Starting phenix.real_space_refine
on Thu Feb  5 00:18:01 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9o95_70242/02_2026/9o95_70242.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9o95_70242/02_2026/9o95_70242.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9o95_70242/02_2026/9o95_70242.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9o95_70242/02_2026/9o95_70242.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9o95_70242/02_2026/9o95_70242.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9o95_70242/02_2026/9o95_70242.map"
  }
  resolution = 3.2
  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=   0.002 sd=   0.223
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: 6
    Type Number    sf(0)   Gaussians
     S      40      5.16       5
     Cl      4      4.86       5
     C    4380      2.51       5
     N    1120      2.21       5
     O    1126      1.98       5
     H    6970      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 13640
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 6818
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 444, 6818
          Classifications: {'peptide': 444}
          Link IDs: {'PTRANS': 19, 'TRANS': 424}
    Chain: "B"
      Number of atoms: 6818
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 444, 6818
          Classifications: {'peptide': 444}
          Link IDs: {'PTRANS': 19, 'TRANS': 424}
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' CL': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' CL': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 2.88, per 1000 atoms: 0.21
  Number of scatterers: 13640
  At special positions: 0
  Unit cell: (76.26, 113.98, 74.62, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Cl      4     17.00
     S      40     16.00
     O    1126      8.00
     N    1120      7.00
     C    4380      6.00
     H    6970      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.10
  Conformation dependent library (CDL) restraints added in 592.0 milliseconds
  

  1768 Ramachandran restraints generated.
    884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1548

  Finding SS restraints...
    Secondary structure from input PDB file:
      48 helices and 0 sheets defined
      84.8% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.24
  Creating SS restraints...
    Processing helix  chain 'A' and resid 17 through 26
    Processing helix  chain 'A' and resid 32 through 67
    Processing helix  chain 'A' and resid 74 through 101
      removed outlier: 3.634A  pdb=" N   SER A  86 " --> pdb=" O   ALA A  82 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   GLY A  93 " --> pdb=" O   LEU A  89 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 102 through 105
    Processing helix  chain 'A' and resid 108 through 117
    Processing helix  chain 'A' and resid 123 through 141
      Proline residue:  A 129  - end of helix
    Processing helix  chain 'A' and resid 147 through 167
    Processing helix  chain 'A' and resid 170 through 191
      removed outlier: 3.550A  pdb=" N   ARG A 174 " --> pdb=" O   GLY A 170 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 192 through 204
      removed outlier: 3.583A  pdb=" N   ILE A 200 " --> pdb=" O   GLY A 196 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 214 through 233
      removed outlier: 3.742A  pdb=" N   PHE A 232 " --> pdb=" O   MET A 228 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 248 through 250
      No H-bonds generated for 'chain 'A' and resid 248 through 250'
    Processing helix  chain 'A' and resid 251 through 285
      removed outlier: 3.966A  pdb=" N   TYR A 255 " --> pdb=" O   THR A 251 " (cutoff:3.500A)
      Proline residue:  A 267  - end of helix
      removed outlier: 3.611A  pdb=" N   HIS A 281 " --> pdb=" O   GLN A 277 " (cutoff:3.500A)
      removed outlier: 4.019A  pdb=" N   ARG A 282 " --> pdb=" O   ASP A 278 " (cutoff:3.500A)
      removed outlier: 4.105A  pdb=" N   VAL A 283 " --> pdb=" O   LEU A 279 " (cutoff:3.500A)
      removed outlier: 3.926A  pdb=" N   HIS A 284 " --> pdb=" O   LEU A 280 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 287 through 309
    Processing helix  chain 'A' and resid 310 through 313
    Processing helix  chain 'A' and resid 318 through 325
      removed outlier: 4.336A  pdb=" N   ILE A 322 " --> pdb=" O   ASN A 318 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 329 through 349
    Processing helix  chain 'A' and resid 356 through 379
      removed outlier: 3.529A  pdb=" N   VAL A 374 " --> pdb=" O   ALA A 370 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 380 through 383
      removed outlier: 3.601A  pdb=" N   HIS A 383 " --> pdb=" O   PRO A 380 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 380 through 383'
    Processing helix  chain 'A' and resid 385 through 395
      removed outlier: 4.180A  pdb=" N   PHE A 389 " --> pdb=" O   GLU A 385 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   ALA A 390 " --> pdb=" O   ALA A 386 " (cutoff:3.500A)
      removed outlier: 4.415A  pdb=" N   GLY A 395 " --> pdb=" O   ILE A 391 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 395 through 402
      removed outlier: 3.560A  pdb=" N   ALA A 399 " --> pdb=" O   GLY A 395 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 404 through 417
    Processing helix  chain 'A' and resid 418 through 420
      No H-bonds generated for 'chain 'A' and resid 418 through 420'
    Processing helix  chain 'A' and resid 421 through 439
    Processing helix  chain 'A' and resid 443 through 459
      removed outlier: 3.680A  pdb=" N   GLU A 459 " --> pdb=" O   LYS A 455 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 18 through 26
    Processing helix  chain 'B' and resid 32 through 67
    Processing helix  chain 'B' and resid 74 through 101
      removed outlier: 3.634A  pdb=" N   SER B  86 " --> pdb=" O   ALA B  82 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   GLY B  93 " --> pdb=" O   LEU B  89 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 102 through 105
    Processing helix  chain 'B' and resid 108 through 117
    Processing helix  chain 'B' and resid 123 through 141
      Proline residue:  B 129  - end of helix
    Processing helix  chain 'B' and resid 147 through 167
    Processing helix  chain 'B' and resid 170 through 191
      removed outlier: 3.551A  pdb=" N   ARG B 174 " --> pdb=" O   GLY B 170 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 192 through 204
      removed outlier: 3.579A  pdb=" N   ILE B 200 " --> pdb=" O   GLY B 196 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 214 through 233
      removed outlier: 3.742A  pdb=" N   PHE B 232 " --> pdb=" O   MET B 228 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 248 through 250
      No H-bonds generated for 'chain 'B' and resid 248 through 250'
    Processing helix  chain 'B' and resid 251 through 285
      removed outlier: 3.954A  pdb=" N   TYR B 255 " --> pdb=" O   THR B 251 " (cutoff:3.500A)
      Proline residue:  B 267  - end of helix
      removed outlier: 3.611A  pdb=" N   HIS B 281 " --> pdb=" O   GLN B 277 " (cutoff:3.500A)
      removed outlier: 4.015A  pdb=" N   ARG B 282 " --> pdb=" O   ASP B 278 " (cutoff:3.500A)
      removed outlier: 4.102A  pdb=" N   VAL B 283 " --> pdb=" O   LEU B 279 " (cutoff:3.500A)
      removed outlier: 3.924A  pdb=" N   HIS B 284 " --> pdb=" O   LEU B 280 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 287 through 309
    Processing helix  chain 'B' and resid 310 through 313
    Processing helix  chain 'B' and resid 318 through 325
      removed outlier: 4.336A  pdb=" N   ILE B 322 " --> pdb=" O   ASN B 318 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 329 through 349
    Processing helix  chain 'B' and resid 356 through 379
      removed outlier: 3.529A  pdb=" N   VAL B 374 " --> pdb=" O   ALA B 370 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 380 through 383
      removed outlier: 3.600A  pdb=" N   HIS B 383 " --> pdb=" O   PRO B 380 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 380 through 383'
    Processing helix  chain 'B' and resid 385 through 395
      removed outlier: 4.179A  pdb=" N   PHE B 389 " --> pdb=" O   GLU B 385 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   ALA B 390 " --> pdb=" O   ALA B 386 " (cutoff:3.500A)
      removed outlier: 4.415A  pdb=" N   GLY B 395 " --> pdb=" O   ILE B 391 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 395 through 402
      removed outlier: 3.559A  pdb=" N   ALA B 399 " --> pdb=" O   GLY B 395 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 404 through 417
    Processing helix  chain 'B' and resid 418 through 420
      No H-bonds generated for 'chain 'B' and resid 418 through 420'
    Processing helix  chain 'B' and resid 421 through 439
    Processing helix  chain 'B' and resid 443 through 459
      removed outlier: 3.683A  pdb=" N   GLU B 459 " --> pdb=" O   LYS B 455 " (cutoff:3.500A)

