Starting phenix.real_space_refine
on Tue Mar  3 16:26:25 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6vyi_21461/03_2026/6vyi_21461.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6vyi_21461/03_2026/6vyi_21461.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6vyi_21461/03_2026/6vyi_21461.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6vyi_21461/03_2026/6vyi_21461.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6vyi_21461/03_2026/6vyi_21461.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6vyi_21461/03_2026/6vyi_21461.map"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.011
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: 5
    Type Number    sf(0)   Gaussians
     P       4      5.49       5
     S      42      5.16       5
     C    4620      2.51       5
     N    1136      2.21       5
     O    1114      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6916
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3360
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 406, 3360
          Classifications: {'peptide': 406}
          Link IDs: {'PTRANS': 18, 'TRANS': 387}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 3360
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 406, 3360
          Classifications: {'peptide': 406}
          Link IDs: {'PTRANS': 18, 'TRANS': 387}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 147
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 147
          Unusual residues: {'6OU': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "B"
      Number of atoms: 49
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 49
          Unusual residues: {'6OU': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.31, per 1000 atoms: 0.19
  Number of scatterers: 6916
  At special positions: 0
  Unit cell: (109.725, 91.575, 81.675, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      42     16.00
     P       4     15.00
     O    1114      8.00
     N    1136      7.00
     C    4620      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=2, symmetry=0
  Number of additional bonds: simple=2, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.53
  Conformation dependent library (CDL) restraints added in 258.9 milliseconds
  

