Starting phenix.real_space_refine
on Tue Mar  3 14:03:54 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wks_32568/03_2026/7wks_32568.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wks_32568/03_2026/7wks_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wks_32568/03_2026/7wks_32568.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wks_32568/03_2026/7wks_32568.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wks_32568/03_2026/7wks_32568.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wks_32568/03_2026/7wks_32568.map"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
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-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 1.41, per 1000 atoms: 0.24
  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: 0.35
  Conformation dependent library (CDL) restraints added in 304.4 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: 0.09
  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: 0.75

  Time building geometry restraints manager: 0.48 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'B'
  selection = chain 'A'
}

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:             0.850
  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:          0.100
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.430
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.800
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.77 (0.31), 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
 ARG   0.008   0.000   ARG B 207 
 TYR   0.006   0.001   TYR A 635 
 PHE   0.010   0.001   PHE A 566 
 TRP   0.010   0.001   TRP A 506 
 HIS   0.001   0.000   HIS B 514 

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

*********************** 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  : 0.205 
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: 0.6151 (mt)
REVERT: A  610 ASN cc_start: 0.8314 (t0) cc_final: 0.7889 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 113
  average time/residue: 0.5599
  time to fit residues: 66.0564
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  : 0.133 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 53 optimal weight:    9.9990
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    0.5980
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    0.0050
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    0.7980
   chunk 61 optimal weight:    0.9980
   chunk 45 optimal weight:    5.9990
   chunk 27 optimal weight:    1.9990
   overall best weight:    0.6794

-------------------------------------------------------------------------------
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 = 0.3887 r_free = 0.3887 target = 0.162918 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.128998 restraints weight = 7256.179|
|-----------------------------------------------------------------------------|
r_work (start): 0.3514 rms_B_bonded: 1.66
r_work: 0.3408 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.3291 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.3291
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8143
moved from start:          0.0851

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   6018  Z= 0.117
  Angle     :  0.520   6.336   8200  Z= 0.268
  Chirality :  0.037   0.133    990
  Planarity :  0.004   0.038    990
  Dihedral  :  4.095  15.043    800
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 6.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.54 %
    Favored  : 99.46 %
  Rotamer:
    Outliers :  0.94 %
    Allowed  :  9.72 %
    Favored  : 89.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.08 (0.32), residues: 746
  helix:  1.87 (0.22), residues: 564
  sheet:  1.81 (0.80), residues: 42
  loop : -0.76 (0.58), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 565 
 TYR   0.006   0.001   TYR A 635 
 PHE   0.009   0.001   PHE A  92 
 TRP   0.008   0.001   TRP A 506 
 HIS   0.000   0.000   HIS B 612 

Details of bonding type rmsd
  covalent geometry    : bond        0.00231 ( 6018)
  covalent geometry    : angle       0.52029 ( 8200)
  hydrogen bonds       : bond        0.04045 (  434)
  hydrogen bonds       : angle       4.92689 ( 1302)

*********************** 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
  113 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 107
  time to evaluate  : 0.208 
Fit side-chains
REVERT: B  160 LEU cc_start: 0.6965 (tm) cc_final: 0.5909 (mt)
REVERT: B  176 LYS cc_start: 0.7135 (mmtt) cc_final: 0.6229 (ttpp)
REVERT: B  610 ASN cc_start: 0.8522 (t0) cc_final: 0.8129 (t0)
REVERT: A  176 LYS cc_start: 0.7244 (mmtt) cc_final: 0.6351 (ttpp)
REVERT: A  610 ASN cc_start: 0.8506 (t0) cc_final: 0.8122 (t0)
  outliers start: 6
  outliers final: 2
  residues processed: 109
  average time/residue: 0.4959
  time to fit residues: 56.7996
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  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  159 MET
Chi-restraints excluded: chain A residue  159 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 14 optimal weight:    0.9980
   chunk 40 optimal weight:    6.9990
   chunk 71 optimal weight:    0.0970
   chunk 12 optimal weight:    5.9990
   chunk 21 optimal weight:    0.0670
   chunk 45 optimal weight:    0.9990
   chunk 32 optimal weight:    0.9980
   chunk 59 optimal weight:    0.9980
   chunk 33 optimal weight:    0.3980
   chunk 57 optimal weight:    9.9990
   chunk 23 optimal weight:    3.9990
   overall best weight:    0.5116