    523 hydrogen bonds defined for protein.
    1557 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: 2.14

  Time building geometry restraints manager: 1.61 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 6964
        1.03 -     1.23: 7
        1.23 -     1.42: 2735
        1.42 -     1.61: 4000
        1.61 -     1.81: 74
  Bond restraints: 13780
  Sorted by residual:
  bond pdb=" N   ARG A  17 "
       pdb=" CA  ARG A  17 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 3.00e+00
  bond pdb=" N   ARG B  17 "
       pdb=" CA  ARG B  17 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.76e+00
  bond pdb=" C   ARG B 205 "
       pdb=" N   PRO B 206 "
    ideal  model  delta    sigma   weight residual
    1.330  1.349 -0.019 1.19e-02 7.06e+03 2.54e+00
  bond pdb=" C   ARG A 205 "
       pdb=" N   PRO A 206 "
    ideal  model  delta    sigma   weight residual
    1.330  1.349 -0.019 1.19e-02 7.06e+03 2.46e+00
  bond pdb=" N   ARG A  17 "
       pdb=" H   ARG A  17 "
    ideal  model  delta    sigma   weight residual
    0.860  0.891 -0.031 2.00e-02 2.50e+03 2.35e+00
  ... (remaining 13775 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     6.98: 25022
        6.98 -    13.96: 0
       13.96 -    20.94: 0
       20.94 -    27.92: 0
       27.92 -    34.90: 6
  Bond angle restraints: 25028
  Sorted by residual:
  angle pdb=" C   LEU B 304 "
        pdb=" CA  LEU B 304 "
        pdb=" HA  LEU B 304 "
      ideal   model   delta    sigma   weight residual
     109.00   74.10   34.90 3.00e+00 1.11e-01 1.35e+02
  angle pdb=" C   LEU A 304 "
        pdb=" CA  LEU A 304 "
        pdb=" HA  LEU A 304 "
      ideal   model   delta    sigma   weight residual
     109.00   74.20   34.80 3.00e+00 1.11e-01 1.35e+02
  angle pdb=" CB  LEU A 304 "
        pdb=" CA  LEU A 304 "
        pdb=" HA  LEU A 304 "
      ideal   model   delta    sigma   weight residual
     109.00   74.54   34.46 3.00e+00 1.11e-01 1.32e+02
  angle pdb=" CB  LEU B 304 "
        pdb=" CA  LEU B 304 "
        pdb=" HA  LEU B 304 "
      ideal   model   delta    sigma   weight residual
     109.00   74.60   34.40 3.00e+00 1.11e-01 1.32e+02
  angle pdb=" N   LEU A 304 "
        pdb=" CA  LEU A 304 "
        pdb=" HA  LEU A 304 "
      ideal   model   delta    sigma   weight residual
     110.00   76.04   33.96 3.00e+00 1.11e-01 1.28e+02
  ... (remaining 25023 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.87: 5623
       16.87 -    33.75: 424
       33.75 -    50.62: 192
       50.62 -    67.49: 137
       67.49 -    84.37: 24
  Dihedral angle restraints: 6400
    sinusoidal: 3498
      harmonic: 2902
  Sorted by residual:
  dihedral pdb=" C   LEU B 304 "
           pdb=" N   LEU B 304 "
           pdb=" CA  LEU B 304 "
           pdb=" CB  LEU B 304 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -132.02    9.42     0      2.50e+00 1.60e-01 1.42e+01
  dihedral pdb=" C   LEU A 304 "
           pdb=" N   LEU A 304 "
           pdb=" CA  LEU A 304 "
           pdb=" CB  LEU A 304 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -131.99    9.39     0      2.50e+00 1.60e-01 1.41e+01
  dihedral pdb=" CA  GLU A 203 "
           pdb=" C   GLU A 203 "
           pdb=" N   MET A 204 "
           pdb=" CA  MET A 204 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -162.94  -17.06     0      5.00e+00 4.00e-02 1.16e+01
  ... (remaining 6397 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.073: 1020
       0.073 -    0.146: 64
       0.146 -    0.220: 0
       0.220 -    0.293: 0
       0.293 -    0.366: 2
  Chirality restraints: 1086
  Sorted by residual:
  chirality pdb=" CA  LEU B 304 "
            pdb=" N   LEU B 304 "
            pdb=" C   LEU B 304 "
            pdb=" CB  LEU B 304 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.14    0.37 2.00e-01 2.50e+01 3.35e+00
  chirality pdb=" CA  LEU A 304 "
            pdb=" N   LEU A 304 "
            pdb=" C   LEU A 304 "
            pdb=" CB  LEU A 304 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.15    0.36 2.00e-01 2.50e+01 3.29e+00
  chirality pdb=" CA  ILE A 213 "
            pdb=" N   ILE A 213 "
            pdb=" C   ILE A 213 "
            pdb=" CB  ILE A 213 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.77e-01
  ... (remaining 1083 not shown)

