -0.95 (0.57), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 506 
 HIS   0.001   0.000   HIS A   5 
 PHE   0.014   0.001   PHE B 603 
 TYR   0.005   0.001   TYR A   8 
 ARG   0.001   0.000   ARG B 512 

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

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

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 100
  time to evaluate  : 0.676 
Fit side-chains
REVERT: B  160 LEU cc_start: 0.7062 (tm) cc_final: 0.5900 (mt)
REVERT: B  176 LYS cc_start: 0.7256 (mmtt) cc_final: 0.6397 (ttpp)
REVERT: B  472 ASN cc_start: 0.5185 (t0) cc_final: 0.4575 (t0)
REVERT: B  610 ASN cc_start: 0.8456 (t0) cc_final: 0.8030 (t0)
REVERT: A  160 LEU cc_start: 0.7043 (tm) cc_final: 0.5900 (mt)
REVERT: A  176 LYS cc_start: 0.7245 (mmtt) cc_final: 0.6394 (ttpp)
REVERT: A  472 ASN cc_start: 0.5191 (t0) cc_final: 0.4584 (t0)
REVERT: A  544 MET cc_start: 0.8613 (ttt) cc_final: 0.8314 (ttp)
REVERT: A  610 ASN cc_start: 0.8451 (t0) cc_final: 0.8055 (t0)
  outliers start: 8
  outliers final: 1
  residues processed: 106
  average time/residue: 0.9711
  time to fit residues: 109.0657
Evaluate side-chains
  96 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 95
  time to evaluate  : 1.003 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  159 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 29 optimal weight:    7.9990
   chunk 46 optimal weight:    9.9990
   chunk 34 optimal weight:    3.9990
   chunk 8 optimal weight:    9.9990
   chunk 69 optimal weight:    0.9980
   chunk 6 optimal weight:    2.9990
   chunk 26 optimal weight:    0.5980
   chunk 1 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9980
   chunk 72 optimal weight:    4.9990
   chunk 14 optimal weight:    3.9990
   overall best weight:    1.5184

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

Flipped N/Q/H residues before XYZ refinement:
B  68 ASN
A  68 ASN
A 612 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.159862 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.127006 restraints weight = 7100.525|
|-----------------------------------------------------------------------------|
r_work (start): 0.3451 rms_B_bonded: 1.62
r_work: 0.3338 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.3221 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.3221
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8226
moved from start:          0.1827

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   6018  Z= 0.225
  Angle     :  0.562   6.241   8200  Z= 0.294
  Chirality :  0.039   0.145    990
  Planarity :  0.004   0.039    990
  Dihedral  :  4.176  15.907    800
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 6.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.21 %
    Favored  : 98.79 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 17.71 %
    Favored  : 80.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.73 (0.31), residues: 746
  helix:  1.65 (0.22), residues: 556
  sheet:  1.81 (0.75), residues: 42
  loop : -0.96 (0.54), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 506 
 HIS   0.001   0.000   HIS A 187 
 PHE   0.016   0.002   PHE B 603 
 TYR   0.007   0.001   TYR B 635 
 ARG   0.001   0.000   ARG A 565 

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

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

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 103
  time to evaluate  : 0.699 
Fit side-chains
REVERT: B  176 LYS cc_start: 0.7365 (mmtt) cc_final: 0.6539 (ttpp)
REVERT: B  472 ASN cc_start: 0.5233 (t0) cc_final: 0.4720 (t0)
REVERT: B  610 ASN cc_start: 0.8453 (t0) cc_final: 0.8030 (t0)
REVERT: A  176 LYS cc_start: 0.7281 (mmtt) cc_final: 0.6452 (ttpp)
REVERT: A  472 ASN cc_start: 0.5234 (t0) cc_final: 0.4720 (t0)
REVERT: A  610 ASN cc_start: 0.8450 (t0) cc_final: 0.8040 (t0)
  outliers start: 10
  outliers final: 2
  residues processed: 109
  average time/residue: 1.0090
  time to fit residues: 116.2409
Evaluate side-chains
  101 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 99
  time to evaluate  : 0.616 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  568 THR
Chi-restraints excluded: chain A residue  568 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 72 optimal weight:    0.7980
   chunk 69 optimal weight:    1.9990
   chunk 38 optimal weight:    4.9990
   chunk 5 optimal weight:    3.9990
   chunk 46 optimal weight:   10.0000
   chunk 67 optimal weight:    3.9990
   chunk 30 optimal weight:    1.9990
   chunk 34 optimal weight:    3.9990
   chunk 65 optimal weight:    3.9990
   chunk 1 optimal weight:    0.4980
   chunk 13 optimal weight:    0.7980
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:
B  68 ASN
A  68 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.159396 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.126250 restraints weight = 7093.206|
|-----------------------------------------------------------------------------|
r_work (start): 0.3443 rms_B_bonded: 1.68
r_work: 0.3328 rms_B_bonded: 2.48 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: 0.8173
moved from start:          0.1851

