Starting phenix.real_space_refine
on Thu Jun  5 09:39:00 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9epo_19881/06_2025/9epo_19881.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9epo_19881/06_2025/9epo_19881.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=1.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9epo_19881/06_2025/9epo_19881.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9epo_19881/06_2025/9epo_19881.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9epo_19881/06_2025/9epo_19881.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9epo_19881/06_2025/9epo_19881.cif"
  }
  resolution = 1.9
  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=   0.010
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      48      5.16       5
     C    3870      2.51       5
     N     910      2.21       5
     O    1032      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-5710/modules/chem_data/mon_lib"
  Total number of atoms: 5860
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 2795
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 346, 2795
          Classifications: {'peptide': 346}
          Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 328}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 2795
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 346, 2795
          Classifications: {'peptide': 346}
          Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 328}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 88
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 88
          Unusual residues: {'PLM': 1, 'Y01': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "D"
      Number of atoms: 88
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 88
          Unusual residues: {'PLM': 1, 'Y01': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "A"
      Number of atoms: 47
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 47, 47
          Classifications: {'water': 47}
          Link IDs: {None: 46}
    Chain: "D"
      Number of atoms: 47
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 47, 47
          Classifications: {'water': 47}
          Link IDs: {None: 46}
  Time building chain proxies: 5.35, per 1000 atoms: 0.91
  Number of scatterers: 5860
  At special positions: 0
  Unit cell: (91.368, 98.136, 59.5584, 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      48     16.00
     O    1032      8.00
     N     910      7.00
     C    3870      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=8, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 210 " - pdb=" SG  CYS A 230 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 234 " - pdb=" SG  CYS A 315 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 336 " - pdb=" SG  CYS A 411 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 508 " - pdb=" SG  CYS A 515 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 210 " - pdb=" SG  CYS D 230 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 234 " - pdb=" SG  CYS D 315 " distance=2.02
    Simple disulfide: pdb=" SG  CYS D 336 " - pdb=" SG  CYS D 411 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 508 " - pdb=" SG  CYS D 515 " distance=2.03

  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: 1.77
  Conformation dependent library (CDL) restraints added in 888.1 milliseconds
  

  1368 Ramachandran restraints generated.
    684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1280

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 6 sheets defined
      72.3% alpha, 2.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.60
  Creating SS restraints...
    Processing helix  chain 'A' and resid 211 through 215
    Processing helix  chain 'A' and resid 217 through 221
    Processing helix  chain 'A' and resid 246 through 277
    Processing helix  chain 'A' and resid 286 through 310
      removed outlier: 3.828A  pdb=" N   ILE A 290 " --> pdb=" O   GLU A 286 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 333 through 366
    Processing helix  chain 'A' and resid 370 through 376
    Processing helix  chain 'A' and resid 377 through 399
      Proline residue:  A 389  - end of helix
    Processing helix  chain 'A' and resid 417 through 425
    Processing helix  chain 'A' and resid 425 through 451
    Processing helix  chain 'A' and resid 465 through 508
      removed outlier: 3.781A  pdb=" N   THR A 479 " --> pdb=" O   SER A 475 " (cutoff:3.500A)
      removed outlier: 4.080A  pdb=" N   VAL A 480 " --> pdb=" O   VAL A 476 " (cutoff:3.500A)
      Proline residue:  A 481  - end of helix
      removed outlier: 5.340A  pdb=" N   GLU A 497 " --> pdb=" O   GLN A 493 " (cutoff:3.500A)
      removed outlier: 5.527A  pdb=" N   HIS A 498 " --> pdb=" O   ALA A 494 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 526 through 543
      removed outlier: 4.653A  pdb=" N   VAL A 540 " --> pdb=" O   MET A 536 " (cutoff:3.500A)
      removed outlier: 5.494A  pdb=" N   GLY A 541 " --> pdb=" O   THR A 537 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 543 through 549
    Processing helix  chain 'A' and resid 550 through 563
    Processing helix  chain 'D' and resid 211 through 215
    Processing helix  chain 'D' and resid 217 through 221
    Processing helix  chain 'D' and resid 246 through 277
    Processing helix  chain 'D' and resid 286 through 310
      removed outlier: 3.828A  pdb=" N   ILE D 290 " --> pdb=" O   GLU D 286 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 333 through 366
    Processing helix  chain 'D' and resid 370 through 376
    Processing helix  chain 'D' and resid 377 through 399
      Proline residue:  D 389  - end of helix
    Processing helix  chain 'D' and resid 417 through 425
    Processing helix  chain 'D' and resid 425 through 451
    Processing helix  chain 'D' and resid 465 through 508
      removed outlier: 3.782A  pdb=" N   THR D 479 " --> pdb=" O   SER D 475 " (cutoff:3.500A)
      removed outlier: 4.080A  pdb=" N   VAL D 480 " --> pdb=" O   VAL D 476 " (cutoff:3.500A)
      Proline residue:  D 481  - end of helix
      removed outlier: 5.341A  pdb=" N   GLU D 497 " --> pdb=" O   GLN D 493 " (cutoff:3.500A)
      removed outlier: 5.528A  pdb=" N   HIS D 498 " --> pdb=" O   ALA D 494 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 526 through 543
      removed outlier: 4.653A  pdb=" N   VAL D 540 " --> pdb=" O   MET D 536 " (cutoff:3.500A)
      removed outlier: 5.494A  pdb=" N   GLY D 541 " --> pdb=" O   THR D 537 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 543 through 549
    Processing helix  chain 'D' and resid 550 through 563
    Processing sheet with id=AA1, first strand: chain 'A' and resid 223 through 224
    Processing sheet with id=AA2, first strand: chain 'A' and resid 315 through 316
      removed outlier: 3.631A  pdb=" N   THR A 326 " --> pdb=" O   VAL A 316 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 402 through 404
    Processing sheet with id=AA4, first strand: chain 'D' and resid 223 through 224
    Processing sheet with id=AA5, first strand: chain 'D' and resid 315 through 316
      removed outlier: 3.631A  pdb=" N   THR D 326 " --> pdb=" O   VAL D 316 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 402 through 404

    384 hydrogen bonds defined for protein.
    1122 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: 1.91