  Planarity restraints: 2008
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 423 "    0.023 5.00e-02 4.00e+02   3.42e-02 1.87e+00
        pdb=" N   PRO A 424 "   -0.059 5.00e-02 4.00e+02
        pdb=" CA  PRO A 424 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A 424 "    0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 423 "   -0.023 5.00e-02 4.00e+02   3.41e-02 1.86e+00
        pdb=" N   PRO B 424 "    0.059 5.00e-02 4.00e+02
        pdb=" CA  PRO B 424 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO B 424 "   -0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 149 "   -0.022 5.00e-02 4.00e+02   3.26e-02 1.70e+00
        pdb=" N   PRO A 150 "    0.056 5.00e-02 4.00e+02
        pdb=" CA  PRO A 150 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A 150 "   -0.018 5.00e-02 4.00e+02
  ... (remaining 2005 not shown)

  Histogram of nonbonded interaction distances:
        1.60 -     2.20: 679
        2.20 -     2.80: 27377
        2.80 -     3.40: 38360
        3.40 -     4.00: 49358
        4.00 -     4.60: 78422
  Nonbonded interactions: 194196
  Sorted by model distance:
  nonbonded pdb=" HH  TYR A 419 "
            pdb=" OE1 GLU B 414 "
     model   vdw
     1.601 2.450
  nonbonded pdb=" OE1 GLU A 414 "
            pdb=" HH  TYR B 419 "
     model   vdw
     1.601 2.450
  nonbonded pdb=" O   GLN B 153 "
            pdb="HD21 ASN B 157 "
     model   vdw
     1.641 2.450
  nonbonded pdb=" O   GLN A 153 "
            pdb="HD21 ASN A 157 "
     model   vdw
     1.641 2.450
  nonbonded pdb=" HA  LEU B 304 "
            pdb=" HB3 LEU B 304 "
     model   vdw
     1.645 1.952
  ... (remaining 194191 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.660
  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:             0.090
  Extract box with map and model:          0.210
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     13.190
  Find NCS groups from input model:        0.080
  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:1.300
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.640
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8389
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      :  0.003   0.034   6810  Z= 0.142
  Angle     :  0.512   4.275   9242  Z= 0.299
  Chirality :  0.039   0.366   1086
  Planarity :  0.004   0.034   1160
  Dihedral  : 13.894  80.367   2404
  Min Nonbonded Distance : 2.084

Molprobity Statistics.
  All-atom Clashscore : 2.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Rotamer:
    Outliers :  0.30 %
    Allowed  :  6.87 %
    Favored  : 92.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.67 (0.29), residues: 884
  helix:  2.64 (0.21), residues: 664
  sheet:  None (None), residues: 0
  loop : -1.10 (0.39), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  17 
 TYR   0.011   0.001   TYR B  75 
 PHE   0.011   0.001   PHE A 307 
 TRP   0.007   0.001   TRP A 253 
 HIS   0.002   0.001   HIS B  70 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 6810)
  covalent geometry    : angle       0.51170 ( 9242)
  hydrogen bonds       : bond        0.14653 (  523)
  hydrogen bonds       : angle       5.14860 ( 1557)

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

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

  1768 Ramachandran restraints generated.
    884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1768 Ramachandran restraints generated.
    884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 74
  time to evaluate  : 0.306 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  391 ILE cc_start: 0.8505 (mt) cc_final: 0.8247 (mm)
REVERT: B  391 ILE cc_start: 0.8509 (mt) cc_final: 0.8253 (mm)
  outliers start: 2
  outliers final: 1
  residues processed: 74
  average time/residue: 0.2544
  time to fit residues: 23.5759
Evaluate side-chains
  71 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 70
  time to evaluate  : 0.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  455 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 49 optimal weight:    5.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    6.9990
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    0.8980
   chunk 45 optimal weight:    1.9990
   chunk 74 optimal weight:    0.7980
   overall best weight:    1.5386