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.165150 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.132181 restraints weight = 7092.090|
|-----------------------------------------------------------------------------|
r_work (start): 0.3525 rms_B_bonded: 1.62
r_work: 0.3418 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.3303 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.3303
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8117
moved from start:          0.1175

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   6018  Z= 0.102
  Angle     :  0.489   7.011   8200  Z= 0.248
  Chirality :  0.036   0.123    990
  Planarity :  0.004   0.037    990
  Dihedral  :  3.988  14.946    800
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 5.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.07 %
    Favored  : 98.93 %
  Rotamer:
    Outliers :  0.78 %
    Allowed  : 12.54 %
    Favored  : 86.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.27 (0.32), residues: 746
  helix:  2.00 (0.22), residues: 564
  sheet:  1.93 (0.77), residues: 42
  loop : -0.71 (0.58), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 493 
 TYR   0.004   0.001   TYR A   8 
 PHE   0.009   0.001   PHE A  92 
 TRP   0.007   0.001   TRP A 506 
 HIS   0.000   0.000   HIS A   5 

Details of bonding type rmsd
  covalent geometry    : bond        0.00204 ( 6018)
  covalent geometry    : angle       0.48933 ( 8200)
  hydrogen bonds       : bond        0.03686 (  434)
  hydrogen bonds       : angle       4.76186 ( 1302)

*********************** 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
  105 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 100
  time to evaluate  : 0.164 
Fit side-chains
REVERT: B  160 LEU cc_start: 0.6994 (tm) cc_final: 0.5847 (mt)
REVERT: B  176 LYS cc_start: 0.7225 (mmtt) cc_final: 0.6379 (ttpp)
REVERT: B  610 ASN cc_start: 0.8452 (t0) cc_final: 0.8025 (t0)
REVERT: A  160 LEU cc_start: 0.6889 (tm) cc_final: 0.5771 (mt)
REVERT: A  176 LYS cc_start: 0.7232 (mmtt) cc_final: 0.6384 (ttpp)
REVERT: A  544 MET cc_start: 0.8579 (ttt) cc_final: 0.8308 (ttp)
REVERT: A  610 ASN cc_start: 0.8457 (t0) cc_final: 0.8039 (t0)
  outliers start: 5
  outliers final: 1
  residues processed: 103
  average time/residue: 0.4806
  time to fit residues: 51.9435
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  : 0.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  201 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 18 optimal weight:    7.9990
   chunk 48 optimal weight:    4.9990
   chunk 73 optimal weight:    0.8980
   chunk 22 optimal weight:    3.9990
   chunk 41 optimal weight:    3.9990
   chunk 28 optimal weight:    3.9990
   chunk 65 optimal weight:    2.9990
   chunk 7 optimal weight:    4.9990
   chunk 46 optimal weight:    9.9990
   chunk 51 optimal weight:    0.4980
   chunk 52 optimal weight:    2.9990
   overall best weight:    2.2786

-------------------------------------------------------------------------------
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
A  68 ASN
A 112 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.155290 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.121846 restraints weight = 7263.852|
|-----------------------------------------------------------------------------|
r_work (start): 0.3430 rms_B_bonded: 1.62
r_work: 0.3317 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.3201 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.3201
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8245
moved from start:          0.1536

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   6018  Z= 0.190
  Angle     :  0.588   5.892   8200  Z= 0.305
  Chirality :  0.041   0.165    990
  Planarity :  0.005   0.043    990
  Dihedral  :  4.225  16.389    800
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 5.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.80 %
    Favored  : 99.20 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 14.42 %
    Favored  : 83.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.67 (0.31), residues: 746
  helix:  1.57 (0.21), residues: 564
  sheet:  1.84 (0.78), residues: 42
  loop : -0.92 (0.55), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 489 
 TYR   0.008   0.001   TYR B 635 
 PHE   0.014   0.002   PHE B 603 
 TRP   0.011   0.002   TRP B 506 
 HIS   0.002   0.001   HIS B 187 