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1564

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 0 sheets defined
      78.1% alpha, 0.0% 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 77 through 81
      removed outlier: 3.627A  pdb=" N   GLY A  81 " --> pdb=" O   SER A  78 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 87 through 113
      removed outlier: 3.505A  pdb=" N   CYS A  92 " --> pdb=" O   ILE A  88 " (cutoff:3.500A)
      removed outlier: 5.739A  pdb=" N   ARG A 102 " --> pdb=" O   LEU A  98 " (cutoff:3.500A)
      removed outlier: 5.845A  pdb=" N   LEU A 103 " --> pdb=" O   SER A  99 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 115 through 127
      removed outlier: 3.607A  pdb=" N   GLN A 119 " --> pdb=" O   VAL A 115 " (cutoff:3.500A)
      removed outlier: 3.886A  pdb=" N   VAL A 121 " --> pdb=" O   PRO A 117 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   ASP A 127 " --> pdb=" O   LEU A 123 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 131 through 155
      removed outlier: 4.299A  pdb=" N   ASN A 141 " --> pdb=" O   VAL A 137 " (cutoff:3.500A)
      removed outlier: 4.557A  pdb=" N   VAL A 142 " --> pdb=" O   ILE A 138 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   PHE A 143 " --> pdb=" O   ALA A 139 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 160 through 185
      Proline residue:  A 179  - end of helix
    Processing helix  chain 'A' and resid 190 through 226
      removed outlier: 3.693A  pdb=" N   ARG A 222 " --> pdb=" O   CYS A 218 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 248 through 257
      removed outlier: 3.785A  pdb=" N   PHE A 257 " --> pdb=" O   TYR A 253 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 274 through 300
    Processing helix  chain 'A' and resid 300 through 307
      removed outlier: 4.089A  pdb=" N   SER A 307 " --> pdb=" O   THR A 303 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 315 through 343
      removed outlier: 3.838A  pdb=" N   LYS A 325 " --> pdb=" O   GLU A 321 " (cutoff:3.500A)
      removed outlier: 4.961A  pdb=" N   VAL A 328 " --> pdb=" O   LEU A 324 " (cutoff:3.500A)
      Proline residue:  A 329  - end of helix
    Processing helix  chain 'A' and resid 343 through 353
    Processing helix  chain 'A' and resid 369 through 375
    Processing helix  chain 'A' and resid 378 through 389
    Processing helix  chain 'A' and resid 390 through 396
    Processing helix  chain 'A' and resid 399 through 420
    Processing helix  chain 'A' and resid 428 through 448
      removed outlier: 3.700A  pdb=" N   THR A 432 " --> pdb=" O   LEU A 428 " (cutoff:3.500A)
      removed outlier: 4.071A  pdb=" N   ILE A 438 " --> pdb=" O   MET A 434 " (cutoff:3.500A)
      Proline residue:  A 439  - end of helix
    Processing helix  chain 'A' and resid 449 through 463
    Processing helix  chain 'A' and resid 465 through 479
      removed outlier: 3.717A  pdb=" N   VAL A 469 " --> pdb=" O   GLN A 465 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 77 through 81
      removed outlier: 3.626A  pdb=" N   GLY B  81 " --> pdb=" O   SER B  78 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 87 through 113
      removed outlier: 3.505A  pdb=" N   CYS B  92 " --> pdb=" O   ILE B  88 " (cutoff:3.500A)
      removed outlier: 5.739A  pdb=" N   ARG B 102 " --> pdb=" O   LEU B  98 " (cutoff:3.500A)
      removed outlier: 5.845A  pdb=" N   LEU B 103 " --> pdb=" O   SER B  99 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 115 through 127
      removed outlier: 3.606A  pdb=" N   GLN B 119 " --> pdb=" O   VAL B 115 " (cutoff:3.500A)
      removed outlier: 3.887A  pdb=" N   VAL B 121 " --> pdb=" O   PRO B 117 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   ASP B 127 " --> pdb=" O   LEU B 123 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 131 through 155
      removed outlier: 4.298A  pdb=" N   ASN B 141 " --> pdb=" O   VAL B 137 " (cutoff:3.500A)
      removed outlier: 4.557A  pdb=" N   VAL B 142 " --> pdb=" O   ILE B 138 " (cutoff:3.500A)
      removed outlier: 3.982A  pdb=" N   PHE B 143 " --> pdb=" O   ALA B 139 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 160 through 185
      Proline residue:  B 179  - end of helix
    Processing helix  chain 'B' and resid 190 through 226
      removed outlier: 3.693A  pdb=" N   ARG B 222 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 248 through 257
      removed outlier: 3.786A  pdb=" N   PHE B 257 " --> pdb=" O   TYR B 253 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 274 through 300
    Processing helix  chain 'B' and resid 300 through 307
      removed outlier: 4.089A  pdb=" N   SER B 307 " --> pdb=" O   THR B 303 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 315 through 343
      removed outlier: 3.838A  pdb=" N   LYS B 325 " --> pdb=" O   GLU B 321 " (cutoff:3.500A)
      removed outlier: 4.961A  pdb=" N   VAL B 328 " --> pdb=" O   LEU B 324 " (cutoff:3.500A)
      Proline residue:  B 329  - end of helix
    Processing helix  chain 'B' and resid 343 through 353
    Processing helix  chain 'B' and resid 369 through 375
    Processing helix  chain 'B' and resid 378 through 389
    Processing helix  chain 'B' and resid 390 through 396
    Processing helix  chain 'B' and resid 399 through 420
    Processing helix  chain 'B' and resid 428 through 448
      removed outlier: 3.699A  pdb=" N   THR B 432 " --> pdb=" O   LEU B 428 " (cutoff:3.500A)
      removed outlier: 4.071A  pdb=" N   ILE B 438 " --> pdb=" O   MET B 434 " (cutoff:3.500A)
      Proline residue:  B 439  - end of helix
    Processing helix  chain 'B' and resid 449 through 463
    Processing helix  chain 'B' and resid 465 through 479
      removed outlier: 3.718A  pdb=" N   VAL B 469 " --> pdb=" O   GLN B 465 " (cutoff:3.500A)

    438 hydrogen bonds defined for protein.
    1308 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.06

