Starting phenix.real_space_refine
on Thu Jul 24 08:45:02 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wks_32568/07_2025/7wks_32568.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wks_32568/07_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_32568/07_2025/7wks_32568.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wks_32568/07_2025/7wks_32568.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wks_32568/07_2025/7wks_32568.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wks_32568/07_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-5711/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: 4.00, per 1000 atoms: 0.68
  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: 1.43
  Conformation dependent library (CDL) restraints added in 900.2 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: 0.64
  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: 1.60

  Time building geometry restraints manager: 1.70 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:             0.690
  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:         0.050
  Set scattering table:                    0.060
  Process input model:                     17.560
  Find NCS groups from input model:        0.110
  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:13.000
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.720
-------------------------------------------------------------------------------
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= 0.120
  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.10981 (  434)
  hydrogen bonds       : angle       5.70492 ( 1302)
  covalent geometry    : bond        0.00238 ( 6018)
  covalent geometry    : angle       0.54254 ( 8200)

*********************** 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  : 0.685 
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: 1.1756
  time to fit residues: 139.1725
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  : 0.713 
-------------------------------------------------------------------------------
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 = 50)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.125914 restraints weight = 7092.211|
|-----------------------------------------------------------------------------|
r_work (start): 0.3472 rms_B_bonded: 1.63
r_work: 0.3363 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.3247 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.3247
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8171
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= 0.139
  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04538 (  434)
  hydrogen bonds       : angle       5.07952 ( 1302)
  covalent geometry    : bond        0.00314 ( 6018)
  covalent geometry    : angle       0.55170 ( 8200)

*********************** 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  : 0.666 
Fit side-chains
REVERT: B  160 LEU cc_start: 0.6969 (tm) cc_final: 0.5917 (mt)
REVERT: B  176 LYS cc_start: 0.7164 (mmtt) cc_final: 0.6252 (ttpp)
REVERT: B  610 ASN cc_start: 0.8521 (t0) cc_final: 0.8139 (t0)
REVERT: A  176 LYS cc_start: 0.7200 (mmtt) cc_final: 0.6284 (ttpp)
REVERT: A  585 ASP cc_start: 0.7590 (m-30) cc_final: 0.7356 (m-30)
REVERT: A  610 ASN cc_start: 0.8511 (t0) cc_final: 0.8132 (t0)
  outliers start: 10
  outliers final: 5
  residues processed: 116
  average time/residue: 1.3395
  time to fit residues: 163.1086
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  : 0.667 
-------------------------------------------------------------------------------
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:    0.3980
   chunk 42 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   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:    6.9990
   overall best weight:    2.0788

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

Flipped N/Q/H residues before XYZ refinement:
B  68 ASN
B 112 ASN
B 472 ASN
A  68 ASN
A 112 ASN
A 472 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.157016 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.123789 restraints weight = 7122.109|
|-----------------------------------------------------------------------------|
r_work (start): 0.3425 rms_B_bonded: 1.67
r_work: 0.3310 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3192 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.3192
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8203
moved from start:          0.1483

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   6018  Z= 0.177
  Angle     :  0.587   7.163   8200  Z= 0.306
  Chirality :  0.040   0.162    990
  Planarity :  0.005   0.042    990
  Dihedral  :  4.288  16.107    800
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.34 %
    Favored  : 98.66 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 13.17 %
    Favored  : 84.95 %
  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:  1.56 (0.30), residues: 746
  helix:  1.53 (0.21), residues: 562
  sheet:  1.75 (0.79), residues: 42
  loop : -1.09 (0.54), residues: 142

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B 506 
 HIS   0.002   0.001   HIS A 187 
 PHE   0.012   0.002   PHE A  92 
 TYR   0.008   0.001   TYR B 635 
 ARG   0.001   0.000   ARG B 493 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05024 (  434)
  hydrogen bonds       : angle       5.29588 ( 1302)
  covalent geometry    : bond        0.00428 ( 6018)
  covalent geometry    : angle       0.58676 ( 8200)

