Starting phenix.real_space_refine
on Wed Sep 17 06:07:35 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9epo_19881/09_2025/9epo_19881.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9epo_19881/09_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_19881/09_2025/9epo_19881.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9epo_19881/09_2025/9epo_19881.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9epo_19881/09_2025/9epo_19881.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9epo_19881/09_2025/9epo_19881.cif"
  }
  resolution = 1.9
  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=   0.010
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-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 1.68, per 1000 atoms: 0.29
  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: 0.58
  Conformation dependent library (CDL) restraints added in 340.7 milliseconds
  
  Enol-peptide restraints added in 1.2 microseconds
  

  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: 0.18
  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: 0.91

  Time building geometry restraints manager: 0.75 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: 0.01
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 206 through 701)
  selection = (chain 'D' and resid 206 through 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:             3.580
  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:          0.150
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     7.560
  Find NCS groups from input model:        0.120
  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:6.240
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.710
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.051   0.002   ARG A 223 
 TYR   0.101   0.012   TYR A 491 
 PHE   0.079   0.004   PHE A 439 
 TRP   0.093   0.010   TRP D 354 
 HIS   0.022   0.004   HIS D 371 

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

*********************** 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  : 0.133 
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: 0.8778
  time to fit residues: 113.5925
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  : 0.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    0.5980
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    0.7980
   chunk 38 optimal weight:    4.9990
   chunk 61 optimal weight:    0.8980
   chunk 45 optimal weight:    8.9990
   chunk 27 optimal weight:    3.9990
   overall best weight:    0.8380

-------------------------------------------------------------------------------
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 = 0.4038 r_free = 0.4038 target = 0.167107 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.137425 restraints weight = 4689.017|
|-----------------------------------------------------------------------------|
r_work (start): 0.3704 rms_B_bonded: 1.00
r_work: 0.3600 rms_B_bonded: 1.53 restraints_weight: 0.5000
r_work: 0.3512 rms_B_bonded: 2.48 restraints_weight: 0.2500
r_work (final): 0.3512
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8204
moved from start:          0.2078

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   5968  Z= 0.146
  Angle     :  0.550   5.984   8126  Z= 0.292
  Chirality :  0.040   0.127    878
  Planarity :  0.005   0.029    972
  Dihedral  :  7.004  53.973   1078
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 3.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.58 %
    Favored  : 99.42 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.11 (0.31), residues: 684
  helix:  2.41 (0.23), residues: 454
  sheet: -4.54 (0.45), residues: 20
  loop : -0.24 (0.37), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D 212 
 TYR   0.012   0.002   TYR A 491 
 PHE   0.015   0.002   PHE D 340 
 TRP   0.015   0.002   TRP D 256 
 HIS   0.003   0.001   HIS D 498 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 5960)
  covalent geometry    : angle       0.54965 ( 8110)
  SS BOND              : bond        0.00415 (    8)
  SS BOND              : angle       0.66585 (   16)
  hydrogen bonds       : bond        0.05121 (  384)
  hydrogen bonds       : angle       4.80517 ( 1122)

*********************** 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
  118 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 109
  time to evaluate  : 0.224 
Fit side-chains
REVERT: A  212 ARG cc_start: 0.7145 (ttp80) cc_final: 0.6837 (ptm-80)
REVERT: A  215 LYS cc_start: 0.8197 (mtpm) cc_final: 0.7542 (mtmm)
REVERT: A  248 GLU cc_start: 0.7660 (pm20) cc_final: 0.7166 (tm-30)
REVERT: A  279 MET cc_start: 0.7672 (mtm) cc_final: 0.7343 (mtp)
REVERT: A  379 GLN cc_start: 0.7644 (mt0) cc_final: 0.7414 (pt0)
REVERT: A  466 LYS cc_start: 0.8268 (tttt) cc_final: 0.8050 (tttm)
REVERT: A  501 ARG cc_start: 0.7683 (ttp80) cc_final: 0.7467 (ttp80)
REVERT: D  212 ARG cc_start: 0.7149 (ttp80) cc_final: 0.6839 (ptm-80)
REVERT: D  215 LYS cc_start: 0.8209 (mtpm) cc_final: 0.7553 (mtmm)
REVERT: D  248 GLU cc_start: 0.7680 (pm20) cc_final: 0.7202 (tm-30)
REVERT: D  279 MET cc_start: 0.7653 (mtm) cc_final: 0.7334 (mtp)
REVERT: D  379 GLN cc_start: 0.7661 (mt0) cc_final: 0.7414 (pt0)
REVERT: D  466 LYS cc_start: 0.8259 (tttt) cc_final: 0.8046 (tttm)
REVERT: D  501 ARG cc_start: 0.7680 (ttp80) cc_final: 0.7465 (ttp80)
  outliers start: 9
  outliers final: 2
  residues processed: 114
  average time/residue: 0.9959
  time to fit residues: 116.5979
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  : 0.175 
-------------------------------------------------------------------------------
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 46 optimal weight:    5.9990
   chunk 8 optimal weight:    1.9990
   chunk 52 optimal weight:    0.7980
   chunk 24 optimal weight:    3.9990
   chunk 32 optimal weight:    2.9990
   chunk 19 optimal weight:    0.3980
   chunk 27 optimal weight:    0.9990
   chunk 67 optimal weight:    0.7980
   chunk 23 optimal weight:    0.7980
   chunk 17 optimal weight:    4.9990
   chunk 64 optimal weight:    3.9990
   overall best weight:    0.7582