Details of bonding type rmsd
  covalent geometry    : bond        0.00464 ( 6018)
  covalent geometry    : angle       0.58799 ( 8200)
  hydrogen bonds       : bond        0.05031 (  434)
  hydrogen bonds       : angle       5.23665 ( 1302)

*********************** 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
  119 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 104
  time to evaluate  : 0.137 
Fit side-chains
REVERT: B  160 LEU cc_start: 0.7055 (tm) cc_final: 0.5928 (mt)
REVERT: B  176 LYS cc_start: 0.7221 (mmtt) cc_final: 0.6311 (ttpp)
REVERT: B  472 ASN cc_start: 0.5073 (t0) cc_final: 0.4545 (t0)
REVERT: B  610 ASN cc_start: 0.8446 (t0) cc_final: 0.8040 (t0)
REVERT: A  160 LEU cc_start: 0.7037 (tm) cc_final: 0.5870 (mt)
REVERT: A  176 LYS cc_start: 0.7344 (mmtt) cc_final: 0.6494 (ttpp)
REVERT: A  472 ASN cc_start: 0.5066 (t0) cc_final: 0.4541 (t0)
REVERT: A  610 ASN cc_start: 0.8451 (t0) cc_final: 0.8065 (t0)
  outliers start: 15
  outliers final: 4
  residues processed: 117
  average time/residue: 0.4499
  time to fit residues: 55.3107
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  : 0.165 
-------------------------------------------------------------------------------
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 13 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9990
   chunk 12 optimal weight:    1.9990
   chunk 45 optimal weight:    5.9990
   chunk 71 optimal weight:    0.5980
   chunk 66 optimal weight:    5.9990
   chunk 36 optimal weight:    0.8980
   chunk 53 optimal weight:    0.3980
   chunk 38 optimal weight:    0.9990
   chunk 33 optimal weight:    0.7980
   chunk 16 optimal weight:    8.9990
   overall best weight:    0.7382

-------------------------------------------------------------------------------
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 = 0.3847 r_free = 0.3847 target = 0.159723 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.126367 restraints weight = 7309.002|
|-----------------------------------------------------------------------------|
r_work (start): 0.3470 rms_B_bonded: 1.65
r_work: 0.3359 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.3240 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.3240
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8178
moved from start:          0.1557

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   6018  Z= 0.116
  Angle     :  0.524   5.892   8200  Z= 0.271
  Chirality :  0.037   0.132    990
  Planarity :  0.004   0.039    990
  Dihedral  :  4.136  15.612    800
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 6.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.34 %
    Favored  : 98.66 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  : 16.30 %
    Favored  : 82.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.91 (0.31), residues: 746
  helix:  1.80 (0.22), residues: 556
  sheet:  1.64 (0.77), residues: 42
  loop : -0.85 (0.55), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 512 
 TYR   0.006   0.001   TYR B 635 
 PHE   0.014   0.001   PHE B 603 
 TRP   0.009   0.001   TRP B 506 
 HIS   0.001   0.000   HIS A 203 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 6018)
  covalent geometry    : angle       0.52425 ( 8200)
  hydrogen bonds       : bond        0.04004 (  434)
  hydrogen bonds       : angle       5.02304 ( 1302)

*********************** 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
  107 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 100
  time to evaluate  : 0.208 
Fit side-chains
REVERT: B  160 LEU cc_start: 0.7038 (tm) cc_final: 0.5897 (mt)
REVERT: B  176 LYS cc_start: 0.7279 (mmtt) cc_final: 0.6433 (ttpp)
REVERT: B  472 ASN cc_start: 0.5130 (t0) cc_final: 0.4559 (t0)
REVERT: B  610 ASN cc_start: 0.8439 (t0) cc_final: 0.8027 (t0)
REVERT: A  160 LEU cc_start: 0.6977 (tm) cc_final: 0.5803 (mt)
REVERT: A  176 LYS cc_start: 0.7273 (mmtt) cc_final: 0.6425 (ttpp)
REVERT: A  472 ASN cc_start: 0.5123 (t0) cc_final: 0.4554 (t0)
REVERT: A  610 ASN cc_start: 0.8458 (t0) cc_final: 0.8061 (t0)
  outliers start: 7
  outliers final: 1
  residues processed: 106
  average time/residue: 0.4155
  time to fit residues: 46.5881
Evaluate side-chains
  95 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 94
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  159 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 48 optimal weight:    0.0870
   chunk 29 optimal weight:    0.0010
   chunk 6 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9990
   chunk 35 optimal weight:    0.5980
   chunk 54 optimal weight:    9.9990
   chunk 18 optimal weight:    7.9990
   chunk 4 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9980
   chunk 53 optimal weight:    1.9990
   overall best weight:    0.5366