  Time building geometry restraints manager: 2.07 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 907
        1.32 -     1.45: 1766
        1.45 -     1.58: 3215
        1.58 -     1.70: 0
        1.70 -     1.83: 72
  Bond restraints: 5960
  Sorted by residual:
  bond pdb=" CA  VAL A 388 "
       pdb=" C   VAL A 388 "
    ideal  model  delta    sigma   weight residual
    1.523  1.543 -0.020 9.20e-03 1.18e+04 4.81e+00
  bond pdb=" CA  VAL D 388 "
       pdb=" C   VAL D 388 "
    ideal  model  delta    sigma   weight residual
    1.523  1.542 -0.019 9.20e-03 1.18e+04 4.12e+00
  bond pdb=" C   VAL A 388 "
       pdb=" O   VAL A 388 "
    ideal  model  delta    sigma   weight residual
    1.242  1.226  0.016 8.60e-03 1.35e+04 3.62e+00
  bond pdb=" C   VAL D 388 "
       pdb=" O   VAL D 388 "
    ideal  model  delta    sigma   weight residual
    1.242  1.226  0.016 8.60e-03 1.35e+04 3.46e+00
  bond pdb=" CA  VAL D 388 "
       pdb=" CB  VAL D 388 "
    ideal  model  delta    sigma   weight residual
    1.539  1.530  0.009 5.40e-03 3.43e+04 2.88e+00
  ... (remaining 5955 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.79: 7726
        1.79 -     3.58: 303
        3.58 -     5.37: 61
        5.37 -     7.16: 18
        7.16 -     8.95: 2
  Bond angle restraints: 8110
  Sorted by residual:
  angle pdb=" C   GLU D 248 "
        pdb=" N   GLU D 249 "
        pdb=" CA  GLU D 249 "
      ideal   model   delta    sigma   weight residual
     120.31  114.65    5.66 1.52e+00 4.33e-01 1.39e+01
  angle pdb=" C   GLU A 248 "
        pdb=" N   GLU A 249 "
        pdb=" CA  GLU A 249 "
      ideal   model   delta    sigma   weight residual
     120.31  114.67    5.64 1.52e+00 4.33e-01 1.38e+01
  angle pdb=" C   ILE D 290 "
        pdb=" N   PHE D 291 "
        pdb=" CA  PHE D 291 "
      ideal   model   delta    sigma   weight residual
     120.31  114.80    5.51 1.52e+00 4.33e-01 1.31e+01
  angle pdb=" C   ILE A 290 "
        pdb=" N   PHE A 291 "
        pdb=" CA  PHE A 291 "
      ideal   model   delta    sigma   weight residual
     120.31  114.84    5.47 1.52e+00 4.33e-01 1.29e+01
  angle pdb=" C   TYR A 489 "
        pdb=" N   PHE A 490 "
        pdb=" CA  PHE A 490 "
      ideal   model   delta    sigma   weight residual
     120.28  125.05   -4.77 1.34e+00 5.57e-01 1.27e+01
  ... (remaining 8105 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.91: 3463
       17.91 -    35.83: 127
       35.83 -    53.74: 27
       53.74 -    71.66: 5
       71.66 -    89.57: 2
  Dihedral angle restraints: 3624
    sinusoidal: 1622
      harmonic: 2002
  Sorted by residual:
  dihedral pdb=" CA  TYR A 324 "
           pdb=" C   TYR A 324 "
           pdb=" N   ARG A 325 "
           pdb=" CA  ARG A 325 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.47   22.53     0      5.00e+00 4.00e-02 2.03e+01
  dihedral pdb=" CA  TYR D 324 "
           pdb=" C   TYR D 324 "
           pdb=" N   ARG D 325 "
           pdb=" CA  ARG D 325 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.52   22.48     0      5.00e+00 4.00e-02 2.02e+01
  dihedral pdb=" CA  TYR D 244 "
           pdb=" C   TYR D 244 "
           pdb=" N   PHE D 245 "
           pdb=" CA  PHE D 245 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -165.13  -14.87     0      5.00e+00 4.00e-02 8.84e+00
  ... (remaining 3621 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.087: 800
       0.087 -    0.173: 56
       0.173 -    0.260: 14
       0.260 -    0.346: 4
       0.346 -    0.433: 4
  Chirality restraints: 878
  Sorted by residual:
  chirality pdb=" CB  VAL A 473 "
            pdb=" CA  VAL A 473 "
            pdb=" CG1 VAL A 473 "
            pdb=" CG2 VAL A 473 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.20   -0.43 2.00e-01 2.50e+01 4.68e+00
  chirality pdb=" CB  VAL D 473 "
            pdb=" CA  VAL D 473 "
            pdb=" CG1 VAL D 473 "
            pdb=" CG2 VAL D 473 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.20   -0.43 2.00e-01 2.50e+01 4.68e+00
  chirality pdb=" CG  LEU A 383 "
            pdb=" CB  LEU A 383 "
            pdb=" CD1 LEU A 383 "
            pdb=" CD2 LEU A 383 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.19   -0.40 2.00e-01 2.50e+01 3.92e+00
  ... (remaining 875 not shown)

  Planarity restraints: 972
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 491 "   -0.024 2.00e-02 2.50e+03   4.47e-02 4.00e+01
        pdb=" CG  TYR A 491 "    0.004 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 491 "    0.003 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 491 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 491 "   -0.011 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 491 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 491 "    0.101 2.00e-02 2.50e+03
        pdb=" OH  TYR A 491 "   -0.071 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR D 491 "   -0.024 2.00e-02 2.50e+03   4.47e-02 3.99e+01
        pdb=" CG  TYR D 491 "    0.004 2.00e-02 2.50e+03
        pdb=" CD1 TYR D 491 "    0.003 2.00e-02 2.50e+03
        pdb=" CD2 TYR D 491 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE1 TYR D 491 "   -0.011 2.00e-02 2.50e+03
        pdb=" CE2 TYR D 491 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ  TYR D 491 "    0.101 2.00e-02 2.50e+03
        pdb=" OH  TYR D 491 "   -0.071 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP D 354 "   -0.005 2.00e-02 2.50e+03   3.92e-02 3.83e+01
        pdb=" CG  TRP D 354 "    0.011 2.00e-02 2.50e+03
        pdb=" CD1 TRP D 354 "    0.015 2.00e-02 2.50e+03
        pdb=" CD2 TRP D 354 "    0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP D 354 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP D 354 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE3 TRP D 354 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP D 354 "   -0.067 2.00e-02 2.50e+03
        pdb=" CZ3 TRP D 354 "   -0.042 2.00e-02 2.50e+03
        pdb=" CH2 TRP D 354 "    0.093 2.00e-02 2.50e+03
  ... (remaining 969 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.69: 148
        2.69 -     3.24: 5979
        3.24 -     3.80: 9782
        3.80 -     4.35: 13043
        4.35 -     4.90: 21642
  Nonbonded interactions: 50594
  Sorted by model distance:
  nonbonded pdb=" O   HOH D 843 "
            pdb=" O   HOH D 845 "
     model   vdw
     2.140 3.040
  nonbonded pdb=" O   HOH A 842 "
            pdb=" O   HOH A 845 "
     model   vdw
     2.141 3.040
  nonbonded pdb=" OH  TYR D 489 "
            pdb=" O   HOH D 801 "
     model   vdw
     2.292 3.040
  nonbonded pdb=" OH  TYR A 489 "
            pdb=" O   HOH A 801 "
     model   vdw
     2.293 3.040
  nonbonded pdb=" O   HOH A 816 "
            pdb=" O   HOH A 841 "
     model   vdw
     2.301 3.040
  ... (remaining 50589 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' and (resid 206 through 563 or resid 701))
  selection = (chain 'D' and (resid 206 through 563 or resid 701))
}