-------------------------------------------------------------------------------
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 = 0.4026 r_free = 0.4026 target = 0.166004 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.135833 restraints weight = 4609.080|
|-----------------------------------------------------------------------------|
r_work (start): 0.3683 rms_B_bonded: 1.02
r_work: 0.3580 rms_B_bonded: 1.56 restraints_weight: 0.5000
r_work: 0.3492 rms_B_bonded: 2.52 restraints_weight: 0.2500
r_work (final): 0.3492
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8233
moved from start:          0.2492

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   5968  Z= 0.134
  Angle     :  0.524   6.722   8126  Z= 0.277
  Chirality :  0.038   0.123    878
  Planarity :  0.004   0.030    972
  Dihedral  :  7.135  55.611   1078
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 3.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.17 %
    Favored  : 98.83 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  :  9.35 %
    Favored  : 88.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    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 aren not related in a simple way.
  whole:  2.23 (0.30), residues: 684
  helix:  2.48 (0.23), residues: 454
  sheet: -4.24 (0.48), residues: 20
  loop : -0.16 (0.37), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D 281 
 TYR   0.014   0.001   TYR D 491 
 PHE   0.015   0.001   PHE D 340 
 TRP   0.015   0.001   TRP A 256 
 HIS   0.002   0.001   HIS A 562 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 5960)
  covalent geometry    : angle       0.52341 ( 8110)
  SS BOND              : bond        0.00335 (    8)
  SS BOND              : angle       0.73098 (   16)
  hydrogen bonds       : bond        0.05034 (  384)
  hydrogen bonds       : angle       4.68572 ( 1122)

*********************** 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
  112 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 100
  time to evaluate  : 0.169 
Fit side-chains
REVERT: A  248 GLU cc_start: 0.7658 (pm20) cc_final: 0.7234 (tm-30)
REVERT: A  279 MET cc_start: 0.7728 (mtm) cc_final: 0.7402 (mtp)
REVERT: A  379 GLN cc_start: 0.7733 (mt0) cc_final: 0.7481 (pt0)
REVERT: A  466 LYS cc_start: 0.8326 (tttt) cc_final: 0.8113 (tttm)
REVERT: D  248 GLU cc_start: 0.7663 (pm20) cc_final: 0.7242 (tm-30)
REVERT: D  279 MET cc_start: 0.7721 (mtm) cc_final: 0.7411 (mtp)
REVERT: D  379 GLN cc_start: 0.7733 (mt0) cc_final: 0.7471 (pt0)
REVERT: D  466 LYS cc_start: 0.8318 (tttt) cc_final: 0.8105 (tttm)
REVERT: D  559 ARG cc_start: 0.6787 (ttp-110) cc_final: 0.6501 (mtm-85)
  outliers start: 12
  outliers final: 4
  residues processed: 104
  average time/residue: 1.0274
  time to fit residues: 109.6878
Evaluate side-chains
  103 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 99
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 35 optimal weight:    0.0870
   chunk 52 optimal weight:    0.6980
   chunk 16 optimal weight:    8.9990
   chunk 36 optimal weight:    5.9990
   chunk 24 optimal weight:    7.9990
   chunk 3 optimal weight:    3.9990
   chunk 23 optimal weight:    0.5980
   chunk 55 optimal weight:    3.9990
   chunk 28 optimal weight:    3.9990
   chunk 47 optimal weight:    0.6980
   chunk 7 optimal weight:    1.9990
   overall best weight:    0.8160