-------------------------------------------------------------------------------
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 = 0.3892 r_free = 0.3892 target = 0.163650 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.130668 restraints weight = 7198.296|
|-----------------------------------------------------------------------------|
r_work (start): 0.3497 rms_B_bonded: 1.64
r_work: 0.3388 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3269 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.3269
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8167
moved from start:          0.1641

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.048   6018  Z= 0.109
  Angle     :  0.510   5.801   8200  Z= 0.265
  Chirality :  0.037   0.122    990
  Planarity :  0.004   0.037    990
  Dihedral  :  4.050  15.377    800
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.07 %
    Favored  : 98.93 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 16.93 %
    Favored  : 81.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.07 (0.31), residues: 746
  helix:  1.88 (0.22), residues: 558
  sheet:  1.61 (0.73), residues: 42
  loop : -0.67 (0.57), residues: 146

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 512 
 TYR   0.005   0.001   TYR B 635 
 PHE   0.013   0.001   PHE B 603 
 TRP   0.008   0.001   TRP A 506 
 HIS   0.001   0.000   HIS A   5 

Details of bonding type rmsd
  covalent geometry    : bond        0.00234 ( 6018)
  covalent geometry    : angle       0.50967 ( 8200)
  hydrogen bonds       : bond        0.03686 (  434)
  hydrogen bonds       : angle       4.93917 ( 1302)

*********************** 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
  106 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 98
  time to evaluate  : 0.216 
Fit side-chains
REVERT: B  160 LEU cc_start: 0.7065 (tm) cc_final: 0.5908 (mt)
REVERT: B  176 LYS cc_start: 0.7264 (mmtt) cc_final: 0.6442 (ttpp)
REVERT: B  472 ASN cc_start: 0.5240 (t0) cc_final: 0.4669 (t0)
REVERT: B  610 ASN cc_start: 0.8430 (t0) cc_final: 0.8023 (t0)
REVERT: A  160 LEU cc_start: 0.7037 (tm) cc_final: 0.5869 (mt)
REVERT: A  176 LYS cc_start: 0.7224 (mmtt) cc_final: 0.6417 (ttpp)
REVERT: A  472 ASN cc_start: 0.5227 (t0) cc_final: 0.4660 (t0)
REVERT: A  544 MET cc_start: 0.8582 (ttt) cc_final: 0.8265 (ttp)
REVERT: A  610 ASN cc_start: 0.8429 (t0) cc_final: 0.8031 (t0)
  outliers start: 8
  outliers final: 0
  residues processed: 104
  average time/residue: 0.3957
  time to fit residues: 43.6077
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  : 0.198 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 38 optimal weight:    5.9990
   chunk 40 optimal weight:    0.4980
   chunk 65 optimal weight:    0.2980
   chunk 50 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9980
   chunk 42 optimal weight:    2.9990
   chunk 49 optimal weight:    1.9990
   chunk 29 optimal weight:   10.0000
   chunk 19 optimal weight:    1.9990
   chunk 15 optimal weight:    8.9990
   chunk 70 optimal weight:    0.0770
   overall best weight:    0.7740

-------------------------------------------------------------------------------
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 = 0.3855 r_free = 0.3855 target = 0.160595 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.127315 restraints weight = 7230.101|
|-----------------------------------------------------------------------------|
r_work (start): 0.3490 rms_B_bonded: 1.64
r_work: 0.3381 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3261 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.3261
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8156
moved from start:          0.1631