  Time building geometry restraints manager: 0.73 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: 1018
        1.32 -     1.44: 2138
        1.44 -     1.56: 3894
        1.56 -     1.68: 8
        1.68 -     1.80: 68
  Bond restraints: 7126
  Sorted by residual:
  bond pdb=" O22 6OU A 502 "
       pdb=" P23 6OU A 502 "
    ideal  model  delta    sigma   weight residual
    1.643  1.557  0.086 2.00e-02 2.50e+03 1.83e+01
  bond pdb=" O22 6OU B 501 "
       pdb=" P23 6OU B 501 "
    ideal  model  delta    sigma   weight residual
    1.643  1.566  0.077 2.00e-02 2.50e+03 1.47e+01
  bond pdb=" O22 6OU A 501 "
       pdb=" P23 6OU A 501 "
    ideal  model  delta    sigma   weight residual
    1.643  1.568  0.075 2.00e-02 2.50e+03 1.40e+01
  bond pdb=" O22 6OU A 503 "
       pdb=" P23 6OU A 503 "
    ideal  model  delta    sigma   weight residual
    1.643  1.573  0.070 2.00e-02 2.50e+03 1.23e+01
  bond pdb=" C27 6OU A 503 "
       pdb=" C28 6OU A 503 "
    ideal  model  delta    sigma   weight residual
    1.512  1.563 -0.051 2.00e-02 2.50e+03 6.57e+00
  ... (remaining 7121 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.49: 9555
        3.49 -     6.98: 79
        6.98 -    10.46: 3
       10.46 -    13.95: 6
       13.95 -    17.44: 5
  Bond angle restraints: 9648
  Sorted by residual:
  angle pdb=" C21 6OU A 502 "
        pdb=" O22 6OU A 502 "
        pdb=" P23 6OU A 502 "
      ideal   model   delta    sigma   weight residual
     117.17  134.61  -17.44 3.00e+00 1.11e-01 3.38e+01
  angle pdb=" C21 6OU A 501 "
        pdb=" O22 6OU A 501 "
        pdb=" P23 6OU A 501 "
      ideal   model   delta    sigma   weight residual
     117.17  134.50  -17.33 3.00e+00 1.11e-01 3.34e+01
  angle pdb=" O22 6OU A 503 "
        pdb=" P23 6OU A 503 "
        pdb=" O26 6OU A 503 "
      ideal   model   delta    sigma   weight residual
      93.95  110.09  -16.14 3.00e+00 1.11e-01 2.89e+01
  angle pdb=" C21 6OU B 501 "
        pdb=" O22 6OU B 501 "
        pdb=" P23 6OU B 501 "
      ideal   model   delta    sigma   weight residual
     117.17  131.43  -14.26 3.00e+00 1.11e-01 2.26e+01
  angle pdb=" O22 6OU B 501 "
        pdb=" P23 6OU B 501 "
        pdb=" O26 6OU B 501 "
      ideal   model   delta    sigma   weight residual
      93.95  108.05  -14.10 3.00e+00 1.11e-01 2.21e+01
  ... (remaining 9643 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.83: 4045
       34.83 -    69.66: 109
       69.66 -   104.49: 21
      104.49 -   139.31: 11
      139.31 -   174.14: 4
  Dihedral angle restraints: 4190
    sinusoidal: 1778
      harmonic: 2412
  Sorted by residual:
  dihedral pdb=" CA  GLY A  87 "
           pdb=" C   GLY A  87 "
           pdb=" N   ILE A  88 "
           pdb=" CA  ILE A  88 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.65   23.35     0      5.00e+00 4.00e-02 2.18e+01
  dihedral pdb=" CA  GLY B  87 "
           pdb=" C   GLY B  87 "
           pdb=" N   ILE B  88 "
           pdb=" CA  ILE B  88 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.67   23.33     0      5.00e+00 4.00e-02 2.18e+01
  dihedral pdb=" C19 6OU B 501 "
           pdb=" C20 6OU B 501 "
           pdb=" C21 6OU B 501 "
           pdb=" O22 6OU B 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -59.00  115.14 -174.14     1      3.00e+01 1.11e-03 2.13e+01
  ... (remaining 4187 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.051: 751
       0.051 -    0.102: 242
       0.102 -    0.153: 35
       0.153 -    0.204: 1
       0.204 -    0.255: 3
  Chirality restraints: 1032
  Sorted by residual:
  chirality pdb=" C20 6OU A 503 "
            pdb=" C19 6OU A 503 "
            pdb=" C21 6OU A 503 "
            pdb=" O30 6OU A 503 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.35    2.60   -0.25 2.00e-01 2.50e+01 1.62e+00
  chirality pdb=" C20 6OU B 501 "
            pdb=" C19 6OU B 501 "
            pdb=" C21 6OU B 501 "
            pdb=" O30 6OU B 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.35    2.57   -0.23 2.00e-01 2.50e+01 1.29e+00
  chirality pdb=" C20 6OU A 502 "
            pdb=" C19 6OU A 502 "
            pdb=" C21 6OU A 502 "
            pdb=" O30 6OU A 502 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.35    2.56   -0.22 2.00e-01 2.50e+01 1.20e+00
  ... (remaining 1029 not shown)