-------------------------------------------------------------------------------
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 = 0.3041 r_free = 0.3041 target = 0.102522 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2799 r_free = 0.2799 target = 0.084948 restraints weight = 23690.795|
|-----------------------------------------------------------------------------|
r_work (start): 0.2805 rms_B_bonded: 1.80
r_work: 0.2706 rms_B_bonded: 2.05 restraints_weight: 0.5000
r_work: 0.2583 rms_B_bonded: 3.52 restraints_weight: 0.2500
r_work (final): 0.2583
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8406
moved from start:          0.0585

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   6810  Z= 0.181
  Angle     :  0.507   4.360   9242  Z= 0.279
  Chirality :  0.041   0.338   1086
  Planarity :  0.005   0.043   1160
  Dihedral  :  4.281  47.819    950
  Min Nonbonded Distance : 2.340

Molprobity Statistics.
  All-atom Clashscore : 1.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  7.31 %
    Favored  : 92.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.28 (0.28), residues: 884
  helix:  2.33 (0.20), residues: 678
  sheet:  None (None), residues: 0
  loop : -1.42 (0.39), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  17 
 TYR   0.011   0.002   TYR A 419 
 PHE   0.014   0.001   PHE A 307 
 TRP   0.006   0.001   TRP B 253 
 HIS   0.003   0.001   HIS A  70 

Details of bonding type rmsd
  covalent geometry    : bond        0.00434 ( 6810)
  covalent geometry    : angle       0.50696 ( 9242)
  hydrogen bonds       : bond        0.06547 (  523)
  hydrogen bonds       : angle       4.48232 ( 1557)

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

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

  1768 Ramachandran restraints generated.
    884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1768 Ramachandran restraints generated.
    884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 73
  time to evaluate  : 0.235 
Fit side-chains
REVERT: A  391 ILE cc_start: 0.8347 (mt) cc_final: 0.8147 (mm)
REVERT: A  417 ASP cc_start: 0.8261 (t0) cc_final: 0.7861 (t0)
REVERT: B  417 ASP cc_start: 0.8267 (t0) cc_final: 0.7860 (t0)
  outliers start: 1
  outliers final: 1
  residues processed: 73
  average time/residue: 0.2319
  time to fit residues: 21.6046
Evaluate side-chains
  70 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 69
  time to evaluate  : 0.231 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  455 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 69 optimal weight:    0.5980
   chunk 38 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9980
   chunk 18 optimal weight:    0.9980
   chunk 23 optimal weight:    0.5980
   chunk 2 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   chunk 57 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   chunk 63 optimal weight:    1.9990
   chunk 84 optimal weight:    0.9990
   overall best weight:    0.8382

-------------------------------------------------------------------------------
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 = 0.3073 r_free = 0.3073 target = 0.104951 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2833 r_free = 0.2833 target = 0.087299 restraints weight = 23551.434|
|-----------------------------------------------------------------------------|
r_work (start): 0.2839 rms_B_bonded: 1.80
r_work: 0.2741 rms_B_bonded: 2.06 restraints_weight: 0.5000
r_work: 0.2617 rms_B_bonded: 3.53 restraints_weight: 0.2500
r_work (final): 0.2617
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8353
moved from start:          0.0895

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6810  Z= 0.124
  Angle     :  0.455   4.370   9242  Z= 0.247
  Chirality :  0.040   0.333   1086
  Planarity :  0.005   0.044   1160
  Dihedral  :  3.726  16.552    946
  Min Nonbonded Distance : 2.367

Molprobity Statistics.
  All-atom Clashscore : 1.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  0.45 %
    Allowed  :  8.21 %
    Favored  : 91.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.60 (0.28), residues: 884
  helix:  2.59 (0.20), residues: 678
  sheet:  None (None), residues: 0
  loop : -1.45 (0.39), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  17 
 TYR   0.005   0.001   TYR B  75 
 PHE   0.011   0.001   PHE B  37 
 TRP   0.004   0.001   TRP B 253 
 HIS   0.002   0.001   HIS A  70 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 6810)
  covalent geometry    : angle       0.45532 ( 9242)
  hydrogen bonds       : bond        0.05321 (  523)
  hydrogen bonds       : angle       4.16257 ( 1557)

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

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

  1768 Ramachandran restraints generated.
    884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1768 Ramachandran restraints generated.
    884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 65
  time to evaluate  : 0.322 
Fit side-chains
REVERT: A  417 ASP cc_start: 0.8235 (t0) cc_final: 0.7804 (t0)
REVERT: B  417 ASP cc_start: 0.8235 (t0) cc_final: 0.7806 (t0)
  outliers start: 3
  outliers final: 1
  residues processed: 67
  average time/residue: 0.2658
  time to fit residues: 22.0362
Evaluate side-chains
  63 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 62
  time to evaluate  : 0.384 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  455 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 80 optimal weight:    0.5980
   chunk 33 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 15 optimal weight:    3.9990
   chunk 58 optimal weight:    1.9990
   chunk 52 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9990
   chunk 40 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9980
   chunk 18 optimal weight:    2.9990
   chunk 47 optimal weight:    1.9990
   overall best weight:    1.3186

-------------------------------------------------------------------------------
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 = 0.3083 r_free = 0.3083 target = 0.104907 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2847 r_free = 0.2847 target = 0.087701 restraints weight = 23710.621|
|-----------------------------------------------------------------------------|
r_work (start): 0.2820 rms_B_bonded: 1.74
r_work: 0.2723 rms_B_bonded: 1.99 restraints_weight: 0.5000
r_work: 0.2603 rms_B_bonded: 3.40 restraints_weight: 0.2500
r_work (final): 0.2603
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8442
moved from start:          0.1009