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:             24.020
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.250
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     20.230
  Find NCS groups from input model:        0.320
  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:             0.010
  Load rotamer database and sin/cos tables:13.390
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   58.360
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5703
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   5968  Z= 0.268
  Angle     :  0.859   8.950   8126  Z= 0.500
  Chirality :  0.063   0.433    878
  Planarity :  0.010   0.077    972
  Dihedral  : 10.139  89.573   2320
  Min Nonbonded Distance : 2.140

Molprobity Statistics.
  All-atom Clashscore : 1.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.29 %
    Favored  : 99.71 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.02 %
    Favored  : 98.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    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:  1.04 (0.31), residues: 684
  helix:  1.37 (0.23), residues: 474
  sheet: -4.83 (0.46), residues: 20
  loop : -0.23 (0.44), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.093   0.010   TRP D 354 
 HIS   0.022   0.004   HIS D 371 
 PHE   0.079   0.004   PHE A 439 
 TYR   0.101   0.012   TYR A 491 
 ARG   0.051   0.002   ARG A 223 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.12076 (  384)
  hydrogen bonds       : angle       6.17861 ( 1122)
  SS BOND              : bond        0.00790 (    8)
  SS BOND              : angle       1.00436 (   16)
  covalent geometry    : bond        0.00517 ( 5960)
  covalent geometry    : angle       0.85898 ( 8110)

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

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

  1368 Ramachandran restraints generated.
    684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1368 Ramachandran restraints generated.
    684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 126
  time to evaluate  : 0.751 
Fit side-chains
REVERT: A  372 GLU cc_start: 0.5997 (mp0) cc_final: 0.5706 (mt-10)
REVERT: A  379 GLN cc_start: 0.5239 (mt0) cc_final: 0.4620 (pt0)
REVERT: A  380 TYR cc_start: 0.5769 (m-80) cc_final: 0.5076 (m-80)
REVERT: A  418 VAL cc_start: 0.6116 (t) cc_final: 0.5710 (p)
REVERT: A  466 LYS cc_start: 0.6705 (tttt) cc_final: 0.6329 (tttm)
REVERT: A  497 GLU cc_start: 0.6049 (mt-10) cc_final: 0.5760 (pm20)
REVERT: D  372 GLU cc_start: 0.6013 (mp0) cc_final: 0.5730 (mt-10)
REVERT: D  379 GLN cc_start: 0.5249 (mt0) cc_final: 0.4626 (pt0)
REVERT: D  380 TYR cc_start: 0.5775 (m-80) cc_final: 0.5081 (m-80)
REVERT: D  418 VAL cc_start: 0.6116 (t) cc_final: 0.5710 (p)
REVERT: D  466 LYS cc_start: 0.6701 (tttt) cc_final: 0.6326 (tttm)
REVERT: D  497 GLU cc_start: 0.6058 (mt-10) cc_final: 0.5733 (pm20)
  outliers start: 0
  outliers final: 0
  residues processed: 126
  average time/residue: 2.4213
  time to fit residues: 314.4619
Evaluate side-chains
  101 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 1.967 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 57 optimal weight:    2.9990
   chunk 51 optimal weight:    2.9990
   chunk 28 optimal weight:    4.9990
   chunk 17 optimal weight:    0.9980
   chunk 34 optimal weight:    8.9990
   chunk 27 optimal weight:    0.9990
   chunk 53 optimal weight:    0.9980
   chunk 20 optimal weight:    0.8980
   chunk 32 optimal weight:    0.7980
   chunk 39 optimal weight:    0.6980
   chunk 61 optimal weight:    3.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
A 329 GLN
D 329 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4034 r_free = 0.4034 target = 0.166708 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.137022 restraints weight = 4633.597|
|-----------------------------------------------------------------------------|
r_work (start): 0.3699 rms_B_bonded: 1.00
r_work: 0.3594 rms_B_bonded: 1.52 restraints_weight: 0.5000
r_work: 0.3506 rms_B_bonded: 2.46 restraints_weight: 0.2500
r_work (final): 0.3506
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8214
moved from start:          0.2067

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   5968  Z= 0.150
  Angle     :  0.550   5.965   8126  Z= 0.293
  Chirality :  0.040   0.126    878
  Planarity :  0.005   0.029    972
  Dihedral  :  6.984  54.279   1078
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 3.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.88 %
    Favored  : 99.12 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  :  7.82 %
    Favored  : 90.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.10 (0.31), residues: 684
  helix:  2.40 (0.23), residues: 454
  sheet: -4.53 (0.46), residues: 20
  loop : -0.24 (0.37), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 354 
 HIS   0.003   0.001   HIS D 498 
 PHE   0.016   0.002   PHE A 340 
 TYR   0.012   0.002   TYR A 491 
 ARG   0.005   0.001   ARG D 212 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05312 (  384)
  hydrogen bonds       : angle       4.85239 ( 1122)
  SS BOND              : bond        0.00441 (    8)
  SS BOND              : angle       0.64583 (   16)
  covalent geometry    : bond        0.00315 ( 5960)
  covalent geometry    : angle       0.54962 ( 8110)