  Planarity restraints: 1172
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 296 "   -0.008 2.00e-02 2.50e+03   1.66e-02 2.76e+00
        pdb=" C   ILE A 296 "    0.029 2.00e-02 2.50e+03
        pdb=" O   ILE A 296 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   GLN A 297 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE B 296 "    0.008 2.00e-02 2.50e+03   1.65e-02 2.72e+00
        pdb=" C   ILE B 296 "   -0.029 2.00e-02 2.50e+03
        pdb=" O   ILE B 296 "    0.011 2.00e-02 2.50e+03
        pdb=" N   GLN B 297 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR B 243 "    0.026 5.00e-02 4.00e+02   3.87e-02 2.40e+00
        pdb=" N   PRO B 244 "   -0.067 5.00e-02 4.00e+02
        pdb=" CA  PRO B 244 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO B 244 "    0.022 5.00e-02 4.00e+02
  ... (remaining 1169 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 284
        2.71 -     3.25: 7272
        3.25 -     3.80: 11658
        3.80 -     4.35: 14141
        4.35 -     4.90: 24318
  Nonbonded interactions: 57673
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU A 351 "
            pdb=" NH2 ARG A 358 "
     model   vdw
     2.157 3.120
  nonbonded pdb=" OE1 GLU B 351 "
            pdb=" NH2 ARG B 358 "
     model   vdw
     2.158 3.120
  nonbonded pdb=" O   GLU B 416 "
            pdb=" OG  SER B 420 "
     model   vdw
     2.193 3.040
  nonbonded pdb=" O   GLU A 416 "
            pdb=" OG  SER A 420 "
     model   vdw
     2.194 3.040
  nonbonded pdb=" ND2 ASN A 366 "
            pdb=" O   ASN B  84 "
     model   vdw
     2.218 3.120
  ... (remaining 57668 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: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 66 through 501)
  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:             1.340
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.140
  Find NCS groups from input model:        0.100
  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:7.160
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.920
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8405
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      :  0.010   0.086   7128  Z= 0.427
  Angle     :  0.941  17.441   9648  Z= 0.447
  Chirality :  0.048   0.255   1032
  Planarity :  0.005   0.039   1172
  Dihedral  : 19.278 174.143   2626
  Min Nonbonded Distance : 2.157

Molprobity Statistics.
  All-atom Clashscore : 10.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.19 %
    Favored  : 88.81 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  7.14 %
    Favored  : 92.86 %
  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: -2.99 (0.26), residues: 804
  helix: -1.16 (0.19), residues: 592
  sheet:  None (None), residues: 0
  loop : -4.15 (0.33), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 272 
 TYR   0.015   0.002   TYR B 417 
 PHE   0.016   0.002   PHE B 338 
 TRP   0.010   0.002   TRP B 334 
 HIS   0.005   0.001   HIS B 382 

Details of bonding type rmsd
  covalent geometry    : bond        0.00980 ( 7126)
  covalent geometry    : angle       0.94141 ( 9648)
  hydrogen bonds       : bond        0.11351 (  438)
  hydrogen bonds       : angle       6.53297 ( 1308)
  Misc. bond           : bond        0.00040 (    2)

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 119
  time to evaluate  : 0.271 
Fit side-chains
   revert: symmetry clash
REVERT: A  306 ASN cc_start: 0.8273 (m-40) cc_final: 0.7946 (m-40)
REVERT: A  404 ARG cc_start: 0.7495 (mtt-85) cc_final: 0.6765 (mtm110)
REVERT: B  404 ARG cc_start: 0.7480 (mtt-85) cc_final: 0.6777 (mtm110)
  outliers start: 0
  outliers final: 0
  residues processed: 119
  average time/residue: 0.6446
  time to fit residues: 79.9353
Evaluate side-chains
  92 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.198 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    0.7980
   chunk 5 optimal weight:    9.9990
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    0.9980
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.6980
   chunk 45 optimal weight:    9.9990
   chunk 74 optimal weight:    0.8980
   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 100 ASN
A 119 GLN
A 162 GLN
A 239 HIS
** A 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 292 GLN
A 465 GLN
B 119 GLN
B 162 GLN
B 239 HIS
B 266 ASN
B 292 GLN
B 465 GLN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.135199 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.106467 restraints weight = 9595.216|
|-----------------------------------------------------------------------------|
r_work (start): 0.3232 rms_B_bonded: 1.91
r_work: 0.3093 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.2954 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.2954
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8535
moved from start:          0.1659