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6810  Z= 0.157
  Angle     :  0.472   4.347   9242  Z= 0.257
  Chirality :  0.040   0.331   1086
  Planarity :  0.005   0.046   1160
  Dihedral  :  3.724  16.818    946
  Min Nonbonded Distance : 2.374

Molprobity Statistics.
  All-atom Clashscore : 1.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  :  8.36 %
    Favored  : 90.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.50 (0.28), residues: 884
  helix:  2.54 (0.20), residues: 678
  sheet:  None (None), residues: 0
  loop : -1.54 (0.39), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  64 
 TYR   0.008   0.001   TYR B 419 
 PHE   0.013   0.001   PHE A 307 
 TRP   0.005   0.001   TRP B 253 
 HIS   0.002   0.001   HIS B  70 

Details of bonding type rmsd
  covalent geometry    : bond        0.00380 ( 6810)
  covalent geometry    : angle       0.47227 ( 9242)
  hydrogen bonds       : bond        0.05782 (  523)
  hydrogen bonds       : angle       4.16991 ( 1557)

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

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

  1768 Ramachandran restraints generated.
    884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1768 Ramachandran restraints generated.
    884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 67
  time to evaluate  : 0.347 
Fit side-chains
REVERT: A  136 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.7963 (mp)
REVERT: A  417 ASP cc_start: 0.8275 (t0) cc_final: 0.7836 (t0)
REVERT: B  136 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.7977 (mp)
REVERT: B  417 ASP cc_start: 0.8293 (t0) cc_final: 0.7854 (t0)
  outliers start: 5
  outliers final: 3
  residues processed: 71
  average time/residue: 0.2627
  time to fit residues: 23.6769
Evaluate side-chains
  72 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 67
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  219 PHE
Chi-restraints excluded: chain A residue  455 LYS
Chi-restraints excluded: chain B residue  136 LEU
Chi-restraints excluded: chain B residue  219 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 45 optimal weight:    2.9990
   chunk 44 optimal weight:    0.8980
   chunk 13 optimal weight:    2.9990
   chunk 46 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 54 optimal weight:    1.9990
   chunk 18 optimal weight:    2.9990
   chunk 27 optimal weight:    1.9990
   chunk 31 optimal weight:    0.6980
   chunk 55 optimal weight:    0.9980
   overall best weight:    1.3184

-------------------------------------------------------------------------------
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 = 0.3081 r_free = 0.3081 target = 0.104754 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2845 r_free = 0.2845 target = 0.087584 restraints weight = 23660.225|
|-----------------------------------------------------------------------------|
r_work (start): 0.2816 rms_B_bonded: 1.74
r_work: 0.2718 rms_B_bonded: 1.99 restraints_weight: 0.5000
r_work: 0.2597 rms_B_bonded: 3.44 restraints_weight: 0.2500
r_work (final): 0.2597
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8437
moved from start:          0.1161

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6810  Z= 0.151
  Angle     :  0.467   4.276   9242  Z= 0.254
  Chirality :  0.040   0.330   1086
  Planarity :  0.005   0.045   1160
  Dihedral  :  3.724  16.785    946
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 1.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  :  8.81 %
    Favored  : 90.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.45 (0.28), residues: 884
  helix:  2.52 (0.19), residues: 680
  sheet:  None (None), residues: 0
  loop : -1.66 (0.39), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  17 
 TYR   0.007   0.001   TYR B 419 
 PHE   0.012   0.001   PHE A 307 
 TRP   0.005   0.001   TRP A 253 
 HIS   0.002   0.001   HIS B  70 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 6810)
  covalent geometry    : angle       0.46680 ( 9242)
  hydrogen bonds       : bond        0.05680 (  523)
  hydrogen bonds       : angle       4.12162 ( 1557)

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

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

  1768 Ramachandran restraints generated.
    884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1768 Ramachandran restraints generated.
    884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 69
  time to evaluate  : 0.348 
Fit side-chains
REVERT: A  136 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.7916 (mp)
REVERT: A  417 ASP cc_start: 0.8285 (t0) cc_final: 0.7859 (t0)
REVERT: B  136 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.7929 (mp)
REVERT: B  417 ASP cc_start: 0.8296 (t0) cc_final: 0.7881 (t0)
  outliers start: 5
  outliers final: 3
  residues processed: 73
  average time/residue: 0.2572
  time to fit residues: 23.9232
Evaluate side-chains
  72 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 67
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  219 PHE
Chi-restraints excluded: chain A residue  455 LYS
Chi-restraints excluded: chain B residue  136 LEU
Chi-restraints excluded: chain B residue  219 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 56 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 62 optimal weight:    2.9990
   chunk 52 optimal weight:    1.9990
   chunk 11 optimal weight:    0.0570
   chunk 48 optimal weight:    0.7980
   chunk 18 optimal weight:    1.9990
   chunk 72 optimal weight:    1.9990
   chunk 44 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 23 optimal weight:    0.6980
   overall best weight:    1.1102

-------------------------------------------------------------------------------
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 = 0.3070 r_free = 0.3070 target = 0.104280 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2834 r_free = 0.2834 target = 0.087027 restraints weight = 23612.939|
|-----------------------------------------------------------------------------|
r_work (start): 0.2842 rms_B_bonded: 1.76
r_work: 0.2744 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.2621 rms_B_bonded: 3.50 restraints_weight: 0.2500
r_work (final): 0.2621
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8415
moved from start:          0.1234