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

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

  1368 Ramachandran restraints generated.
    684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1368 Ramachandran restraints generated.
    684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 110
  time to evaluate  : 0.586 
Fit side-chains
REVERT: A  212 ARG cc_start: 0.7169 (ttp80) cc_final: 0.6928 (ptt-90)
REVERT: A  215 LYS cc_start: 0.8212 (mtpm) cc_final: 0.7565 (mtmm)
REVERT: A  248 GLU cc_start: 0.7692 (pm20) cc_final: 0.7175 (tm-30)
REVERT: A  279 MET cc_start: 0.7678 (mtm) cc_final: 0.7349 (mtp)
REVERT: A  379 GLN cc_start: 0.7665 (mt0) cc_final: 0.7433 (pt0)
REVERT: A  466 LYS cc_start: 0.8279 (tttt) cc_final: 0.8062 (tttm)
REVERT: D  212 ARG cc_start: 0.7177 (ttp80) cc_final: 0.6931 (ptt-90)
REVERT: D  215 LYS cc_start: 0.8208 (mtpm) cc_final: 0.7557 (mtmm)
REVERT: D  248 GLU cc_start: 0.7710 (pm20) cc_final: 0.7211 (tm-30)
REVERT: D  279 MET cc_start: 0.7661 (mtm) cc_final: 0.7343 (mtp)
REVERT: D  379 GLN cc_start: 0.7681 (mt0) cc_final: 0.7434 (pt0)
REVERT: D  466 LYS cc_start: 0.8263 (tttt) cc_final: 0.8052 (tttm)
  outliers start: 9
  outliers final: 2
  residues processed: 114
  average time/residue: 1.9318
  time to fit residues: 226.4828
Evaluate side-chains
  104 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 102
  time to evaluate  : 0.584 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  505 LEU
Chi-restraints excluded: chain D residue  505 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 65 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9980
   chunk 10 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 4 optimal weight:    2.9990
   chunk 2 optimal weight:    2.9990
   chunk 59 optimal weight:    3.9990
   chunk 24 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   chunk 29 optimal weight:    0.0980
   chunk 54 optimal weight:    0.9990
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
A 329 GLN
D 329 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4010 r_free = 0.4010 target = 0.164593 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.134279 restraints weight = 4641.315|
|-----------------------------------------------------------------------------|
r_work (start): 0.3663 rms_B_bonded: 1.02
r_work: 0.3559 rms_B_bonded: 1.56 restraints_weight: 0.5000
r_work: 0.3470 rms_B_bonded: 2.51 restraints_weight: 0.2500
r_work (final): 0.3470
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8252
moved from start:          0.2507

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   5968  Z= 0.152
  Angle     :  0.545   6.009   8126  Z= 0.291
  Chirality :  0.039   0.121    878
  Planarity :  0.004   0.029    972
  Dihedral  :  7.223  56.927   1078
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 4.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.88 %
    Favored  : 99.12 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  :  9.86 %
    Favored  : 88.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.08 (0.30), residues: 684
  helix:  2.37 (0.23), residues: 454
  sheet: -4.18 (0.51), residues: 20
  loop : -0.25 (0.36), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP D 354 
 HIS   0.002   0.001   HIS A 498 
 PHE   0.017   0.002   PHE A 340 
 TYR   0.014   0.002   TYR A 491 
 ARG   0.005   0.001   ARG A 281 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05350 (  384)
  hydrogen bonds       : angle       4.83651 ( 1122)
  SS BOND              : bond        0.00379 (    8)
  SS BOND              : angle       0.75792 (   16)
  covalent geometry    : bond        0.00326 ( 5960)
  covalent geometry    : angle       0.54476 ( 8110)

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

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

  1368 Ramachandran restraints generated.
    684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1368 Ramachandran restraints generated.
    684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 98
  time to evaluate  : 0.922 
Fit side-chains
REVERT: A  248 GLU cc_start: 0.7677 (pm20) cc_final: 0.7203 (tm-30)
REVERT: A  279 MET cc_start: 0.7735 (OUTLIER) cc_final: 0.7443 (mtp)
REVERT: A  379 GLN cc_start: 0.7759 (mt0) cc_final: 0.7494 (pt0)
REVERT: A  466 LYS cc_start: 0.8332 (tttt) cc_final: 0.8071 (tttm)
REVERT: D  248 GLU cc_start: 0.7674 (pm20) cc_final: 0.7204 (tm-30)
REVERT: D  279 MET cc_start: 0.7737 (mtm) cc_final: 0.7461 (mtp)
REVERT: D  379 GLN cc_start: 0.7761 (mt0) cc_final: 0.7488 (pt0)
REVERT: D  466 LYS cc_start: 0.8323 (tttt) cc_final: 0.8063 (tttm)
REVERT: D  559 ARG cc_start: 0.6857 (ttp-110) cc_final: 0.6560 (mtm-85)
  outliers start: 12
  outliers final: 4
  residues processed: 102
  average time/residue: 2.0263
  time to fit residues: 212.6272
Evaluate side-chains
  103 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 98
  time to evaluate  : 0.663 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  279 MET
Chi-restraints excluded: chain A residue  375 GLU
Chi-restraints excluded: chain A residue  505 LEU
Chi-restraints excluded: chain D residue  375 GLU
Chi-restraints excluded: chain D residue  505 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 22 optimal weight:    0.0970
   chunk 16 optimal weight:    8.9990
   chunk 14 optimal weight:    0.6980
   chunk 64 optimal weight:    0.3980
   chunk 29 optimal weight:   10.0000
   chunk 63 optimal weight:   10.0000
   chunk 12 optimal weight:    4.9990
   chunk 5 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9980
   chunk 4 optimal weight:    0.9990
   chunk 6 optimal weight:    3.9990
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.4055 r_free = 0.4055 target = 0.167690 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.137937 restraints weight = 4752.026|
|-----------------------------------------------------------------------------|
r_work (start): 0.3691 rms_B_bonded: 1.02
r_work: 0.3588 rms_B_bonded: 1.57 restraints_weight: 0.5000
r_work: 0.3500 rms_B_bonded: 2.53 restraints_weight: 0.2500
r_work (final): 0.3500
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8224
moved from start:          0.2715

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   5968  Z= 0.123
  Angle     :  0.506   7.185   8126  Z= 0.265
  Chirality :  0.037   0.117    878
  Planarity :  0.004   0.029    972
  Dihedral  :  7.265  55.385   1078
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 3.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.17 %
    Favored  : 98.83 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 10.37 %
    Favored  : 87.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.39 (0.31), residues: 684
  helix:  2.57 (0.23), residues: 456
  sheet: -4.18 (0.47), residues: 20
  loop : -0.05 (0.38), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP D 256 
 HIS   0.001   0.001   HIS A 498 
 PHE   0.013   0.001   PHE A 340 
 TYR   0.014   0.001   TYR D 491 
 ARG   0.006   0.001   ARG A 281 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04762 (  384)
  hydrogen bonds       : angle       4.57690 ( 1122)
  SS BOND              : bond        0.00331 (    8)
  SS BOND              : angle       0.66078 (   16)
  covalent geometry    : bond        0.00255 ( 5960)
  covalent geometry    : angle       0.50559 ( 8110)