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7128  Z= 0.135
  Angle     :  0.597   7.153   9648  Z= 0.301
  Chirality :  0.039   0.124   1032
  Planarity :  0.005   0.033   1172
  Dihedral  : 17.857 177.716   1082
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 7.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.96 %
    Favored  : 92.04 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 11.34 %
    Favored  : 85.43 %
  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: -0.67 (0.29), residues: 804
  helix:  0.57 (0.22), residues: 590
  sheet:  None (None), residues: 0
  loop : -3.34 (0.34), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 358 
 TYR   0.013   0.001   TYR B 211 
 PHE   0.028   0.002   PHE B 443 
 TRP   0.010   0.001   TRP B 340 
 HIS   0.005   0.001   HIS A 201 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 7126)
  covalent geometry    : angle       0.59668 ( 9648)
  hydrogen bonds       : bond        0.03668 (  438)
  hydrogen bonds       : angle       5.06508 ( 1308)
  Misc. bond           : bond        0.00019 (    2)

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 114
  time to evaluate  : 0.230 
Fit side-chains
REVERT: A  315 ASP cc_start: 0.7976 (t70) cc_final: 0.7680 (t70)
REVERT: A  404 ARG cc_start: 0.7511 (mtt-85) cc_final: 0.6478 (mtm110)
REVERT: B  102 ARG cc_start: 0.7851 (OUTLIER) cc_final: 0.7488 (tpt90)
REVERT: B  315 ASP cc_start: 0.7946 (t70) cc_final: 0.7669 (t70)
REVERT: B  404 ARG cc_start: 0.7504 (mtt-85) cc_final: 0.6457 (mtm110)
  outliers start: 23
  outliers final: 2
  residues processed: 121
  average time/residue: 0.4531
  time to fit residues: 58.2670
Evaluate side-chains
  102 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 99
  time to evaluate  : 0.164 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  248 THR
Chi-restraints excluded: chain B residue  102 ARG
Chi-restraints excluded: chain B residue  248 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 66 optimal weight:    0.7980
   chunk 25 optimal weight:    0.5980
   chunk 68 optimal weight:    0.4980
   chunk 78 optimal weight:    0.8980
   chunk 79 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   chunk 71 optimal weight:    6.9990
   chunk 65 optimal weight:    1.9990
   chunk 38 optimal weight:    3.9990
   chunk 67 optimal weight:    0.7980
   chunk 31 optimal weight:    7.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 162 GLN
A 266 ASN
A 292 GLN
B 162 GLN
B 266 ASN
B 292 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.136491 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.107678 restraints weight = 9486.805|
|-----------------------------------------------------------------------------|
r_work (start): 0.3257 rms_B_bonded: 1.91
r_work: 0.3121 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.2984 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.2984
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8505
moved from start:          0.2231

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7128  Z= 0.122
  Angle     :  0.562   7.140   9648  Z= 0.280
  Chirality :  0.038   0.124   1032
  Planarity :  0.004   0.030   1172
  Dihedral  : 16.319 170.841   1082
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 7.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.46 %
    Favored  : 92.54 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 13.17 %
    Favored  : 82.91 %
  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:  0.22 (0.31), residues: 804
  helix:  1.19 (0.22), residues: 598
  sheet:  None (None), residues: 0
  loop : -3.09 (0.36), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 427 
 TYR   0.012   0.001   TYR A 316 
 PHE   0.011   0.001   PHE B 338 
 TRP   0.014   0.001   TRP B 340 
 HIS   0.004   0.001   HIS A 474 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 7126)
  covalent geometry    : angle       0.56184 ( 9648)
  hydrogen bonds       : bond        0.03390 (  438)
  hydrogen bonds       : angle       4.84990 ( 1308)
  Misc. bond           : bond        0.00063 (    2)