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6810  Z= 0.136
  Angle     :  0.454   4.238   9242  Z= 0.246
  Chirality :  0.040   0.329   1086
  Planarity :  0.005   0.045   1160
  Dihedral  :  3.662  16.626    946
  Min Nonbonded Distance : 2.389

Molprobity Statistics.
  All-atom Clashscore : 1.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  :  9.10 %
    Favored  : 90.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.59 (0.28), residues: 884
  helix:  2.62 (0.19), residues: 680
  sheet:  None (None), residues: 0
  loop : -1.63 (0.39), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  17 
 TYR   0.006   0.001   TYR B 419 
 PHE   0.014   0.001   PHE B 307 
 TRP   0.005   0.001   TRP B 253 
 HIS   0.002   0.001   HIS A  70 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 6810)
  covalent geometry    : angle       0.45418 ( 9242)
  hydrogen bonds       : bond        0.05353 (  523)
  hydrogen bonds       : angle       4.04792 ( 1557)

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

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

  1768 Ramachandran restraints generated.
    884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1768 Ramachandran restraints generated.
    884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 68
  time to evaluate  : 0.362 
Fit side-chains
REVERT: A  136 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.7888 (mp)
REVERT: A  373 MET cc_start: 0.8060 (mtt) cc_final: 0.7832 (mtt)
REVERT: B   65 MET cc_start: 0.6912 (mtp) cc_final: 0.6641 (mtt)
REVERT: B  136 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.7900 (mp)
REVERT: B  373 MET cc_start: 0.8050 (mtt) cc_final: 0.7822 (mtt)
  outliers start: 5
  outliers final: 3
  residues processed: 72
  average time/residue: 0.2417
  time to fit residues: 22.6938
Evaluate side-chains
  73 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 68
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  219 PHE
Chi-restraints excluded: chain A residue  455 LYS
Chi-restraints excluded: chain B residue  136 LEU
Chi-restraints excluded: chain B residue  219 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 37 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 35 optimal weight:    0.5980
   chunk 53 optimal weight:    1.9990
   chunk 74 optimal weight:    1.9990
   chunk 6 optimal weight:    2.9990
   chunk 1 optimal weight:    1.9990
   chunk 36 optimal weight:    0.1980
   chunk 71 optimal weight:    1.9990
   chunk 40 optimal weight:    1.9990
   chunk 2 optimal weight:    0.7980
   overall best weight:    1.1184

-------------------------------------------------------------------------------
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 = 0.3090 r_free = 0.3090 target = 0.105437 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2857 r_free = 0.2857 target = 0.088436 restraints weight = 23303.837|
|-----------------------------------------------------------------------------|
r_work (start): 0.2827 rms_B_bonded: 1.72
r_work: 0.2731 rms_B_bonded: 1.97 restraints_weight: 0.5000
r_work: 0.2610 rms_B_bonded: 3.42 restraints_weight: 0.2500
r_work (final): 0.2610
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8425
moved from start:          0.1324

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6810  Z= 0.137
  Angle     :  0.453   4.214   9242  Z= 0.246
  Chirality :  0.040   0.328   1086
  Planarity :  0.005   0.045   1160
  Dihedral  :  3.648  16.607    946
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 1.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  :  9.70 %
    Favored  : 89.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.63 (0.28), residues: 884
  helix:  2.66 (0.19), residues: 680
  sheet:  None (None), residues: 0
  loop : -1.66 (0.39), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  17 
 TYR   0.007   0.001   TYR B 419 
 PHE   0.013   0.001   PHE A 307 
 TRP   0.005   0.001   TRP A 253 
 HIS   0.002   0.001   HIS B  70 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 6810)
  covalent geometry    : angle       0.45282 ( 9242)
  hydrogen bonds       : bond        0.05359 (  523)
  hydrogen bonds       : angle       4.03687 ( 1557)

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

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

  1768 Ramachandran restraints generated.
    884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1768 Ramachandran restraints generated.
    884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 68
  time to evaluate  : 0.357 
Fit side-chains
REVERT: A   65 MET cc_start: 0.6922 (mtp) cc_final: 0.6660 (mtt)
REVERT: A  136 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.7920 (mp)
REVERT: A  373 MET cc_start: 0.8074 (mtt) cc_final: 0.7863 (mtt)
REVERT: A  417 ASP cc_start: 0.8150 (t0) cc_final: 0.7797 (t0)
REVERT: B   65 MET cc_start: 0.6920 (mtp) cc_final: 0.6650 (mtt)
REVERT: B  136 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.7916 (mp)
REVERT: B  373 MET cc_start: 0.8069 (mtt) cc_final: 0.7856 (mtt)
REVERT: B  417 ASP cc_start: 0.8178 (t0) cc_final: 0.7823 (t0)
  outliers start: 5
  outliers final: 3
  residues processed: 72
  average time/residue: 0.2343
  time to fit residues: 22.1594
Evaluate side-chains
  73 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 68
  time to evaluate  : 0.429 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  219 PHE
Chi-restraints excluded: chain A residue  455 LYS
Chi-restraints excluded: chain B residue  136 LEU
Chi-restraints excluded: chain B residue  219 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 13 optimal weight:    1.9990
   chunk 29 optimal weight:    3.9990
   chunk 50 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9990
   chunk 70 optimal weight:    0.6980
   chunk 1 optimal weight:    1.9990
   chunk 79 optimal weight:    2.9990
   chunk 77 optimal weight:    0.9980
   chunk 25 optimal weight:    0.6980
   overall best weight:    1.0784