*********************** 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
  112 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 100
  time to evaluate  : 0.747 
Fit side-chains
REVERT: B  160 LEU cc_start: 0.7016 (tm) cc_final: 0.5873 (mt)
REVERT: B  176 LYS cc_start: 0.7188 (mmtt) cc_final: 0.6258 (ttpp)
REVERT: B  472 ASN cc_start: 0.5150 (t0) cc_final: 0.4596 (t0)
REVERT: B  610 ASN cc_start: 0.8411 (t0) cc_final: 0.8048 (t0)
REVERT: B  636 ILE cc_start: 0.8102 (mp) cc_final: 0.7894 (mp)
REVERT: A  160 LEU cc_start: 0.6945 (tm) cc_final: 0.5853 (mt)
REVERT: A  176 LYS cc_start: 0.7310 (mmtt) cc_final: 0.6426 (ttpp)
REVERT: A  472 ASN cc_start: 0.5140 (t0) cc_final: 0.4594 (t0)
REVERT: A  610 ASN cc_start: 0.8402 (t0) cc_final: 0.8041 (t0)
REVERT: A  636 ILE cc_start: 0.8088 (mp) cc_final: 0.7884 (mp)
  outliers start: 12
  outliers final: 2
  residues processed: 110
  average time/residue: 1.6682
  time to fit residues: 191.6489
Evaluate side-chains
  94 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 92
  time to evaluate  : 0.807 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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:    0.2980
   chunk 12 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   chunk 50 optimal weight:    1.9990
   chunk 2 optimal weight:    2.9990
   chunk 23 optimal weight:    2.9990
   chunk 70 optimal weight:    2.9990
   chunk 54 optimal weight:    6.9990
   chunk 53 optimal weight:    6.9990
   chunk 40 optimal weight:    4.9990
   chunk 0 optimal weight:    4.9990
   overall best weight:    2.0588

-------------------------------------------------------------------------------
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 = 0.3813 r_free = 0.3813 target = 0.156584 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.122869 restraints weight = 7368.633|
|-----------------------------------------------------------------------------|
r_work (start): 0.3408 rms_B_bonded: 1.73
r_work: 0.3295 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3174 rms_B_bonded: 4.09 restraints_weight: 0.2500
r_work (final): 0.3174
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8216
moved from start:          0.1705

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6018  Z= 0.174
  Angle     :  0.574   5.661   8200  Z= 0.300
  Chirality :  0.040   0.162    990
  Planarity :  0.005   0.042    990
  Dihedral  :  4.332  16.272    800
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 6.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.34 %
    Favored  : 98.66 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 15.52 %
    Favored  : 82.45 %
  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:  1.45 (0.30), residues: 746
  helix:  1.45 (0.21), residues: 562
  sheet:  1.72 (0.82), residues: 42
  loop : -1.17 (0.53), residues: 142

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 506 
 HIS   0.001   0.001   HIS B 187 
 PHE   0.012   0.002   PHE B 189 
 TYR   0.006   0.001   TYR B   8 
 ARG   0.001   0.000   ARG A  70 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04889 (  434)
  hydrogen bonds       : angle       5.31765 ( 1302)
  covalent geometry    : bond        0.00419 ( 6018)
  covalent geometry    : angle       0.57404 ( 8200)