-------------------------------------------------------------------------------
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 = 0.4043 r_free = 0.4043 target = 0.166825 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.136955 restraints weight = 4664.488|
|-----------------------------------------------------------------------------|
r_work (start): 0.3677 rms_B_bonded: 1.01
r_work: 0.3573 rms_B_bonded: 1.56 restraints_weight: 0.5000
r_work: 0.3485 rms_B_bonded: 2.51 restraints_weight: 0.2500
r_work (final): 0.3485
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8240
moved from start:          0.2707

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   5968  Z= 0.135
  Angle     :  0.522   6.089   8126  Z= 0.276
  Chirality :  0.038   0.118    878
  Planarity :  0.004   0.029    972
  Dihedral  :  7.309  55.989   1078
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 4.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.17 %
    Favored  : 98.83 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 10.03 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.28 (0.30), residues: 684
  helix:  2.47 (0.23), residues: 454
  sheet: -4.19 (0.48), residues: 20
  loop : -0.01 (0.38), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D 281 
 TYR   0.014   0.001   TYR D 491 
 PHE   0.015   0.001   PHE D 340 
 TRP   0.014   0.001   TRP D 256 
 HIS   0.002   0.001   HIS D 498 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 5960)
  covalent geometry    : angle       0.52154 ( 8110)
  SS BOND              : bond        0.00345 (    8)
  SS BOND              : angle       0.72553 (   16)
  hydrogen bonds       : bond        0.04993 (  384)
  hydrogen bonds       : angle       4.66972 ( 1122)

*********************** 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: 12
    poor density    : 100
  time to evaluate  : 0.181 
Fit side-chains
REVERT: A  247 GLU cc_start: 0.7186 (OUTLIER) cc_final: 0.6411 (mm-30)
REVERT: A  279 MET cc_start: 0.7768 (OUTLIER) cc_final: 0.7472 (mtp)
REVERT: A  379 GLN cc_start: 0.7743 (mt0) cc_final: 0.7514 (pt0)
REVERT: A  466 LYS cc_start: 0.8314 (tttt) cc_final: 0.8045 (tttm)
REVERT: D  247 GLU cc_start: 0.7191 (OUTLIER) cc_final: 0.6414 (mm-30)
REVERT: D  279 MET cc_start: 0.7779 (OUTLIER) cc_final: 0.7502 (mtp)
REVERT: D  379 GLN cc_start: 0.7754 (mt0) cc_final: 0.7506 (pt0)
REVERT: D  466 LYS cc_start: 0.8309 (tttt) cc_final: 0.8042 (tttm)
REVERT: D  559 ARG cc_start: 0.6920 (ttp-110) cc_final: 0.6660 (mtm-85)
  outliers start: 12
  outliers final: 4
  residues processed: 106
  average time/residue: 1.0207
  time to fit residues: 111.0681
Evaluate side-chains
  102 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 94
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
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  505 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 26 optimal weight:    1.9990
   chunk 61 optimal weight:    2.9990
   chunk 54 optimal weight:    4.9990
   chunk 32 optimal weight:    0.7980
   chunk 30 optimal weight:    5.9990
   chunk 67 optimal weight:    0.0970
   chunk 3 optimal weight:    3.9990
   chunk 51 optimal weight:    2.9990
   chunk 48 optimal weight:    0.5980
   chunk 18 optimal weight:    0.8980
   chunk 43 optimal weight:    0.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 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 = 0.4077 r_free = 0.4077 target = 0.168294 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.139810 restraints weight = 4802.879|
|-----------------------------------------------------------------------------|
r_work (start): 0.3736 rms_B_bonded: 0.98
r_work: 0.3632 rms_B_bonded: 1.52 restraints_weight: 0.5000
r_work: 0.3545 rms_B_bonded: 2.46 restraints_weight: 0.2500
r_work (final): 0.3545
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8243
moved from start:          0.2864