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   6018  Z= 0.112
  Angle     :  0.512   6.227   8200  Z= 0.264
  Chirality :  0.037   0.125    990
  Planarity :  0.004   0.037    990
  Dihedral  :  4.019  15.205    800
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 6.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.07 %
    Favored  : 98.93 %
  Rotamer:
    Outliers :  0.94 %
    Allowed  : 17.08 %
    Favored  : 81.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.07 (0.31), residues: 746
  helix:  1.88 (0.22), residues: 558
  sheet:  1.77 (0.72), residues: 42
  loop : -0.72 (0.56), residues: 146

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 512 
 TYR   0.005   0.001   TYR A   8 
 PHE   0.015   0.001   PHE B 603 
 TRP   0.008   0.001   TRP B 506 
 HIS   0.001   0.000   HIS A 612 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 ( 6018)
  covalent geometry    : angle       0.51200 ( 8200)
  hydrogen bonds       : bond        0.03732 (  434)
  hydrogen bonds       : angle       4.90564 ( 1302)

*********************** 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
  104 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 98
  time to evaluate  : 0.219 
Fit side-chains
REVERT: B  160 LEU cc_start: 0.7023 (tm) cc_final: 0.5864 (mt)
REVERT: B  176 LYS cc_start: 0.7229 (mmtt) cc_final: 0.6404 (ttpp)
REVERT: B  472 ASN cc_start: 0.5239 (t0) cc_final: 0.4667 (t0)
REVERT: B  610 ASN cc_start: 0.8443 (t0) cc_final: 0.8048 (t0)
REVERT: A  160 LEU cc_start: 0.6995 (tm) cc_final: 0.5822 (mt)
REVERT: A  472 ASN cc_start: 0.5223 (t0) cc_final: 0.4655 (t0)
REVERT: A  544 MET cc_start: 0.8604 (ttt) cc_final: 0.8321 (ttp)
REVERT: A  610 ASN cc_start: 0.8434 (t0) cc_final: 0.8031 (t0)
  outliers start: 6
  outliers final: 0
  residues processed: 104
  average time/residue: 0.4054
  time to fit residues: 44.6404
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  : 0.164 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 18 optimal weight:   10.0000
   chunk 53 optimal weight:    0.7980
   chunk 14 optimal weight:    3.9990
   chunk 23 optimal weight:    3.9990
   chunk 58 optimal weight:    1.9990
   chunk 45 optimal weight:    9.9990
   chunk 32 optimal weight:    0.7980
   chunk 48 optimal weight:    1.9990
   chunk 43 optimal weight:    3.9990
   chunk 39 optimal weight:    0.6980
   chunk 67 optimal weight:    1.9990
   overall best weight:    1.2584

-------------------------------------------------------------------------------
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 = 0.3862 r_free = 0.3862 target = 0.160992 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.128098 restraints weight = 7148.862|
|-----------------------------------------------------------------------------|
r_work (start): 0.3471 rms_B_bonded: 1.64
r_work: 0.3361 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.3243 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.3243
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8199
moved from start:          0.1784

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   6018  Z= 0.136
  Angle     :  0.555   6.863   8200  Z= 0.289
  Chirality :  0.039   0.143    990
  Planarity :  0.004   0.039    990
  Dihedral  :  4.105  15.589    800
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 6.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.94 %
    Favored  : 99.06 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  : 18.65 %
    Favored  : 80.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.89 (0.31), residues: 746
  helix:  1.75 (0.22), residues: 556
  sheet:  1.85 (0.71), residues: 42
  loop : -0.79 (0.56), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 565 
 TYR   0.007   0.001   TYR B 635 
 PHE   0.018   0.001   PHE B 603 
 TRP   0.009   0.001   TRP B 506 
 HIS   0.001   0.000   HIS B 187 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 6018)
  covalent geometry    : angle       0.55547 ( 8200)
  hydrogen bonds       : bond        0.04166 (  434)
  hydrogen bonds       : angle       5.06662 ( 1302)