*********************** 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
  116 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 103
  time to evaluate  : 0.705 
Fit side-chains
REVERT: B  160 LEU cc_start: 0.7006 (tm) cc_final: 0.5850 (mt)
REVERT: B  176 LYS cc_start: 0.7272 (mmtt) cc_final: 0.6390 (ttpp)
REVERT: B  472 ASN cc_start: 0.5261 (t0) cc_final: 0.4672 (t0)
REVERT: B  610 ASN cc_start: 0.8436 (t0) cc_final: 0.8031 (t0)
REVERT: A  176 LYS cc_start: 0.7230 (mmtt) cc_final: 0.6344 (ttpp)
REVERT: A  472 ASN cc_start: 0.5200 (t0) cc_final: 0.4627 (t0)
REVERT: A  610 ASN cc_start: 0.8431 (t0) cc_final: 0.7999 (t0)
  outliers start: 13
  outliers final: 4
  residues processed: 112
  average time/residue: 1.1657
  time to fit residues: 137.9878
Evaluate side-chains
  101 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 97
  time to evaluate  : 0.726 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 10 optimal weight:    5.9990
   chunk 11 optimal weight:    0.9990
   chunk 31 optimal weight:    6.9990
   chunk 23 optimal weight:    0.7980
   chunk 24 optimal weight:    0.8980
   chunk 37 optimal weight:    2.9990
   chunk 16 optimal weight:    8.9990
   chunk 68 optimal weight:    0.6980
   chunk 57 optimal weight:    7.9990
   chunk 15 optimal weight:    1.9990
   overall best weight:    0.8582

-------------------------------------------------------------------------------
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 = 0.3850 r_free = 0.3850 target = 0.159896 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.126982 restraints weight = 7123.410|
|-----------------------------------------------------------------------------|
r_work (start): 0.3457 rms_B_bonded: 1.63
r_work: 0.3345 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3229 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.3229
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8217
moved from start:          0.1701

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= 0.118
  Angle     :  0.527   7.345   8200  Z= 0.274
  Chirality :  0.037   0.135    990
  Planarity :  0.004   0.039    990
  Dihedral  :  4.215  15.886    800
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 6.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.34 %
    Favored  : 98.66 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 17.55 %
    Favored  : 81.03 %
  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:  1.71 (0.22), residues: 560
  sheet:  1.74 (0.78), residues: 42
  loop : -1.18 (0.55), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 506 
 HIS   0.001   0.000   HIS A   5 
 PHE   0.009   0.001   PHE A  92 
 TYR   0.008   0.001   TYR B 635 
 ARG   0.001   0.000   ARG A 512 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04072 (  434)
  hydrogen bonds       : angle       5.15250 ( 1302)
  covalent geometry    : bond        0.00256 ( 6018)
  covalent geometry    : angle       0.52662 ( 8200)

*********************** 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
  114 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 105
  time to evaluate  : 1.734 
Fit side-chains
REVERT: B  160 LEU cc_start: 0.7076 (tm) cc_final: 0.5925 (mt)
REVERT: B  176 LYS cc_start: 0.7333 (mmtt) cc_final: 0.6474 (ttpp)
REVERT: B  472 ASN cc_start: 0.5247 (t0) cc_final: 0.4645 (t0)
REVERT: B  610 ASN cc_start: 0.8399 (t0) cc_final: 0.7990 (t0)
REVERT: A  160 LEU cc_start: 0.7088 (tm) cc_final: 0.5970 (mt)
REVERT: A  176 LYS cc_start: 0.7262 (mmtt) cc_final: 0.6429 (ttpp)
REVERT: A  472 ASN cc_start: 0.5244 (t0) cc_final: 0.4646 (t0)
REVERT: A  610 ASN cc_start: 0.8409 (t0) cc_final: 0.8003 (t0)
  outliers start: 9
  outliers final: 3
  residues processed: 111
  average time/residue: 1.5187
  time to fit residues: 179.4485
Evaluate side-chains
  101 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 98
  time to evaluate  : 0.550 
-------------------------------------------------------------------------------
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  568 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 14 optimal weight:    1.9990
   chunk 57 optimal weight:    3.9990
   chunk 63 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 10 optimal weight:    6.9990
   chunk 8 optimal weight:    5.9990
   chunk 73 optimal weight:    0.7980
   chunk 26 optimal weight:    0.2980
   chunk 19 optimal weight:    8.9990
   chunk 52 optimal weight:   10.0000
   chunk 22 optimal weight:    1.9990
   overall best weight:    1.4186

-------------------------------------------------------------------------------
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 = 0.3841 r_free = 0.3841 target = 0.159033 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.125684 restraints weight = 7082.830|
|-----------------------------------------------------------------------------|
r_work (start): 0.3428 rms_B_bonded: 1.68
r_work: 0.3313 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.3194 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.3194
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8190
moved from start:          0.1816