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= 0.126
  Angle     :  0.517   7.543   8126  Z= 0.271
  Chirality :  0.037   0.119    878
  Planarity :  0.004   0.029    972
  Dihedral  :  7.391  58.140   1078
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 4.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.88 %
    Favored  : 99.12 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 10.88 %
    Favored  : 86.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    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 aren not related in a simple way.
  whole:  2.38 (0.30), residues: 684
  helix:  2.57 (0.23), residues: 456
  sheet: -4.15 (0.48), residues: 20
  loop : -0.06 (0.37), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG D 501 
 TYR   0.014   0.001   TYR D 491 
 PHE   0.015   0.001   PHE D 340 
 TRP   0.016   0.001   TRP A 256 
 HIS   0.002   0.001   HIS D 382 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 5960)
  covalent geometry    : angle       0.51639 ( 8110)
  SS BOND              : bond        0.00294 (    8)
  SS BOND              : angle       0.57537 (   16)
  hydrogen bonds       : bond        0.04806 (  384)
  hydrogen bonds       : angle       4.54857 ( 1122)

*********************** 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
  111 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 98
  time to evaluate  : 0.229 
Fit side-chains
REVERT: A  247 GLU cc_start: 0.7208 (OUTLIER) cc_final: 0.6348 (mm-30)
REVERT: A  248 GLU cc_start: 0.7647 (pm20) cc_final: 0.7278 (tm-30)
REVERT: A  279 MET cc_start: 0.7787 (OUTLIER) cc_final: 0.7501 (mtp)
REVERT: A  379 GLN cc_start: 0.7770 (mt0) cc_final: 0.7568 (pt0)
REVERT: A  466 LYS cc_start: 0.8326 (tttt) cc_final: 0.8060 (tttm)
REVERT: D  247 GLU cc_start: 0.7214 (OUTLIER) cc_final: 0.6347 (mm-30)
REVERT: D  248 GLU cc_start: 0.7650 (pm20) cc_final: 0.7271 (tm-30)
REVERT: D  279 MET cc_start: 0.7776 (OUTLIER) cc_final: 0.7454 (mtp)
REVERT: D  379 GLN cc_start: 0.7774 (mt0) cc_final: 0.7566 (pt0)
REVERT: D  466 LYS cc_start: 0.8310 (tttt) cc_final: 0.8049 (tttm)
  outliers start: 13
  outliers final: 4
  residues processed: 103
  average time/residue: 0.9942
  time to fit residues: 105.2287
Evaluate side-chains
  105 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 97
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
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  505 LEU
Chi-restraints excluded: chain D residue  247 GLU
Chi-restraints excluded: chain D residue  279 MET
Chi-restraints excluded: chain D residue  372 GLU
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 50 optimal weight:    0.6980
   chunk 12 optimal weight:    5.9990
   chunk 46 optimal weight:    3.9990
   chunk 14 optimal weight:    0.5980
   chunk 41 optimal weight:    0.4980
   chunk 59 optimal weight:    3.9990
   chunk 55 optimal weight:    5.9990
   chunk 36 optimal weight:    3.9990
   chunk 22 optimal weight:    0.5980
   chunk 32 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9990
   overall best weight:    0.6782

-------------------------------------------------------------------------------
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 = 0.4075 r_free = 0.4075 target = 0.168203 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.139868 restraints weight = 4762.777|
|-----------------------------------------------------------------------------|
r_work (start): 0.3735 rms_B_bonded: 0.98
r_work: 0.3632 rms_B_bonded: 1.51 restraints_weight: 0.5000
r_work: 0.3546 rms_B_bonded: 2.44 restraints_weight: 0.2500
r_work (final): 0.3546
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8242
moved from start:          0.2948

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= 0.125
  Angle     :  0.519   7.816   8126  Z= 0.270
  Chirality :  0.037   0.119    878
  Planarity :  0.004   0.028    972
  Dihedral  :  7.484  59.811   1078
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 3.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.88 %
    Favored  : 99.12 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 10.54 %
    Favored  : 86.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    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 aren not related in a simple way.
  whole:  2.37 (0.30), residues: 684
  helix:  2.59 (0.23), residues: 456
  sheet: -4.13 (0.49), residues: 20
  loop : -0.12 (0.37), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D 501 
 TYR   0.014   0.001   TYR D 491 
 PHE   0.015   0.001   PHE D 340 
 TRP   0.017   0.001   TRP D 256 
 HIS   0.001   0.001   HIS D 562 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 5960)
  covalent geometry    : angle       0.51837 ( 8110)
  SS BOND              : bond        0.00290 (    8)
  SS BOND              : angle       0.67005 (   16)
  hydrogen bonds       : bond        0.04798 (  384)
  hydrogen bonds       : angle       4.53516 ( 1122)