*********************** 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
  104 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 97
  time to evaluate  : 0.210 
Fit side-chains
REVERT: B  176 LYS cc_start: 0.7268 (mmtt) cc_final: 0.6472 (ttpp)
REVERT: B  472 ASN cc_start: 0.5255 (t0) cc_final: 0.4797 (t0)
REVERT: B  610 ASN cc_start: 0.8460 (t0) cc_final: 0.8047 (t0)
REVERT: A  472 ASN cc_start: 0.5245 (t0) cc_final: 0.4765 (t0)
REVERT: A  610 ASN cc_start: 0.8455 (t0) cc_final: 0.8053 (t0)
  outliers start: 7
  outliers final: 1
  residues processed: 103
  average time/residue: 0.4167
  time to fit residues: 45.3851
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  : 0.232 
-------------------------------------------------------------------------------
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 25 optimal weight:    1.9990
   chunk 40 optimal weight:    0.8980
   chunk 48 optimal weight:    1.9990
   chunk 59 optimal weight:    0.8980
   chunk 18 optimal weight:    8.9990
   chunk 66 optimal weight:    0.9990
   chunk 4 optimal weight:    2.9990
   chunk 67 optimal weight:    0.9990
   chunk 69 optimal weight:    0.8980
   chunk 41 optimal weight:    0.8980
   chunk 31 optimal weight:    3.9990
   overall best weight:    0.9182

-------------------------------------------------------------------------------
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 = 0.3879 r_free = 0.3879 target = 0.162596 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.129685 restraints weight = 7166.060|
|-----------------------------------------------------------------------------|
r_work (start): 0.3467 rms_B_bonded: 1.63
r_work: 0.3358 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.3240 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.3240
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8172
moved from start:          0.1763

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   6018  Z= 0.126
  Angle     :  0.578   7.794   8200  Z= 0.294
  Chirality :  0.038   0.135    990
  Planarity :  0.004   0.039    990
  Dihedral  :  4.104  15.306    800
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 6.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.07 %
    Favored  : 98.93 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  : 19.44 %
    Favored  : 80.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.88 (0.31), residues: 746
  helix:  1.74 (0.22), residues: 556
  sheet:  1.88 (0.71), residues: 42
  loop : -0.81 (0.55), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 512 
 TYR   0.008   0.001   TYR B 128 
 PHE   0.021   0.001   PHE A 622 
 TRP   0.009   0.001   TRP B 506 
 HIS   0.001   0.000   HIS A   5 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 6018)
  covalent geometry    : angle       0.57760 ( 8200)
  hydrogen bonds       : bond        0.03941 (  434)
  hydrogen bonds       : angle       5.01738 ( 1302)

*********************** 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
  93 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 91
  time to evaluate  : 0.226 
Fit side-chains
REVERT: B  160 LEU cc_start: 0.6910 (tm) cc_final: 0.5813 (mt)
REVERT: B  176 LYS cc_start: 0.7369 (mmtt) cc_final: 0.6527 (ttpp)
REVERT: B  472 ASN cc_start: 0.5206 (t0) cc_final: 0.4705 (t0)
REVERT: B  610 ASN cc_start: 0.8461 (t0) cc_final: 0.8065 (t0)
REVERT: A  160 LEU cc_start: 0.6907 (tm) cc_final: 0.5800 (mt)
REVERT: A  472 ASN cc_start: 0.5192 (t0) cc_final: 0.4696 (t0)
REVERT: A  544 MET cc_start: 0.8586 (ttt) cc_final: 0.8284 (ttp)
REVERT: A  610 ASN cc_start: 0.8463 (t0) cc_final: 0.8057 (t0)
  outliers start: 2
  outliers final: 0
  residues processed: 93
  average time/residue: 0.4223
  time to fit residues: 41.4868
Evaluate side-chains
  89 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 0.156 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 8 optimal weight:    8.9990
   chunk 44 optimal weight:    2.9990
   chunk 10 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9980
   chunk 25 optimal weight:    4.9990
   chunk 63 optimal weight:    4.9990
   chunk 38 optimal weight:    0.9980
   chunk 7 optimal weight:    2.9990
   chunk 32 optimal weight:    0.7980
   chunk 50 optimal weight:    1.9990
   chunk 59 optimal weight:    0.7980
   overall best weight:    1.1182