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= 0.143
  Angle     :  0.551   6.423   8200  Z= 0.289
  Chirality :  0.039   0.143    990
  Planarity :  0.004   0.039    990
  Dihedral  :  4.210  15.847    800
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 6.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.07 %
    Favored  : 98.93 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 17.87 %
    Favored  : 80.41 %
  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:  1.63 (0.22), residues: 556
  sheet:  1.67 (0.77), residues: 42
  loop : -1.06 (0.54), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 506 
 HIS   0.001   0.000   HIS B 187 
 PHE   0.009   0.001   PHE A  92 
 TYR   0.006   0.001   TYR B 635 
 ARG   0.001   0.000   ARG B 512 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04360 (  434)
  hydrogen bonds       : angle       5.23716 ( 1302)
  covalent geometry    : bond        0.00339 ( 6018)
  covalent geometry    : angle       0.55143 ( 8200)

*********************** 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
  114 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 103
  time to evaluate  : 0.762 
Fit side-chains
REVERT: B  176 LYS cc_start: 0.7265 (mmtt) cc_final: 0.6366 (ttpp)
REVERT: B  472 ASN cc_start: 0.5356 (t0) cc_final: 0.4823 (t0)
REVERT: B  610 ASN cc_start: 0.8423 (t0) cc_final: 0.8002 (t0)
REVERT: A  160 LEU cc_start: 0.7001 (tm) cc_final: 0.5840 (mt)
REVERT: A  176 LYS cc_start: 0.7226 (mmtt) cc_final: 0.6352 (ttpp)
REVERT: A  472 ASN cc_start: 0.5343 (t0) cc_final: 0.4818 (t0)
REVERT: A  610 ASN cc_start: 0.8424 (t0) cc_final: 0.8008 (t0)
  outliers start: 11
  outliers final: 3
  residues processed: 110
  average time/residue: 1.1717
  time to fit residues: 136.3016
Evaluate side-chains
  102 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 99
  time to evaluate  : 0.524 
-------------------------------------------------------------------------------
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  568 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 29 optimal weight:    9.9990
   chunk 46 optimal weight:    9.9990
   chunk 34 optimal weight:    0.0270
   chunk 8 optimal weight:   10.0000
   chunk 69 optimal weight:    1.9990
   chunk 6 optimal weight:    2.9990
   chunk 26 optimal weight:    0.6980
   chunk 1 optimal weight:    0.6980
   chunk 58 optimal weight:    5.9990
   chunk 72 optimal weight:    0.9980
   chunk 14 optimal weight:    0.7980
   overall best weight:    0.6438

-------------------------------------------------------------------------------
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 = 0.3871 r_free = 0.3871 target = 0.161991 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.129146 restraints weight = 7131.974|
|-----------------------------------------------------------------------------|
r_work (start): 0.3474 rms_B_bonded: 1.64
r_work: 0.3364 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.3247 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.3247
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8182
moved from start:          0.1778

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.046   6018  Z= 0.115
  Angle     :  0.532   7.695   8200  Z= 0.275
  Chirality :  0.037   0.131    990
  Planarity :  0.004   0.037    990
  Dihedral  :  4.138  15.571    800
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 7.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.07 %
    Favored  : 98.93 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  : 19.75 %
    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:  1.85 (0.31), residues: 746
  helix:  1.76 (0.22), residues: 560
  sheet:  1.72 (0.75), residues: 42
  loop : -1.04 (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   5 
 PHE   0.015   0.001   PHE A 622 
 TYR   0.006   0.001   TYR B 635 
 ARG   0.001   0.000   ARG A 512 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03824 (  434)
  hydrogen bonds       : angle       5.06368 ( 1302)
  covalent geometry    : bond        0.00250 ( 6018)
  covalent geometry    : angle       0.53203 ( 8200)