*********************** 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: 17
    poor density    : 100
  time to evaluate  : 0.235 
Fit side-chains
REVERT: A  247 GLU cc_start: 0.7188 (OUTLIER) cc_final: 0.6339 (mm-30)
REVERT: A  248 GLU cc_start: 0.7620 (pm20) cc_final: 0.7273 (tm-30)
REVERT: A  279 MET cc_start: 0.7832 (OUTLIER) cc_final: 0.7541 (mtp)
REVERT: A  466 LYS cc_start: 0.8323 (tttt) cc_final: 0.7991 (tttp)
REVERT: D  247 GLU cc_start: 0.7199 (OUTLIER) cc_final: 0.6347 (mm-30)
REVERT: D  248 GLU cc_start: 0.7607 (pm20) cc_final: 0.7260 (tm-30)
REVERT: D  279 MET cc_start: 0.7811 (OUTLIER) cc_final: 0.7506 (mtp)
REVERT: D  281 ARG cc_start: 0.6813 (ptm-80) cc_final: 0.6561 (tmt-80)
REVERT: D  466 LYS cc_start: 0.8314 (tttt) cc_final: 0.7980 (tttp)
  outliers start: 17
  outliers final: 5
  residues processed: 109
  average time/residue: 0.9746
  time to fit residues: 109.2551
Evaluate side-chains
  106 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 97
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
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 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
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 5 optimal weight:    0.9990
   chunk 8 optimal weight:    0.9990
   chunk 16 optimal weight:    1.9990
   chunk 50 optimal weight:    0.8980
   chunk 7 optimal weight:    0.6980
   chunk 20 optimal weight:    3.9990
   chunk 62 optimal weight:    0.8980
   chunk 58 optimal weight:    0.7980
   chunk 17 optimal weight:    1.9990
   chunk 60 optimal weight:    1.9990
   chunk 39 optimal weight:    0.8980
   overall best weight:    0.8380

-------------------------------------------------------------------------------
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 = 0.4074 r_free = 0.4074 target = 0.167652 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.139165 restraints weight = 4759.760|
|-----------------------------------------------------------------------------|
r_work (start): 0.3727 rms_B_bonded: 0.98
r_work: 0.3625 rms_B_bonded: 1.51 restraints_weight: 0.5000
r_work: 0.3538 rms_B_bonded: 2.44 restraints_weight: 0.2500
r_work (final): 0.3538
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8254
moved from start:          0.3026

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   5968  Z= 0.134
  Angle     :  0.539   9.130   8126  Z= 0.281
  Chirality :  0.038   0.120    878
  Planarity :  0.004   0.028    972
  Dihedral  :  7.642  59.771   1078
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 4.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.17 %
    Favored  : 98.83 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 10.71 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.29 (0.30), residues: 684
  helix:  2.52 (0.23), residues: 454
  sheet: -4.06 (0.50), residues: 20
  loop : -0.13 (0.36), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 281 
 TYR   0.015   0.001   TYR D 491 
 PHE   0.017   0.001   PHE A 340 
 TRP   0.016   0.001   TRP D 256 
 HIS   0.002   0.001   HIS D 562 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 5960)
  covalent geometry    : angle       0.53869 ( 8110)
  SS BOND              : bond        0.00300 (    8)
  SS BOND              : angle       0.80516 (   16)
  hydrogen bonds       : bond        0.04972 (  384)
  hydrogen bonds       : angle       4.61492 ( 1122)