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

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

  1368 Ramachandran restraints generated.
    684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1368 Ramachandran restraints generated.
    684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 102
  time to evaluate  : 0.637 
Fit side-chains
REVERT: A  247 GLU cc_start: 0.7171 (OUTLIER) cc_final: 0.6402 (mm-30)
REVERT: A  279 MET cc_start: 0.7764 (mtm) cc_final: 0.7458 (mtp)
REVERT: A  379 GLN cc_start: 0.7737 (mt0) cc_final: 0.7507 (pt0)
REVERT: A  466 LYS cc_start: 0.8309 (tttt) cc_final: 0.8042 (tttm)
REVERT: D  247 GLU cc_start: 0.7176 (OUTLIER) cc_final: 0.6409 (mm-30)
REVERT: D  279 MET cc_start: 0.7761 (OUTLIER) cc_final: 0.7446 (mtp)
REVERT: D  379 GLN cc_start: 0.7728 (mt0) cc_final: 0.7498 (pt0)
REVERT: D  466 LYS cc_start: 0.8294 (tttt) cc_final: 0.8028 (tttm)
REVERT: D  559 ARG cc_start: 0.6896 (ttp-110) cc_final: 0.6603 (mtm-85)
  outliers start: 10
  outliers final: 4
  residues processed: 108
  average time/residue: 2.0252
  time to fit residues: 224.8656
Evaluate side-chains
  106 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 99
  time to evaluate  : 0.638 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  247 GLU
Chi-restraints excluded: chain A residue  505 LEU
Chi-restraints excluded: chain D residue  216 VAL
Chi-restraints excluded: chain D residue  247 GLU
Chi-restraints excluded: chain D residue  279 MET
Chi-restraints excluded: chain D residue  505 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 24 optimal weight:    0.5980
   chunk 57 optimal weight:    0.7980
   chunk 23 optimal weight:    0.6980
   chunk 29 optimal weight:    0.9990
   chunk 27 optimal weight:    3.9990
   chunk 54 optimal weight:    0.9990
   chunk 1 optimal weight:    4.9990
   chunk 67 optimal weight:    0.2980
   chunk 28 optimal weight:    0.7980
   chunk 39 optimal weight:    0.7980
   chunk 59 optimal weight:    2.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 371 HIS
D 371 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.167418 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.137827 restraints weight = 4626.079|
|-----------------------------------------------------------------------------|
r_work (start): 0.3689 rms_B_bonded: 1.01
r_work: 0.3586 rms_B_bonded: 1.54 restraints_weight: 0.5000
r_work: 0.3498 rms_B_bonded: 2.49 restraints_weight: 0.2500
r_work (final): 0.3498
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8227
moved from start:          0.2839

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   5968  Z= 0.124
  Angle     :  0.509   7.311   8126  Z= 0.267
  Chirality :  0.037   0.119    878
  Planarity :  0.004   0.029    972
  Dihedral  :  7.326  58.066   1078
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 3.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.88 %
    Favored  : 99.12 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 10.54 %
    Favored  : 87.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.39 (0.31), residues: 684
  helix:  2.59 (0.23), residues: 456
  sheet: -4.16 (0.48), residues: 20
  loop : -0.08 (0.37), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 256 
 HIS   0.001   0.001   HIS A 382 
 PHE   0.014   0.001   PHE A 340 
 TYR   0.014   0.001   TYR D 491 
 ARG   0.005   0.000   ARG A 501 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04770 (  384)
  hydrogen bonds       : angle       4.51765 ( 1122)
  SS BOND              : bond        0.00291 (    8)
  SS BOND              : angle       0.57004 (   16)
  covalent geometry    : bond        0.00258 ( 5960)
  covalent geometry    : angle       0.50929 ( 8110)

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

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

  1368 Ramachandran restraints generated.
    684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1368 Ramachandran restraints generated.
    684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 102
  time to evaluate  : 0.699 
Fit side-chains
REVERT: A  247 GLU cc_start: 0.7205 (OUTLIER) cc_final: 0.6327 (mm-30)
REVERT: A  248 GLU cc_start: 0.7637 (pm20) cc_final: 0.7214 (tm-30)
REVERT: A  279 MET cc_start: 0.7740 (OUTLIER) cc_final: 0.7420 (mtp)
REVERT: A  281 ARG cc_start: 0.6792 (ptm-80) cc_final: 0.6505 (tmt-80)
REVERT: A  379 GLN cc_start: 0.7733 (mt0) cc_final: 0.7514 (pt0)
REVERT: A  466 LYS cc_start: 0.8302 (tttt) cc_final: 0.8037 (tttm)
REVERT: D  247 GLU cc_start: 0.7207 (OUTLIER) cc_final: 0.6327 (mm-30)
REVERT: D  248 GLU cc_start: 0.7638 (pm20) cc_final: 0.7213 (tm-30)
REVERT: D  279 MET cc_start: 0.7748 (OUTLIER) cc_final: 0.7443 (mtp)
REVERT: D  281 ARG cc_start: 0.6808 (ptm-80) cc_final: 0.6507 (tmt-80)
REVERT: D  379 GLN cc_start: 0.7722 (mt0) cc_final: 0.7505 (pt0)
REVERT: D  466 LYS cc_start: 0.8294 (tttt) cc_final: 0.8029 (tttm)
REVERT: D  559 ARG cc_start: 0.6968 (ttp-110) cc_final: 0.6675 (mtm-85)
  outliers start: 13
  outliers final: 5
  residues processed: 108
  average time/residue: 2.2867
  time to fit residues: 253.9883
Evaluate side-chains
  108 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 99
  time to evaluate  : 0.639 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  247 GLU
Chi-restraints excluded: chain A residue  279 MET
Chi-restraints excluded: chain A residue  505 LEU
Chi-restraints excluded: chain D residue  216 VAL
Chi-restraints excluded: chain D residue  247 GLU
Chi-restraints excluded: chain D residue  279 MET
Chi-restraints excluded: chain D residue  316 VAL
Chi-restraints excluded: chain D residue  505 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 35 optimal weight:    0.0670
   chunk 39 optimal weight:    0.9990
   chunk 18 optimal weight:    0.8980
   chunk 4 optimal weight:    3.9990
   chunk 46 optimal weight:    0.7980
   chunk 28 optimal weight:    1.9990
   chunk 3 optimal weight:    0.6980
   chunk 49 optimal weight:    4.9990
   chunk 45 optimal weight:    0.0060
   chunk 14 optimal weight:    0.5980
   chunk 26 optimal weight:    1.9990
   overall best weight:    0.4334

-------------------------------------------------------------------------------
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 = 0.4095 r_free = 0.4095 target = 0.170075 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.142066 restraints weight = 4754.959|
|-----------------------------------------------------------------------------|
r_work (start): 0.3760 rms_B_bonded: 0.97
r_work: 0.3661 rms_B_bonded: 1.50 restraints_weight: 0.5000
r_work: 0.3576 rms_B_bonded: 2.43 restraints_weight: 0.2500
r_work (final): 0.3576
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8211
moved from start:          0.3002