*********************** 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
  108 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 101
  time to evaluate  : 0.660 
Fit side-chains
REVERT: B  160 LEU cc_start: 0.7048 (tm) cc_final: 0.5925 (mt)
REVERT: B  176 LYS cc_start: 0.7301 (mmtt) cc_final: 0.6443 (ttpp)
REVERT: B  472 ASN cc_start: 0.5326 (t0) cc_final: 0.4786 (t0)
REVERT: B  610 ASN cc_start: 0.8443 (t0) cc_final: 0.8033 (t0)
REVERT: A  160 LEU cc_start: 0.7000 (tm) cc_final: 0.5869 (mt)
REVERT: A  472 ASN cc_start: 0.5321 (t0) cc_final: 0.4785 (t0)
REVERT: A  544 MET cc_start: 0.8589 (ttt) cc_final: 0.8271 (ttp)
REVERT: A  610 ASN cc_start: 0.8423 (t0) cc_final: 0.8017 (t0)
  outliers start: 7
  outliers final: 0
  residues processed: 107
  average time/residue: 0.9608
  time to fit residues: 108.7217
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  : 0.589 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 72 optimal weight:    3.9990
   chunk 69 optimal weight:    0.9980
   chunk 38 optimal weight:    5.9990
   chunk 5 optimal weight:    3.9990
   chunk 46 optimal weight:    9.9990
   chunk 67 optimal weight:    4.9990
   chunk 30 optimal weight:    3.9990
   chunk 34 optimal weight:    2.9990
   chunk 65 optimal weight:    4.9990
   chunk 1 optimal weight:    0.5980
   chunk 13 optimal weight:    1.9990
   overall best weight:    2.1186

-------------------------------------------------------------------------------
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 494 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.156853 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.123782 restraints weight = 7157.399|
|-----------------------------------------------------------------------------|
r_work (start): 0.3425 rms_B_bonded: 1.64
r_work: 0.3310 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.3193 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.3193
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8260
moved from start:          0.2001

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.059   6018  Z= 0.183
  Angle     :  0.605   6.942   8200  Z= 0.317
  Chirality :  0.041   0.153    990
  Planarity :  0.005   0.041    990
  Dihedral  :  4.265  16.345    800
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 7.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 19.59 %
    Favored  : 78.68 %
  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:  1.54 (0.31), residues: 746
  helix:  1.52 (0.21), residues: 556
  sheet:  1.77 (0.77), residues: 42
  loop : -1.04 (0.53), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 506 
 HIS   0.002   0.001   HIS B 187 
 PHE   0.012   0.002   PHE A 189 
 TYR   0.007   0.002   TYR A   8 
 ARG   0.002   0.000   ARG A 565 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04801 (  434)
  hydrogen bonds       : angle       5.35591 ( 1302)
  covalent geometry    : bond        0.00452 ( 6018)
  covalent geometry    : angle       0.60455 ( 8200)

*********************** 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
  110 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 99
  time to evaluate  : 0.611 
Fit side-chains
REVERT: B  160 LEU cc_start: 0.7086 (tm) cc_final: 0.5987 (mt)
REVERT: B  176 LYS cc_start: 0.7409 (mmtt) cc_final: 0.6574 (ttpp)
REVERT: B  472 ASN cc_start: 0.5355 (t0) cc_final: 0.4870 (t0)
REVERT: B  473 MET cc_start: 0.5864 (OUTLIER) cc_final: 0.5588 (tpt)
REVERT: B  610 ASN cc_start: 0.8457 (t0) cc_final: 0.8038 (t0)
REVERT: A  472 ASN cc_start: 0.5316 (t0) cc_final: 0.4856 (t0)
REVERT: A  473 MET cc_start: 0.5846 (OUTLIER) cc_final: 0.5588 (tpt)
REVERT: A  610 ASN cc_start: 0.8478 (t0) cc_final: 0.8064 (t0)
  outliers start: 11
  outliers final: 2
  residues processed: 106
  average time/residue: 1.0009
  time to fit residues: 112.0772
Evaluate side-chains
  100 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 96
  time to evaluate  : 0.710 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  473 MET
Chi-restraints excluded: chain B residue  568 THR
Chi-restraints excluded: chain A residue  473 MET
Chi-restraints excluded: chain A 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:    0.8980
   chunk 29 optimal weight:    4.9990
   chunk 62 optimal weight:    4.9990
   chunk 70 optimal weight:    0.6980
   chunk 37 optimal weight:    3.9990
   chunk 46 optimal weight:   10.0000
   chunk 26 optimal weight:    0.7980
   chunk 73 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9990
   chunk 72 optimal weight:    0.9980
   chunk 44 optimal weight:    0.6980
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 = 0.3853 r_free = 0.3853 target = 0.160493 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.127194 restraints weight = 7137.781|
|-----------------------------------------------------------------------------|
r_work (start): 0.3462 rms_B_bonded: 1.70
r_work: 0.3351 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3231 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.3231
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8164
moved from start:          0.1944