*********************** 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
  117 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 100
  time to evaluate  : 0.145 
Fit side-chains
REVERT: A  247 GLU cc_start: 0.7227 (OUTLIER) cc_final: 0.6454 (mm-30)
REVERT: A  279 MET cc_start: 0.7813 (OUTLIER) cc_final: 0.7504 (mtp)
REVERT: A  466 LYS cc_start: 0.8331 (tttt) cc_final: 0.7990 (tttp)
REVERT: D  247 GLU cc_start: 0.7228 (OUTLIER) cc_final: 0.6449 (mm-30)
REVERT: D  279 MET cc_start: 0.7841 (OUTLIER) cc_final: 0.7528 (mtp)
REVERT: D  281 ARG cc_start: 0.6905 (ptm-80) cc_final: 0.6587 (tmt-80)
REVERT: D  466 LYS cc_start: 0.8320 (tttt) cc_final: 0.7978 (tttp)
  outliers start: 17
  outliers final: 13
  residues processed: 108
  average time/residue: 0.9322
  time to fit residues: 103.4349
Evaluate side-chains
  115 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 98
  time to evaluate  : 0.136 
-------------------------------------------------------------------------------
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  263 LEU
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  375 GLU
Chi-restraints excluded: chain A residue  379 GLN
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  263 LEU
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  379 GLN
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 41 optimal weight:    0.4980
   chunk 1 optimal weight:    1.9990
   chunk 56 optimal weight:    0.8980
   chunk 24 optimal weight:   10.0000
   chunk 30 optimal weight:    0.7980
   chunk 13 optimal weight:    0.5980
   chunk 23 optimal weight:    0.6980
   chunk 9 optimal weight:    0.8980
   chunk 4 optimal weight:    2.9990
   chunk 18 optimal weight:    0.8980
   chunk 26 optimal weight:    1.9990
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.4078 r_free = 0.4078 target = 0.168014 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.139722 restraints weight = 4753.654|
|-----------------------------------------------------------------------------|
r_work (start): 0.3734 rms_B_bonded: 0.98
r_work: 0.3631 rms_B_bonded: 1.51 restraints_weight: 0.5000
r_work: 0.3546 rms_B_bonded: 2.43 restraints_weight: 0.2500
r_work (final): 0.3546
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8245
moved from start:          0.3086

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= 0.128
  Angle     :  0.548  10.587   8126  Z= 0.282
  Chirality :  0.037   0.119    878
  Planarity :  0.004   0.028    972
  Dihedral  :  7.631  59.669   1078
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 4.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.17 %
    Favored  : 98.83 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 10.88 %
    Favored  : 86.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    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 aren not related in a simple way.
  whole:  2.31 (0.30), residues: 684
  helix:  2.54 (0.23), residues: 456
  sheet: -4.01 (0.51), residues: 20
  loop : -0.17 (0.36), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 281 
 TYR   0.015   0.001   TYR A 491 
 PHE   0.016   0.001   PHE D 340 
 TRP   0.016   0.001   TRP A 256 
 HIS   0.002   0.001   HIS A 498 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 5960)
  covalent geometry    : angle       0.54752 ( 8110)
  SS BOND              : bond        0.00288 (    8)
  SS BOND              : angle       0.72188 (   16)
  hydrogen bonds       : bond        0.04821 (  384)
  hydrogen bonds       : angle       4.56217 ( 1122)

*********************** 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
  119 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 101
  time to evaluate  : 0.158 
Fit side-chains
REVERT: A  247 GLU cc_start: 0.7244 (OUTLIER) cc_final: 0.6368 (mm-30)
REVERT: A  248 GLU cc_start: 0.7698 (pm20) cc_final: 0.7297 (tm-30)
REVERT: A  279 MET cc_start: 0.7810 (OUTLIER) cc_final: 0.7537 (mtp)
REVERT: A  466 LYS cc_start: 0.8324 (tttt) cc_final: 0.7981 (tttp)
REVERT: D  247 GLU cc_start: 0.7253 (OUTLIER) cc_final: 0.6378 (mm-30)
REVERT: D  248 GLU cc_start: 0.7692 (pm20) cc_final: 0.7286 (tm-30)
REVERT: D  279 MET cc_start: 0.7823 (OUTLIER) cc_final: 0.7529 (mtp)
REVERT: D  466 LYS cc_start: 0.8319 (tttt) cc_final: 0.7973 (tttp)
  outliers start: 18
  outliers final: 10
  residues processed: 109
  average time/residue: 0.9440
  time to fit residues: 105.6946
Evaluate side-chains
  111 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 97
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
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  263 LEU
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  263 LEU
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 66 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9980
   chunk 63 optimal weight:    4.9990
   chunk 61 optimal weight:    3.9990
   chunk 27 optimal weight:    3.9990
   chunk 64 optimal weight:    2.9990
   chunk 38 optimal weight:    0.4980
   chunk 26 optimal weight:    1.9990
   chunk 46 optimal weight:    5.9990
   chunk 44 optimal weight:    2.9990
   chunk 4 optimal weight:    3.9990
   overall best weight:    1.8986