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   5968  Z= 0.110
  Angle     :  0.492   7.864   8126  Z= 0.254
  Chirality :  0.036   0.118    878
  Planarity :  0.004   0.028    972
  Dihedral  :  7.301  59.935   1078
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 3.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.88 %
    Favored  : 99.12 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 10.88 %
    Favored  : 86.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.54 (0.31), residues: 684
  helix:  2.73 (0.23), residues: 456
  sheet: -4.18 (0.47), residues: 20
  loop : -0.07 (0.37), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 256 
 HIS   0.001   0.000   HIS D 562 
 PHE   0.012   0.001   PHE A 340 
 TYR   0.015   0.001   TYR D 491 
 ARG   0.005   0.001   ARG D 501 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04410 (  384)
  hydrogen bonds       : angle       4.36105 ( 1122)
  SS BOND              : bond        0.00259 (    8)
  SS BOND              : angle       0.53641 (   16)
  covalent geometry    : bond        0.00223 ( 5960)
  covalent geometry    : angle       0.49211 ( 8110)

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

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

  1368 Ramachandran restraints generated.
    684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1368 Ramachandran restraints generated.
    684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 103
  time to evaluate  : 0.574 
Fit side-chains
REVERT: A  247 GLU cc_start: 0.7181 (OUTLIER) cc_final: 0.6366 (mm-30)
REVERT: A  248 GLU cc_start: 0.7616 (pm20) cc_final: 0.7303 (tm-30)
REVERT: A  279 MET cc_start: 0.7745 (OUTLIER) cc_final: 0.7446 (mtp)
REVERT: A  281 ARG cc_start: 0.6892 (ptm-80) cc_final: 0.6604 (tmt-80)
REVERT: A  466 LYS cc_start: 0.8304 (tttt) cc_final: 0.7975 (tttp)
REVERT: D  247 GLU cc_start: 0.7178 (OUTLIER) cc_final: 0.6359 (mm-30)
REVERT: D  248 GLU cc_start: 0.7604 (pm20) cc_final: 0.7296 (tm-30)
REVERT: D  279 MET cc_start: 0.7737 (OUTLIER) cc_final: 0.7441 (mtp)
REVERT: D  281 ARG cc_start: 0.6872 (ptm-80) cc_final: 0.6591 (tmt-80)
REVERT: D  466 LYS cc_start: 0.8301 (tttt) cc_final: 0.7975 (tttp)
  outliers start: 14
  outliers final: 4
  residues processed: 109
  average time/residue: 2.1425
  time to fit residues: 239.7949
Evaluate side-chains
  108 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 100
  time to evaluate  : 0.694 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  247 GLU
Chi-restraints excluded: chain A residue  279 MET
Chi-restraints excluded: chain A residue  316 VAL
Chi-restraints excluded: chain A residue  372 GLU
Chi-restraints excluded: chain D residue  247 GLU
Chi-restraints excluded: chain D residue  279 MET
Chi-restraints excluded: chain D residue  316 VAL
Chi-restraints excluded: chain D residue  372 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 59 optimal weight:    0.8980
   chunk 39 optimal weight:    0.7980
   chunk 6 optimal weight:    0.9980
   chunk 27 optimal weight:    3.9990
   chunk 7 optimal weight:    0.7980
   chunk 54 optimal weight:    0.9980
   chunk 20 optimal weight:    1.9990
   chunk 16 optimal weight:    3.9990
   chunk 37 optimal weight:    3.9990
   chunk 8 optimal weight:    0.9980
   chunk 41 optimal weight:    0.0980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.4084 r_free = 0.4084 target = 0.168637 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.140208 restraints weight = 4733.435|
|-----------------------------------------------------------------------------|
r_work (start): 0.3740 rms_B_bonded: 0.98
r_work: 0.3637 rms_B_bonded: 1.51 restraints_weight: 0.5000
r_work: 0.3552 rms_B_bonded: 2.43 restraints_weight: 0.2500
r_work (final): 0.3552
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8239
moved from start:          0.3016

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   5968  Z= 0.127
  Angle     :  0.525   8.984   8126  Z= 0.273
  Chirality :  0.037   0.119    878
  Planarity :  0.004   0.028    972
  Dihedral  :  7.417  59.842   1078
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 3.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.17 %
    Favored  : 98.83 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 11.22 %
    Favored  : 86.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.42 (0.31), residues: 684
  helix:  2.62 (0.23), residues: 456
  sheet: -4.15 (0.49), residues: 20
  loop : -0.10 (0.37), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 256 
 HIS   0.002   0.001   HIS D 562 
 PHE   0.016   0.001   PHE A 340 
 TYR   0.014   0.001   TYR D 491 
 ARG   0.005   0.000   ARG A 501 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04785 (  384)
  hydrogen bonds       : angle       4.52039 ( 1122)
  SS BOND              : bond        0.00280 (    8)
  SS BOND              : angle       0.81615 (   16)
  covalent geometry    : bond        0.00265 ( 5960)
  covalent geometry    : angle       0.52392 ( 8110)

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

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

  1368 Ramachandran restraints generated.
    684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1368 Ramachandran restraints generated.
    684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 100
  time to evaluate  : 0.692 
Fit side-chains
REVERT: A  247 GLU cc_start: 0.7192 (OUTLIER) cc_final: 0.6445 (mm-30)
REVERT: A  279 MET cc_start: 0.7778 (OUTLIER) cc_final: 0.7469 (mtp)
REVERT: A  466 LYS cc_start: 0.8312 (tttt) cc_final: 0.7980 (tttp)
REVERT: D  247 GLU cc_start: 0.7188 (OUTLIER) cc_final: 0.6438 (mm-30)
REVERT: D  279 MET cc_start: 0.7774 (OUTLIER) cc_final: 0.7470 (mtp)
REVERT: D  466 LYS cc_start: 0.8314 (tttt) cc_final: 0.7982 (tttp)
  outliers start: 14
  outliers final: 8
  residues processed: 106
  average time/residue: 2.0532
  time to fit residues: 224.2477
Evaluate side-chains
  109 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 97
  time to evaluate  : 0.615 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  247 GLU
Chi-restraints excluded: chain A residue  279 MET
Chi-restraints excluded: chain A residue  316 VAL
Chi-restraints excluded: chain A residue  372 GLU
Chi-restraints excluded: chain A residue  505 LEU
Chi-restraints excluded: chain D residue  216 VAL
Chi-restraints excluded: chain D residue  247 GLU
Chi-restraints excluded: chain D residue  279 MET
Chi-restraints excluded: chain D residue  316 VAL
Chi-restraints excluded: chain D residue  372 GLU
Chi-restraints excluded: chain D residue  505 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 62 optimal weight:    0.9980
   chunk 19 optimal weight:    0.0570
   chunk 12 optimal weight:    0.6980
   chunk 10 optimal weight:    3.9990
   chunk 18 optimal weight:    0.6980
   chunk 24 optimal weight:    9.9990
   chunk 48 optimal weight:    0.5980
   chunk 40 optimal weight:    5.9990
   chunk 3 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9990
   chunk 65 optimal weight:    4.9990
   overall best weight:    0.6098