-------------------------------------------------------------------------------
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 = 0.3867 r_free = 0.3867 target = 0.161411 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.128650 restraints weight = 7202.699|
|-----------------------------------------------------------------------------|
r_work (start): 0.3476 rms_B_bonded: 1.64
r_work: 0.3366 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.3249 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.3249
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8181
moved from start:          0.1875

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= 0.134
  Angle     :  0.591   8.036   8200  Z= 0.303
  Chirality :  0.039   0.159    990
  Planarity :  0.004   0.040    990
  Dihedral  :  4.125  15.513    800
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 6.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.21 %
    Favored  : 98.79 %
  Rotamer:
    Outliers :  0.78 %
    Allowed  : 19.28 %
    Favored  : 79.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.79 (0.31), residues: 746
  helix:  1.68 (0.22), residues: 556
  sheet:  1.81 (0.71), residues: 42
  loop : -0.82 (0.55), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 565 
 TYR   0.008   0.001   TYR B 128 
 PHE   0.021   0.001   PHE B 603 
 TRP   0.009   0.001   TRP A 506 
 HIS   0.001   0.000   HIS A 187 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 6018)
  covalent geometry    : angle       0.59123 ( 8200)
  hydrogen bonds       : bond        0.04071 (  434)
  hydrogen bonds       : angle       5.08408 ( 1302)

********************** 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: 5
    poor density    : 98
  time to evaluate  : 0.225 
Fit side-chains
REVERT: B  160 LEU cc_start: 0.6937 (tm) cc_final: 0.5818 (mt)
REVERT: B  472 ASN cc_start: 0.5210 (t0) cc_final: 0.4732 (t0)
REVERT: B  610 ASN cc_start: 0.8477 (t0) cc_final: 0.8068 (t0)
REVERT: A  160 LEU cc_start: 0.6924 (tm) cc_final: 0.5789 (mt)
REVERT: A  472 ASN cc_start: 0.5172 (t0) cc_final: 0.4711 (t0)
REVERT: A  610 ASN cc_start: 0.8470 (t0) cc_final: 0.8077 (t0)
  outliers start: 5
  outliers final: 1
  residues processed: 102
  average time/residue: 0.4827
  time to fit residues: 51.8621
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  : 0.145 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  568 THR
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 3 optimal weight:    0.7980
   chunk 4 optimal weight:    1.9990
   chunk 28 optimal weight:    0.6980
   chunk 17 optimal weight:    3.9990
   chunk 15 optimal weight:    4.9990
   chunk 2 optimal weight:    3.9990
   chunk 61 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 63 optimal weight:    0.7980
   chunk 16 optimal weight:    8.9990
   overall best weight:    1.2584

-------------------------------------------------------------------------------
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 = 0.3852 r_free = 0.3852 target = 0.160185 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.127314 restraints weight = 7135.928|
|-----------------------------------------------------------------------------|
r_work (start): 0.3469 rms_B_bonded: 1.63
r_work: 0.3360 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.3240 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.3240
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8202
moved from start:          0.1875

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059   6018  Z= 0.140
  Angle     :  0.596   7.672   8200  Z= 0.305
  Chirality :  0.039   0.156    990
  Planarity :  0.004   0.040    990
  Dihedral  :  4.166  15.485    800
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 6.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.47 %
    Favored  : 98.53 %
  Rotamer:
    Outliers :  0.78 %
    Allowed  : 19.44 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.72 (0.31), residues: 746
  helix:  1.63 (0.22), residues: 556
  sheet:  1.82 (0.72), residues: 42
  loop : -0.85 (0.55), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 512 
 TYR   0.011   0.001   TYR A 128 
 PHE   0.022   0.001   PHE B 603 
 TRP   0.009   0.001   TRP A 506 
 HIS   0.001   0.000   HIS B 187 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 6018)
  covalent geometry    : angle       0.59584 ( 8200)
  hydrogen bonds       : bond        0.04147 (  434)
  hydrogen bonds       : angle       5.12495 ( 1302)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1943.48 seconds
wall clock time: 33 minutes 44.50 seconds (2024.50 seconds total)