-------------------------------------------------------------------------------
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 = 0.3092 r_free = 0.3092 target = 0.105633 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2861 r_free = 0.2861 target = 0.088759 restraints weight = 23382.580|
|-----------------------------------------------------------------------------|
r_work (start): 0.2848 rms_B_bonded: 1.69
r_work: 0.2754 rms_B_bonded: 1.96 restraints_weight: 0.5000
r_work: 0.2632 rms_B_bonded: 3.40 restraints_weight: 0.2500
r_work (final): 0.2632
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8453
moved from start:          0.1327

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6810  Z= 0.134
  Angle     :  0.449   4.198   9242  Z= 0.243
  Chirality :  0.040   0.328   1086
  Planarity :  0.005   0.044   1160
  Dihedral  :  3.626  16.588    946
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 1.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  :  9.70 %
    Favored  : 89.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.68 (0.28), residues: 884
  helix:  2.70 (0.19), residues: 680
  sheet:  None (None), residues: 0
  loop : -1.64 (0.39), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  17 
 TYR   0.007   0.001   TYR B 419 
 PHE   0.012   0.001   PHE A 307 
 TRP   0.005   0.001   TRP B 253 
 HIS   0.002   0.001   HIS A  70 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 6810)
  covalent geometry    : angle       0.44867 ( 9242)
  hydrogen bonds       : bond        0.05275 (  523)
  hydrogen bonds       : angle       4.01395 ( 1557)

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

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

  1768 Ramachandran restraints generated.
    884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1768 Ramachandran restraints generated.
    884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 68
  time to evaluate  : 0.357 
Fit side-chains
REVERT: A   65 MET cc_start: 0.6959 (mtp) cc_final: 0.6682 (mtt)
REVERT: A  136 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.7964 (mp)
REVERT: A  212 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8308 (tt)
REVERT: A  373 MET cc_start: 0.8121 (mtt) cc_final: 0.7903 (mtt)
REVERT: B   65 MET cc_start: 0.6949 (mtp) cc_final: 0.6671 (mtt)
REVERT: B  136 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.7965 (mp)
REVERT: B  212 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8302 (tt)
REVERT: B  373 MET cc_start: 0.8118 (mtt) cc_final: 0.7899 (mtt)
  outliers start: 7
  outliers final: 3
  residues processed: 74
  average time/residue: 0.2216
  time to fit residues: 21.6096
Evaluate side-chains
  75 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 68
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  212 LEU
Chi-restraints excluded: chain A residue  219 PHE
Chi-restraints excluded: chain A residue  455 LYS
Chi-restraints excluded: chain B residue  136 LEU
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  219 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 71 optimal weight:    1.9990
   chunk 6 optimal weight:    2.9990
   chunk 20 optimal weight:    1.9990
   chunk 22 optimal weight:    0.7980
   chunk 67 optimal weight:    0.9980
   chunk 34 optimal weight:    1.9990
   chunk 56 optimal weight:    1.9990
   chunk 41 optimal weight:    1.9990
   chunk 25 optimal weight:    0.6980
   chunk 74 optimal weight:    1.9990
   chunk 62 optimal weight:    2.9990
   overall best weight:    1.2984

-------------------------------------------------------------------------------
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 = 0.3081 r_free = 0.3081 target = 0.104824 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2848 r_free = 0.2848 target = 0.087826 restraints weight = 23573.252|
|-----------------------------------------------------------------------------|
r_work (start): 0.2818 rms_B_bonded: 1.72
r_work: 0.2722 rms_B_bonded: 1.97 restraints_weight: 0.5000
r_work: 0.2600 rms_B_bonded: 3.42 restraints_weight: 0.2500
r_work (final): 0.2600
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8440
moved from start:          0.1391

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   6810  Z= 0.152
  Angle     :  0.466   4.775   9242  Z= 0.252
  Chirality :  0.040   0.328   1086
  Planarity :  0.005   0.045   1160
  Dihedral  :  3.669  16.676    946
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 1.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  :  9.70 %
    Favored  : 89.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.58 (0.28), residues: 884
  helix:  2.63 (0.19), residues: 680
  sheet:  None (None), residues: 0
  loop : -1.69 (0.39), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  17 
 TYR   0.008   0.001   TYR B 419 
 PHE   0.011   0.001   PHE B 219 
 TRP   0.005   0.001   TRP A 253 
 HIS   0.002   0.001   HIS A 234 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 ( 6810)
  covalent geometry    : angle       0.46634 ( 9242)
  hydrogen bonds       : bond        0.05571 (  523)
  hydrogen bonds       : angle       4.05958 ( 1557)

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

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

  1768 Ramachandran restraints generated.
    884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1768 Ramachandran restraints generated.
    884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 65
  time to evaluate  : 0.382 
Fit side-chains
REVERT: A   65 MET cc_start: 0.6928 (mtp) cc_final: 0.6639 (mtt)
REVERT: A  136 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.7941 (mp)
REVERT: A  212 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8300 (tt)
REVERT: A  373 MET cc_start: 0.8090 (mtt) cc_final: 0.7869 (mtt)
REVERT: A  417 ASP cc_start: 0.8159 (t0) cc_final: 0.7818 (t0)
REVERT: B   65 MET cc_start: 0.6942 (mtp) cc_final: 0.6652 (mtt)
REVERT: B  136 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.7939 (mp)
REVERT: B  212 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8295 (tt)
REVERT: B  373 MET cc_start: 0.8090 (mtt) cc_final: 0.7867 (mtt)
REVERT: B  417 ASP cc_start: 0.8184 (t0) cc_final: 0.7851 (t0)
  outliers start: 7
  outliers final: 3
  residues processed: 71
  average time/residue: 0.2105
  time to fit residues: 19.8393
Evaluate side-chains
  72 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 65
  time to evaluate  : 0.376 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  212 LEU
Chi-restraints excluded: chain A residue  219 PHE
Chi-restraints excluded: chain A residue  455 LYS
Chi-restraints excluded: chain B residue  136 LEU
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  219 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 1 optimal weight:    0.7980
   chunk 82 optimal weight:    0.9990
   chunk 78 optimal weight:    0.9980
   chunk 87 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9980
   chunk 30 optimal weight:    1.9990
   chunk 64 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9990
   chunk 42 optimal weight:    0.9980
   chunk 34 optimal weight:    1.9990
   chunk 75 optimal weight:    0.7980
   overall best weight:    0.9180