-------------------------------------------------------------------------------
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 = 0.4087 r_free = 0.4087 target = 0.168937 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.140781 restraints weight = 4702.177|
|-----------------------------------------------------------------------------|
r_work (start): 0.3747 rms_B_bonded: 0.97
r_work: 0.3645 rms_B_bonded: 1.50 restraints_weight: 0.5000
r_work: 0.3561 rms_B_bonded: 2.42 restraints_weight: 0.2500
r_work (final): 0.3561
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8230
moved from start:          0.3072

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043   5968  Z= 0.120
  Angle     :  0.522   9.709   8126  Z= 0.269
  Chirality :  0.037   0.118    878
  Planarity :  0.004   0.028    972
  Dihedral  :  7.383  59.568   1078
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 4.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.17 %
    Favored  : 98.83 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 11.56 %
    Favored  : 85.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.41 (0.31), residues: 684
  helix:  2.62 (0.23), residues: 456
  sheet: -4.19 (0.49), residues: 20
  loop : -0.11 (0.37), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP D 256 
 HIS   0.002   0.001   HIS D 562 
 PHE   0.015   0.001   PHE A 340 
 TYR   0.015   0.001   TYR D 491 
 ARG   0.007   0.001   ARG A 559 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04649 (  384)
  hydrogen bonds       : angle       4.46425 ( 1122)
  SS BOND              : bond        0.00273 (    8)
  SS BOND              : angle       0.74783 (   16)
  covalent geometry    : bond        0.00250 ( 5960)
  covalent geometry    : angle       0.52112 ( 8110)

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

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

  1368 Ramachandran restraints generated.
    684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1368 Ramachandran restraints generated.
    684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 102
  time to evaluate  : 0.598 
Fit side-chains
REVERT: A  247 GLU cc_start: 0.7256 (OUTLIER) cc_final: 0.6362 (mm-30)
REVERT: A  248 GLU cc_start: 0.7682 (pm20) cc_final: 0.7285 (tm-30)
REVERT: A  279 MET cc_start: 0.7770 (OUTLIER) cc_final: 0.7468 (mtp)
REVERT: A  466 LYS cc_start: 0.8323 (tttt) cc_final: 0.7980 (tttp)
REVERT: D  247 GLU cc_start: 0.7252 (OUTLIER) cc_final: 0.6356 (mm-30)
REVERT: D  248 GLU cc_start: 0.7668 (pm20) cc_final: 0.7283 (tm-30)
REVERT: D  279 MET cc_start: 0.7775 (OUTLIER) cc_final: 0.7475 (mtp)
REVERT: D  466 LYS cc_start: 0.8310 (tttt) cc_final: 0.7966 (tttp)
  outliers start: 15
  outliers final: 8
  residues processed: 108
  average time/residue: 2.1327
  time to fit residues: 236.9107
Evaluate side-chains
  111 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 99
  time to evaluate  : 0.586 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  247 GLU
Chi-restraints excluded: chain A residue  279 MET
Chi-restraints excluded: chain A residue  316 VAL
Chi-restraints excluded: chain A residue  372 GLU
Chi-restraints excluded: chain A residue  505 LEU
Chi-restraints excluded: chain D residue  216 VAL
Chi-restraints excluded: chain D residue  247 GLU
Chi-restraints excluded: chain D residue  279 MET
Chi-restraints excluded: chain D residue  316 VAL
Chi-restraints excluded: chain D residue  372 GLU
Chi-restraints excluded: chain D residue  505 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 61 optimal weight:    3.9990
   chunk 23 optimal weight:    0.7980
   chunk 51 optimal weight:    0.9990
   chunk 40 optimal weight:    3.9990
   chunk 43 optimal weight:    1.9990
   chunk 21 optimal weight:    0.5980
   chunk 49 optimal weight:    3.9990
   chunk 36 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9990
   chunk 32 optimal weight:    2.9990
   chunk 12 optimal weight:    0.3980
   overall best weight:    0.7584

-------------------------------------------------------------------------------
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 = 0.4080 r_free = 0.4080 target = 0.168259 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.139704 restraints weight = 4719.083|
|-----------------------------------------------------------------------------|
r_work (start): 0.3734 rms_B_bonded: 0.99
r_work: 0.3632 rms_B_bonded: 1.52 restraints_weight: 0.5000
r_work: 0.3546 rms_B_bonded: 2.45 restraints_weight: 0.2500
r_work (final): 0.3546
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8247
moved from start:          0.3075

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   5968  Z= 0.130
  Angle     :  0.552  10.328   8126  Z= 0.284
  Chirality :  0.037   0.119    878
  Planarity :  0.004   0.028    972
  Dihedral  :  7.469  58.063   1078
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 4.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.17 %
    Favored  : 98.83 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 12.41 %
    Favored  : 85.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.35 (0.31), residues: 684
  helix:  2.56 (0.23), residues: 456
  sheet: -4.14 (0.49), residues: 20
  loop : -0.11 (0.37), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP D 256 
 HIS   0.002   0.001   HIS D 562 
 PHE   0.016   0.001   PHE D 340 
 TYR   0.015   0.001   TYR D 491 
 ARG   0.005   0.001   ARG D 501 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04831 (  384)
  hydrogen bonds       : angle       4.54080 ( 1122)
  SS BOND              : bond        0.00280 (    8)
  SS BOND              : angle       0.73771 (   16)
  covalent geometry    : bond        0.00276 ( 5960)
  covalent geometry    : angle       0.55151 ( 8110)

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

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

  1368 Ramachandran restraints generated.
    684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1368 Ramachandran restraints generated.
    684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 100
  time to evaluate  : 0.514 
Fit side-chains
REVERT: A  247 GLU cc_start: 0.7227 (OUTLIER) cc_final: 0.6368 (mm-30)
REVERT: A  248 GLU cc_start: 0.7696 (pm20) cc_final: 0.7296 (tm-30)
REVERT: A  279 MET cc_start: 0.7803 (OUTLIER) cc_final: 0.7494 (mtp)
REVERT: A  466 LYS cc_start: 0.8334 (tttt) cc_final: 0.7995 (tttp)
REVERT: D  247 GLU cc_start: 0.7219 (OUTLIER) cc_final: 0.6361 (mm-30)
REVERT: D  248 GLU cc_start: 0.7690 (pm20) cc_final: 0.7291 (tm-30)
REVERT: D  279 MET cc_start: 0.7809 (OUTLIER) cc_final: 0.7508 (mtp)
REVERT: D  466 LYS cc_start: 0.8322 (tttt) cc_final: 0.7983 (tttp)
  outliers start: 14
  outliers final: 8
  residues processed: 106
  average time/residue: 1.9265
  time to fit residues: 210.4446
Evaluate side-chains
  108 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 96
  time to evaluate  : 0.809 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  247 GLU
Chi-restraints excluded: chain A residue  279 MET
Chi-restraints excluded: chain A residue  316 VAL
Chi-restraints excluded: chain A residue  372 GLU
Chi-restraints excluded: chain A residue  505 LEU
Chi-restraints excluded: chain D residue  216 VAL
Chi-restraints excluded: chain D residue  247 GLU
Chi-restraints excluded: chain D residue  279 MET
Chi-restraints excluded: chain D residue  316 VAL
Chi-restraints excluded: chain D residue  372 GLU
Chi-restraints excluded: chain D residue  505 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 58 optimal weight:   10.0000
   chunk 16 optimal weight:    0.8980
   chunk 44 optimal weight:    0.0970
   chunk 28 optimal weight:    0.9980
   chunk 38 optimal weight:    0.9990
   chunk 29 optimal weight:    0.2980
   chunk 62 optimal weight:    0.9990
   chunk 22 optimal weight:    0.7980
   chunk 4 optimal weight:    3.9990
   chunk 9 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9980
   overall best weight:    0.6178