-------------------------------------------------------------------------------
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 = 0.4045 r_free = 0.4045 target = 0.164922 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.135930 restraints weight = 4751.029|
|-----------------------------------------------------------------------------|
r_work (start): 0.3686 rms_B_bonded: 0.99
r_work: 0.3581 rms_B_bonded: 1.51 restraints_weight: 0.5000
r_work: 0.3492 rms_B_bonded: 2.43 restraints_weight: 0.2500
r_work (final): 0.3492
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8297
moved from start:          0.3088

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.074   5968  Z= 0.204
  Angle     :  0.640  10.583   8126  Z= 0.335
  Chirality :  0.042   0.132    878
  Planarity :  0.005   0.032    972
  Dihedral  :  8.212  57.784   1078
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 4.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.88 %
    Favored  : 99.12 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 11.22 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.09 (0.30), residues: 684
  helix:  2.21 (0.23), residues: 454
  sheet:  None (None), residues: 0
  loop : -0.28 (0.34), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 281 
 TYR   0.014   0.002   TYR D 491 
 PHE   0.024   0.002   PHE A 340 
 TRP   0.014   0.002   TRP A 354 
 HIS   0.003   0.001   HIS A 562 

Details of bonding type rmsd
  covalent geometry    : bond        0.00452 ( 5960)
  covalent geometry    : angle       0.63952 ( 8110)
  SS BOND              : bond        0.00397 (    8)
  SS BOND              : angle       0.80908 (   16)
  hydrogen bonds       : bond        0.05885 (  384)
  hydrogen bonds       : angle       5.01445 ( 1122)

*********************** 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
  117 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 99
  time to evaluate  : 0.285 
Fit side-chains
REVERT: A  247 GLU cc_start: 0.7273 (OUTLIER) cc_final: 0.6356 (mm-30)
REVERT: A  248 GLU cc_start: 0.7712 (pm20) cc_final: 0.7245 (tm-30)
REVERT: A  279 MET cc_start: 0.7879 (OUTLIER) cc_final: 0.7588 (mtp)
REVERT: A  466 LYS cc_start: 0.8356 (tttt) cc_final: 0.8007 (tttp)
REVERT: D  247 GLU cc_start: 0.7261 (OUTLIER) cc_final: 0.6326 (mm-30)
REVERT: D  248 GLU cc_start: 0.7711 (pm20) cc_final: 0.7235 (tm-30)
REVERT: D  279 MET cc_start: 0.7877 (OUTLIER) cc_final: 0.7586 (mtp)
REVERT: D  466 LYS cc_start: 0.8349 (tttt) cc_final: 0.7998 (tttp)
  outliers start: 18
  outliers final: 8
  residues processed: 107
  average time/residue: 0.9670
  time to fit residues: 106.4425
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  : 0.236 
-------------------------------------------------------------------------------
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  263 LEU
Chi-restraints excluded: chain A residue  279 MET
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  263 LEU
Chi-restraints excluded: chain D residue  279 MET
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 66 optimal weight:    0.5980
   chunk 21 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9980
   chunk 63 optimal weight:    4.9990
   chunk 30 optimal weight:    3.9990
   chunk 45 optimal weight:    2.9990
   chunk 2 optimal weight:    8.9990
   chunk 28 optimal weight:    0.9990
   chunk 20 optimal weight:    0.8980
   chunk 49 optimal weight:    4.9990
   chunk 62 optimal weight:    0.7980
   overall best weight:    0.8582

-------------------------------------------------------------------------------
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 = 0.4066 r_free = 0.4066 target = 0.166871 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.138228 restraints weight = 4804.399|
|-----------------------------------------------------------------------------|
r_work (start): 0.3717 rms_B_bonded: 1.00
r_work: 0.3613 rms_B_bonded: 1.52 restraints_weight: 0.5000
r_work: 0.3526 rms_B_bonded: 2.46 restraints_weight: 0.2500
r_work (final): 0.3526
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8265
moved from start:          0.3121