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6018  Z= 0.122
  Angle     :  0.554   7.116   8200  Z= 0.287
  Chirality :  0.038   0.126    990
  Planarity :  0.004   0.039    990
  Dihedral  :  4.178  15.668    800
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 6.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.21 %
    Favored  : 98.79 %
  Rotamer:
    Outliers :  0.63 %
    Allowed  : 21.16 %
    Favored  : 78.21 %
  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:  1.78 (0.31), residues: 746
  helix:  1.69 (0.22), residues: 556
  sheet:  1.86 (0.76), residues: 42
  loop : -0.93 (0.54), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 506 
 HIS   0.001   0.000   HIS A   5 
 PHE   0.014   0.001   PHE A 622 
 TYR   0.007   0.001   TYR A 128 
 ARG   0.001   0.000   ARG A 512 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03958 (  434)
  hydrogen bonds       : angle       5.13367 ( 1302)
  covalent geometry    : bond        0.00273 ( 6018)
  covalent geometry    : angle       0.55404 ( 8200)

*********************** 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
  104 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 100
  time to evaluate  : 0.654 
Fit side-chains
REVERT: B  160 LEU cc_start: 0.6987 (tm) cc_final: 0.5893 (mt)
REVERT: B  472 ASN cc_start: 0.5313 (t0) cc_final: 0.4898 (t0)
REVERT: B  473 MET cc_start: 0.5907 (OUTLIER) cc_final: 0.5667 (tpt)
REVERT: B  544 MET cc_start: 0.8574 (ttt) cc_final: 0.8294 (ttp)
REVERT: B  610 ASN cc_start: 0.8452 (t0) cc_final: 0.8026 (t0)
REVERT: A  160 LEU cc_start: 0.6957 (tm) cc_final: 0.5823 (mt)
REVERT: A  472 ASN cc_start: 0.5310 (t0) cc_final: 0.4895 (t0)
REVERT: A  473 MET cc_start: 0.5886 (OUTLIER) cc_final: 0.5664 (tpt)
REVERT: A  544 MET cc_start: 0.8559 (ttt) cc_final: 0.8237 (ttp)
REVERT: A  610 ASN cc_start: 0.8435 (t0) cc_final: 0.8033 (t0)
  outliers start: 4
  outliers final: 0
  residues processed: 102
  average time/residue: 1.0152
  time to fit residues: 109.4993
Evaluate side-chains
  93 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 91
  time to evaluate  : 0.613 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  473 MET
Chi-restraints excluded: chain A residue  473 MET
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:    0.8980
   chunk 34 optimal weight:    4.9990
   chunk 24 optimal weight:    0.8980
   chunk 32 optimal weight:    0.8980
   chunk 65 optimal weight:    0.0870
   chunk 26 optimal weight:    0.9980
   chunk 46 optimal weight:    9.9990
   chunk 51 optimal weight:    0.9980
   chunk 43 optimal weight:    0.6980
   chunk 33 optimal weight:    0.3980
   overall best weight:    0.5958