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6018  Z= 0.203
  Angle     :  0.579   7.808   8200  Z= 0.296
  Chirality :  0.039   0.137    990
  Planarity :  0.004   0.039    990
  Dihedral  :  4.180  15.628    800
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 6.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.07 %
    Favored  : 98.93 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  : 19.12 %
    Favored  : 79.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.75 (0.31), residues: 746
  helix:  1.67 (0.22), residues: 556
  sheet:  1.89 (0.74), residues: 42
  loop : -0.93 (0.55), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 506 
 HIS   0.001   0.000   HIS A 612 
 PHE   0.019   0.001   PHE A 622 
 TYR   0.007   0.001   TYR B 128 
 ARG   0.001   0.000   ARG B 512 

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

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

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 98
  time to evaluate  : 0.639 
Fit side-chains
REVERT: B  160 LEU cc_start: 0.6973 (tm) cc_final: 0.5861 (mt)
REVERT: B  472 ASN cc_start: 0.5244 (t0) cc_final: 0.4714 (t0)
REVERT: B  610 ASN cc_start: 0.8459 (t0) cc_final: 0.8036 (t0)
REVERT: A  472 ASN cc_start: 0.5234 (t0) cc_final: 0.4710 (t0)
REVERT: A  610 ASN cc_start: 0.8455 (t0) cc_final: 0.8037 (t0)
  outliers start: 7
  outliers final: 1
  residues processed: 104
  average time/residue: 1.0388
  time to fit residues: 113.8008
Evaluate side-chains
  94 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 93
  time to evaluate  : 0.702 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  568 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 65 optimal weight:    0.2980
   chunk 29 optimal weight:    3.9990
   chunk 62 optimal weight:    3.9990
   chunk 70 optimal weight:    0.8980
   chunk 37 optimal weight:    3.9990
   chunk 46 optimal weight:    9.9990
   chunk 26 optimal weight:    2.9990
   chunk 73 optimal weight:    1.9990
   chunk 11 optimal weight:    2.9990
   chunk 72 optimal weight:    0.5980
   chunk 44 optimal weight:    0.9980
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
B  68 ASN
A  68 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.161736 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.128910 restraints weight = 7114.828|
|-----------------------------------------------------------------------------|
r_work (start): 0.3474 rms_B_bonded: 1.63
r_work: 0.3365 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.3245 rms_B_bonded: 3.95 restraints_weight: 0.2500
r_work (final): 0.3245
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8186
moved from start:          0.1857

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   6018  Z= 0.188
  Angle     :  0.570   7.570   8200  Z= 0.293
  Chirality :  0.038   0.134    990
  Planarity :  0.004   0.039    990
  Dihedral  :  4.156  15.528    800
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 6.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.94 %
    Favored  : 99.06 %
  Rotamer:
    Outliers :  0.94 %
    Allowed  : 19.91 %
    Favored  : 79.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.79 (0.31), residues: 746
  helix:  1.68 (0.22), residues: 560
  sheet:  1.94 (0.72), residues: 42
  loop : -0.96 (0.57), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 506 
 HIS   0.001   0.000   HIS A 612 
 PHE   0.018   0.001   PHE B 603 
 TYR   0.009   0.001   TYR B 128 
 ARG   0.001   0.000   ARG B 512 

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

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

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 97
  time to evaluate  : 0.648 
Fit side-chains
REVERT: B  160 LEU cc_start: 0.6970 (tm) cc_final: 0.5872 (mt)
REVERT: B  472 ASN cc_start: 0.5322 (t0) cc_final: 0.4816 (t0)
REVERT: B  610 ASN cc_start: 0.8457 (t0) cc_final: 0.8052 (t0)
REVERT: A  472 ASN cc_start: 0.5325 (t0) cc_final: 0.4824 (t0)
REVERT: A  544 MET cc_start: 0.8613 (ttt) cc_final: 0.8307 (ttp)
REVERT: A  610 ASN cc_start: 0.8433 (t0) cc_final: 0.8033 (t0)
  outliers start: 6
  outliers final: 0
  residues processed: 101
  average time/residue: 1.0300
  time to fit residues: 109.8087
Evaluate side-chains
  92 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.611 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 15 optimal weight:    7.9990
   chunk 60 optimal weight:    0.9990
   chunk 34 optimal weight:    0.5980
   chunk 24 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9980
   chunk 65 optimal weight:    0.0010
   chunk 26 optimal weight:    0.1980
   chunk 46 optimal weight:   10.0000
   chunk 51 optimal weight:    0.9980
   chunk 43 optimal weight:    2.9990
   chunk 33 optimal weight:    0.5980
   overall best weight:    0.4786