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   5968  Z= 0.138
  Angle     :  0.567  11.171   8126  Z= 0.292
  Chirality :  0.038   0.118    878
  Planarity :  0.004   0.028    972
  Dihedral  :  8.283  59.919   1078
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 4.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.17 %
    Favored  : 98.83 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 11.56 %
    Favored  : 86.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    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 aren not related in a simple way.
  whole:  2.32 (0.30), residues: 684
  helix:  2.41 (0.23), residues: 454
  sheet:  None (None), residues: 0
  loop : -0.25 (0.35), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 281 
 TYR   0.014   0.001   TYR D 491 
 PHE   0.017   0.001   PHE A 340 
 TRP   0.016   0.001   TRP A 256 
 HIS   0.002   0.001   HIS A 562 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 5960)
  covalent geometry    : angle       0.56652 ( 8110)
  SS BOND              : bond        0.00325 (    8)
  SS BOND              : angle       0.73406 (   16)
  hydrogen bonds       : bond        0.05081 (  384)
  hydrogen bonds       : angle       4.71832 ( 1122)

********************** 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
  114 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 101
  time to evaluate  : 0.236 
Fit side-chains
REVERT: A  247 GLU cc_start: 0.7239 (OUTLIER) cc_final: 0.6340 (mm-30)
REVERT: A  248 GLU cc_start: 0.7663 (pm20) cc_final: 0.7268 (tm-30)
REVERT: A  279 MET cc_start: 0.7829 (OUTLIER) cc_final: 0.7541 (mtp)
REVERT: A  466 LYS cc_start: 0.8354 (tttt) cc_final: 0.8009 (tttp)
REVERT: D  247 GLU cc_start: 0.7229 (OUTLIER) cc_final: 0.6332 (mm-30)
REVERT: D  248 GLU cc_start: 0.7664 (pm20) cc_final: 0.7257 (tm-30)
REVERT: D  279 MET cc_start: 0.7822 (OUTLIER) cc_final: 0.7523 (mtp)
REVERT: D  466 LYS cc_start: 0.8340 (tttt) cc_final: 0.7994 (tttp)
  outliers start: 13
  outliers final: 9
  residues processed: 108
  average time/residue: 1.0207
  time to fit residues: 113.2846
Evaluate side-chains
  112 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 99
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
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  263 LEU
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  263 LEU
Chi-restraints excluded: chain D residue  279 MET
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 12 optimal weight:    4.9990
   chunk 48 optimal weight:    0.5980
   chunk 7 optimal weight:    1.9990
   chunk 64 optimal weight:    2.9990
   chunk 59 optimal weight:    2.9990
   chunk 61 optimal weight:    2.9990
   chunk 20 optimal weight:    3.9990
   chunk 19 optimal weight:    1.9990
   chunk 14 optimal weight:    4.9990
   chunk 3 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9990
   overall best weight:    1.5188

-------------------------------------------------------------------------------
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 = 0.4048 r_free = 0.4048 target = 0.165262 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.136578 restraints weight = 4703.184|
|-----------------------------------------------------------------------------|
r_work (start): 0.3695 rms_B_bonded: 0.97
r_work: 0.3588 rms_B_bonded: 1.50 restraints_weight: 0.5000
r_work: 0.3501 rms_B_bonded: 2.41 restraints_weight: 0.2500
r_work (final): 0.3501
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8289
moved from start:          0.3127

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.066   5968  Z= 0.180
  Angle     :  0.621  10.740   8126  Z= 0.324
  Chirality :  0.041   0.126    878
  Planarity :  0.004   0.027    972
  Dihedral  :  8.698  59.960   1078
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 4.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.73 %
    Favored  : 99.27 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 12.07 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.06 (0.30), residues: 684
  helix:  2.20 (0.23), residues: 454
  sheet:  None (None), residues: 0
  loop : -0.33 (0.34), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 281 
 TYR   0.014   0.002   TYR A 491 
 PHE   0.022   0.002   PHE A 340 
 TRP   0.014   0.002   TRP A 354 
 HIS   0.003   0.001   HIS D 498 

Details of bonding type rmsd
  covalent geometry    : bond        0.00397 ( 5960)
  covalent geometry    : angle       0.62106 ( 8110)
  SS BOND              : bond        0.00371 (    8)
  SS BOND              : angle       0.80766 (   16)
  hydrogen bonds       : bond        0.05669 (  384)
  hydrogen bonds       : angle       4.94430 ( 1122)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3644.77 seconds
wall clock time: 62 minutes 42.86 seconds (3762.86 seconds total)