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.162337 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.129675 restraints weight = 7163.770|
|-----------------------------------------------------------------------------|
r_work (start): 0.3486 rms_B_bonded: 1.63
r_work: 0.3378 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3259 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.3259
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8164
moved from start:          0.1950

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060   6018  Z= 0.118
  Angle     :  0.567   7.788   8200  Z= 0.289
  Chirality :  0.038   0.146    990
  Planarity :  0.004   0.037    990
  Dihedral  :  4.108  15.338    800
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 7.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.07 %
    Favored  : 98.93 %
  Rotamer:
    Outliers :  0.63 %
    Allowed  : 21.47 %
    Favored  : 77.90 %
  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:  1.84 (0.31), residues: 746
  helix:  1.73 (0.22), residues: 560
  sheet:  1.94 (0.75), residues: 42
  loop : -1.01 (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   0.029   0.001   PHE A 622 
 TYR   0.008   0.001   TYR A 128 
 ARG   0.002   0.000   ARG A 565 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03748 (  434)
  hydrogen bonds       : angle       5.02054 ( 1302)
  covalent geometry    : bond        0.00264 ( 6018)
  covalent geometry    : angle       0.56691 ( 8200)

********************** 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
  99 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 95
  time to evaluate  : 0.611 
Fit side-chains
REVERT: B  160 LEU cc_start: 0.7015 (tm) cc_final: 0.5915 (mt)
REVERT: B  472 ASN cc_start: 0.5350 (t0) cc_final: 0.4923 (t0)
REVERT: B  544 MET cc_start: 0.8617 (ttt) cc_final: 0.8360 (ttp)
REVERT: B  610 ASN cc_start: 0.8448 (t0) cc_final: 0.8054 (t0)
REVERT: A  472 ASN cc_start: 0.5335 (t0) cc_final: 0.4915 (t0)
REVERT: A  544 MET cc_start: 0.8575 (ttt) cc_final: 0.8283 (ttp)
REVERT: A  610 ASN cc_start: 0.8412 (t0) cc_final: 0.8006 (t0)
  outliers start: 4
  outliers final: 0
  residues processed: 97
  average time/residue: 0.9207
  time to fit residues: 94.8298
Evaluate side-chains
  91 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 0.663 
-------------------------------------------------------------------------------
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:    6.9990
   chunk 30 optimal weight:    3.9990
   chunk 27 optimal weight:    0.9990
   chunk 26 optimal weight:    0.8980
   chunk 33 optimal weight:    0.0970
   chunk 40 optimal weight:    0.9980
   chunk 46 optimal weight:    9.9990
   chunk 25 optimal weight:    0.9980
   chunk 50 optimal weight:    2.9990
   chunk 63 optimal weight:    0.0970
   chunk 58 optimal weight:    6.9990
   overall best weight:    0.6176

-------------------------------------------------------------------------------
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 = 0.160296 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.127931 restraints weight = 7267.100|
|-----------------------------------------------------------------------------|
r_work (start): 0.3469 rms_B_bonded: 1.69
r_work: 0.3358 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3241 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.3241
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8172
moved from start:          0.2008

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062   6018  Z= 0.123
  Angle     :  0.597   8.139   8200  Z= 0.303
  Chirality :  0.039   0.202    990
  Planarity :  0.004   0.036    990
  Dihedral  :  4.112  15.336    800
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 8.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.21 %
    Favored  : 98.79 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  : 23.20 %
    Favored  : 76.49 %
  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:  1.82 (0.31), residues: 746
  helix:  1.71 (0.22), residues: 558
  sheet:  1.99 (0.75), residues: 42
  loop : -0.94 (0.56), residues: 146

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   0.012   0.001   PHE B 603 
 TYR   0.009   0.001   TYR B 128 
 ARG   0.001   0.000   ARG B 512 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03721 (  434)
  hydrogen bonds       : angle       5.00582 ( 1302)
  covalent geometry    : bond        0.00280 ( 6018)
  covalent geometry    : angle       0.59719 ( 8200)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4947.90 seconds
wall clock time: 88 minutes 19.65 seconds (5299.65 seconds total)