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

Flipped N/Q/H residues before XYZ refinement:
B  68 ASN
B 140 GLN
A  68 ASN
A 140 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.164022 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.131140 restraints weight = 7173.456|
|-----------------------------------------------------------------------------|
r_work (start): 0.3508 rms_B_bonded: 1.64
r_work: 0.3399 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.3281 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.3281
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8147
moved from start:          0.1905

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   6018  Z= 0.167
  Angle     :  0.565   7.545   8200  Z= 0.291
  Chirality :  0.038   0.156    990
  Planarity :  0.004   0.038    990
  Dihedral  :  4.109  15.003    800
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 6.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.07 %
    Favored  : 98.93 %
  Rotamer:
    Outliers :  0.94 %
    Allowed  : 20.69 %
    Favored  : 78.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.86 (0.31), residues: 746
  helix:  1.73 (0.22), residues: 560
  sheet:  1.91 (0.72), residues: 42
  loop : -0.90 (0.58), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 506 
 HIS   0.001   0.000   HIS A 612 
 PHE   0.018   0.001   PHE B 603 
 TYR   0.010   0.001   TYR A 128 
 ARG   0.001   0.000   ARG B 489 

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

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

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 97
  time to evaluate  : 0.616 
Fit side-chains
REVERT: B  160 LEU cc_start: 0.6901 (tm) cc_final: 0.5815 (mt)
REVERT: B  472 ASN cc_start: 0.5294 (t0) cc_final: 0.4828 (t0)
REVERT: B  544 MET cc_start: 0.8582 (ttt) cc_final: 0.8321 (ttp)
REVERT: B  610 ASN cc_start: 0.8451 (t0) cc_final: 0.8069 (t0)
REVERT: A  472 ASN cc_start: 0.5293 (t0) cc_final: 0.4840 (t0)
REVERT: A  544 MET cc_start: 0.8611 (ttt) cc_final: 0.8310 (ttp)
REVERT: A  610 ASN cc_start: 0.8426 (t0) cc_final: 0.8050 (t0)
  outliers start: 6
  outliers final: 0
  residues processed: 101
  average time/residue: 0.9597
  time to fit residues: 102.6082
Evaluate side-chains
  93 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 93
  time to evaluate  : 0.660 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 21 optimal weight:    2.9990
   chunk 30 optimal weight:    3.9990
   chunk 27 optimal weight:    0.9980
   chunk 26 optimal weight:    0.5980
   chunk 33 optimal weight:    1.9990
   chunk 40 optimal weight:    2.9990
   chunk 46 optimal weight:    9.9990
   chunk 25 optimal weight:    1.9990
   chunk 50 optimal weight:    0.9990
   chunk 63 optimal weight:    0.9980
   chunk 58 optimal weight:    0.0370
   overall best weight:    0.7260

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

Flipped N/Q/H residues before XYZ refinement:
B  68 ASN
A  68 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.161718 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.128644 restraints weight = 7184.601|
|-----------------------------------------------------------------------------|
r_work (start): 0.3493 rms_B_bonded: 1.65
r_work: 0.3384 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.3265 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.3265
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8157
moved from start:          0.1941

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.065   6018  Z= 0.182
  Angle     :  0.579   8.152   8200  Z= 0.296
  Chirality :  0.038   0.156    990
  Planarity :  0.004   0.038    990
  Dihedral  :  4.082  15.289    800
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 6.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.07 %
    Favored  : 98.93 %
  Rotamer:
    Outliers :  0.78 %
    Allowed  : 21.16 %
    Favored  : 78.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.87 (0.31), residues: 746
  helix:  1.72 (0.22), residues: 558
  sheet:  1.95 (0.72), residues: 42
  loop : -0.82 (0.56), residues: 146

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 506 
 HIS   0.001   0.000   HIS A 612 
 PHE   0.024   0.001   PHE A 622 
 TYR   0.009   0.001   TYR B 128 
 ARG   0.001   0.000   ARG B 512 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4135.97 seconds
wall clock time: 73 minutes 44.15 seconds (4424.15 seconds total)