-------------------------------------------------------------------------------
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 = 0.4085 r_free = 0.4085 target = 0.168757 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.140518 restraints weight = 4797.968|
|-----------------------------------------------------------------------------|
r_work (start): 0.3744 rms_B_bonded: 0.98
r_work: 0.3643 rms_B_bonded: 1.50 restraints_weight: 0.5000
r_work: 0.3558 rms_B_bonded: 2.43 restraints_weight: 0.2500
r_work (final): 0.3558
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8233
moved from start:          0.3129

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   5968  Z= 0.121
  Angle     :  0.531  10.431   8126  Z= 0.273
  Chirality :  0.037   0.119    878
  Planarity :  0.004   0.028    972
  Dihedral  :  7.383  59.850   1078
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 4.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.17 %
    Favored  : 98.83 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 11.73 %
    Favored  : 85.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.36 (0.31), residues: 684
  helix:  2.58 (0.23), residues: 456
  sheet: -4.13 (0.50), residues: 20
  loop : -0.13 (0.37), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP D 256 
 HIS   0.002   0.001   HIS D 562 
 PHE   0.015   0.001   PHE A 340 
 TYR   0.015   0.001   TYR D 491 
 ARG   0.010   0.001   ARG A 559 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04683 (  384)
  hydrogen bonds       : angle       4.51408 ( 1122)
  SS BOND              : bond        0.00270 (    8)
  SS BOND              : angle       0.70206 (   16)
  covalent geometry    : bond        0.00252 ( 5960)
  covalent geometry    : angle       0.53058 ( 8110)

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

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

  1368 Ramachandran restraints generated.
    684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1368 Ramachandran restraints generated.
    684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 97
  time to evaluate  : 0.643 
Fit side-chains
REVERT: A  246 LYS cc_start: 0.6895 (mtmm) cc_final: 0.6536 (pttt)
REVERT: A  247 GLU cc_start: 0.7209 (OUTLIER) cc_final: 0.6374 (mm-30)
REVERT: A  248 GLU cc_start: 0.7677 (pm20) cc_final: 0.7294 (tm-30)
REVERT: A  279 MET cc_start: 0.7789 (OUTLIER) cc_final: 0.7486 (mtp)
REVERT: A  466 LYS cc_start: 0.8324 (tttt) cc_final: 0.7990 (tttp)
REVERT: D  247 GLU cc_start: 0.7203 (OUTLIER) cc_final: 0.6366 (mm-30)
REVERT: D  248 GLU cc_start: 0.7671 (pm20) cc_final: 0.7285 (tm-30)
REVERT: D  279 MET cc_start: 0.7798 (OUTLIER) cc_final: 0.7502 (mtp)
REVERT: D  466 LYS cc_start: 0.8311 (tttt) cc_final: 0.7975 (tttp)
  outliers start: 15
  outliers final: 8
  residues processed: 106
  average time/residue: 1.9392
  time to fit residues: 211.7180
Evaluate side-chains
  108 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 96
  time to evaluate  : 0.593 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  247 GLU
Chi-restraints excluded: chain A residue  279 MET
Chi-restraints excluded: chain A residue  316 VAL
Chi-restraints excluded: chain A residue  372 GLU
Chi-restraints excluded: chain A residue  505 LEU
Chi-restraints excluded: chain D residue  216 VAL
Chi-restraints excluded: chain D residue  247 GLU
Chi-restraints excluded: chain D residue  279 MET
Chi-restraints excluded: chain D residue  316 VAL
Chi-restraints excluded: chain D residue  372 GLU
Chi-restraints excluded: chain D residue  505 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 1 optimal weight:    4.9990
   chunk 32 optimal weight:    2.9990
   chunk 17 optimal weight:    5.9990
   chunk 6 optimal weight:    1.9990
   chunk 38 optimal weight:    0.8980
   chunk 57 optimal weight:    0.5980
   chunk 41 optimal weight:    0.7980
   chunk 40 optimal weight:    0.6980
   chunk 34 optimal weight:   10.0000
   chunk 11 optimal weight:    0.7980
   chunk 52 optimal weight:    1.9990
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.4077 r_free = 0.4077 target = 0.167990 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.139649 restraints weight = 4757.119|
|-----------------------------------------------------------------------------|
r_work (start): 0.3733 rms_B_bonded: 0.98
r_work: 0.3630 rms_B_bonded: 1.51 restraints_weight: 0.5000
r_work: 0.3545 rms_B_bonded: 2.42 restraints_weight: 0.2500
r_work (final): 0.3545
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8246
moved from start:          0.3129

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   5968  Z= 0.130
  Angle     :  0.554  12.066   8126  Z= 0.283
  Chirality :  0.037   0.119    878
  Planarity :  0.004   0.029    972
  Dihedral  :  7.465  57.100   1078
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 4.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.17 %
    Favored  : 98.83 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 11.90 %
    Favored  : 85.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.28 (0.31), residues: 684
  helix:  2.52 (0.23), residues: 456
  sheet: -4.07 (0.52), residues: 20
  loop : -0.17 (0.37), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP D 256 
 HIS   0.002   0.001   HIS D 562 
 PHE   0.016   0.001   PHE A 340 
 TYR   0.015   0.001   TYR A 491 
 ARG   0.009   0.001   ARG A 559 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04857 (  384)
  hydrogen bonds       : angle       4.57498 ( 1122)
  SS BOND              : bond        0.00289 (    8)
  SS BOND              : angle       0.72175 (   16)
  covalent geometry    : bond        0.00274 ( 5960)
  covalent geometry    : angle       0.55359 ( 8110)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7719.16 seconds
wall clock time: 133 minutes 56.28 seconds (8036.28 seconds total)