-------------------------------------------------------------------------------
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 = 0.3100 r_free = 0.3100 target = 0.106194 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2869 r_free = 0.2869 target = 0.089305 restraints weight = 23442.691|
|-----------------------------------------------------------------------------|
r_work (start): 0.2855 rms_B_bonded: 1.69
r_work: 0.2761 rms_B_bonded: 1.95 restraints_weight: 0.5000
r_work: 0.2639 rms_B_bonded: 3.40 restraints_weight: 0.2500
r_work (final): 0.2639
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8445
moved from start:          0.1381

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6810  Z= 0.123
  Angle     :  0.439   4.208   9242  Z= 0.238
  Chirality :  0.039   0.328   1086
  Planarity :  0.005   0.044   1160
  Dihedral  :  3.598  16.534    946
  Min Nonbonded Distance : 2.400

Molprobity Statistics.
  All-atom Clashscore : 2.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  :  9.70 %
    Favored  : 89.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.77 (0.29), residues: 884
  helix:  2.76 (0.20), residues: 680
  sheet:  None (None), residues: 0
  loop : -1.59 (0.40), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  17 
 TYR   0.006   0.001   TYR B 419 
 PHE   0.009   0.001   PHE B 219 
 TRP   0.005   0.001   TRP B 253 
 HIS   0.001   0.001   HIS B 175 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 6810)
  covalent geometry    : angle       0.43929 ( 9242)
  hydrogen bonds       : bond        0.05080 (  523)
  hydrogen bonds       : angle       3.97063 ( 1557)

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

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

  1768 Ramachandran restraints generated.
    884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1768 Ramachandran restraints generated.
    884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 65
  time to evaluate  : 0.370 
Fit side-chains
REVERT: A   65 MET cc_start: 0.6917 (mtp) cc_final: 0.6646 (mtt)
REVERT: A  136 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.7958 (mp)
REVERT: A  212 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8300 (tt)
REVERT: A  373 MET cc_start: 0.8127 (mtt) cc_final: 0.7905 (mtt)
REVERT: A  417 ASP cc_start: 0.8171 (t0) cc_final: 0.7828 (t0)
REVERT: B   65 MET cc_start: 0.6940 (mtp) cc_final: 0.6661 (mtt)
REVERT: B  136 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.7953 (mp)
REVERT: B  212 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8296 (tt)
REVERT: B  373 MET cc_start: 0.8125 (mtt) cc_final: 0.7900 (mtt)
REVERT: B  417 ASP cc_start: 0.8200 (t0) cc_final: 0.7865 (t0)
  outliers start: 7
  outliers final: 0
  residues processed: 71
  average time/residue: 0.2128
  time to fit residues: 20.1212
Evaluate side-chains
  69 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 65
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  212 LEU
Chi-restraints excluded: chain B residue  136 LEU
Chi-restraints excluded: chain B residue  212 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 67 optimal weight:    0.4980
   chunk 54 optimal weight:    1.9990
   chunk 5 optimal weight:    3.9990
   chunk 9 optimal weight:    2.9990
   chunk 16 optimal weight:    2.9990
   chunk 71 optimal weight:    1.9990
   chunk 29 optimal weight:    0.6980
   chunk 80 optimal weight:    0.5980
   chunk 48 optimal weight:    1.9990
   chunk 78 optimal weight:    1.9990
   chunk 47 optimal weight:    1.9990
   overall best weight:    1.1584

-------------------------------------------------------------------------------
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 = 0.3093 r_free = 0.3093 target = 0.105684 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2862 r_free = 0.2862 target = 0.088799 restraints weight = 23612.974|
|-----------------------------------------------------------------------------|
r_work (start): 0.2845 rms_B_bonded: 1.70
r_work: 0.2749 rms_B_bonded: 1.98 restraints_weight: 0.5000
r_work: 0.2629 rms_B_bonded: 3.42 restraints_weight: 0.2500
r_work (final): 0.2629
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8471
moved from start:          0.1431

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6810  Z= 0.140
  Angle     :  0.453   4.684   9242  Z= 0.245
  Chirality :  0.040   0.328   1086
  Planarity :  0.005   0.045   1160
  Dihedral  :  3.611  16.625    946
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 2.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  : 10.30 %
    Favored  : 88.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.72 (0.28), residues: 884
  helix:  2.71 (0.19), residues: 680
  sheet:  None (None), residues: 0
  loop : -1.56 (0.40), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  17 
 TYR   0.007   0.001   TYR B 419 
 PHE   0.012   0.001   PHE B 307 
 TRP   0.005   0.001   TRP B 253 
 HIS   0.001   0.001   HIS A  70 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 6810)
  covalent geometry    : angle       0.45288 ( 9242)
  hydrogen bonds       : bond        0.05320 (  523)
  hydrogen bonds       : angle       4.01128 ( 1557)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3010.24 seconds
wall clock time: 51 minutes 47.29 seconds (3107.29 seconds total)