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 133
  time to evaluate  : 0.228 
Fit side-chains
REVERT: A   73 ASP cc_start: 0.8369 (OUTLIER) cc_final: 0.8012 (t0)
REVERT: A   79 ASP cc_start: 0.8484 (p0) cc_final: 0.8171 (p0)
REVERT: A  176 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8760 (tp)
REVERT: A  318 ARG cc_start: 0.7614 (mmp-170) cc_final: 0.7210 (ttm170)
REVERT: A  363 ASP cc_start: 0.8829 (p0) cc_final: 0.8347 (p0)
REVERT: A  400 LYS cc_start: 0.7874 (ttmt) cc_final: 0.7569 (ttmt)
REVERT: A  404 ARG cc_start: 0.7470 (mtt-85) cc_final: 0.6475 (mtm110)
REVERT: B  363 ASP cc_start: 0.8881 (p0) cc_final: 0.8391 (p0)
REVERT: B  402 MET cc_start: 0.8520 (OUTLIER) cc_final: 0.8280 (ttp)
REVERT: B  404 ARG cc_start: 0.7532 (mtt-85) cc_final: 0.6492 (mtm110)
  outliers start: 28
  outliers final: 4
  residues processed: 146
  average time/residue: 0.5140
  time to fit residues: 79.0613
Evaluate side-chains
  116 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 109
  time to evaluate  : 0.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 ASP
Chi-restraints excluded: chain A residue  176 LEU
Chi-restraints excluded: chain A residue  185 LEU
Chi-restraints excluded: chain A residue  251 ASP
Chi-restraints excluded: chain B residue  185 LEU
Chi-restraints excluded: chain B residue  251 ASP
Chi-restraints excluded: chain B residue  402 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 59 optimal weight:    0.0030
   chunk 2 optimal weight:    2.9990
   chunk 23 optimal weight:    7.9990
   chunk 33 optimal weight:    8.9990
   chunk 60 optimal weight:    2.9990
   chunk 65 optimal weight:    0.9980
   chunk 34 optimal weight:    0.7980
   chunk 67 optimal weight:    0.5980
   chunk 27 optimal weight:    0.7980
   chunk 45 optimal weight:   10.0000
   chunk 78 optimal weight:    0.6980
   overall best weight:    0.5790

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

Flipped N/Q/H residues before XYZ refinement:
A 162 GLN
A 266 ASN
A 292 GLN
B 162 GLN
B 266 ASN
B 292 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.142415 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.110264 restraints weight = 9313.724|
|-----------------------------------------------------------------------------|
r_work (start): 0.3331 rms_B_bonded: 2.14
r_work: 0.3172 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work: 0.3025 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.3025
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8248
moved from start:          0.2391

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7128  Z= 0.114
  Angle     :  0.562   7.456   9648  Z= 0.278
  Chirality :  0.037   0.120   1032
  Planarity :  0.004   0.035   1172
  Dihedral  : 15.872 171.513   1082
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.84 %
    Favored  : 93.16 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 16.39 %
    Favored  : 79.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.60 (0.31), residues: 804
  helix:  1.48 (0.22), residues: 598
  sheet:  None (None), residues: 0
  loop : -2.98 (0.37), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 222 
 TYR   0.010   0.001   TYR B 211 
 PHE   0.028   0.001   PHE A 443 
 TRP   0.017   0.001   TRP B 340 
 HIS   0.004   0.001   HIS B 474 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 ( 7126)
  covalent geometry    : angle       0.56192 ( 9648)
  hydrogen bonds       : bond        0.03276 (  438)
  hydrogen bonds       : angle       4.74503 ( 1308)
  Misc. bond           : bond        0.00054 (    2)

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 122
  time to evaluate  : 0.203 
Fit side-chains
REVERT: A   73 ASP cc_start: 0.8365 (OUTLIER) cc_final: 0.8008 (t0)
REVERT: A   79 ASP cc_start: 0.8643 (p0) cc_final: 0.8350 (p0)
REVERT: A  224 LYS cc_start: 0.8686 (ttpp) cc_final: 0.7908 (tmmt)
REVERT: A  363 ASP cc_start: 0.8824 (p0) cc_final: 0.8186 (p0)
REVERT: A  400 LYS cc_start: 0.7441 (ttmt) cc_final: 0.7084 (ttmt)
REVERT: A  404 ARG cc_start: 0.7161 (mtt-85) cc_final: 0.6161 (mtm110)
REVERT: B  224 LYS cc_start: 0.8694 (ttpp) cc_final: 0.7914 (tmmt)
REVERT: B  315 ASP cc_start: 0.7861 (t0) cc_final: 0.7537 (t70)
REVERT: B  404 ARG cc_start: 0.7118 (mtt-85) cc_final: 0.6097 (mtm110)
  outliers start: 26
  outliers final: 10
  residues processed: 136
  average time/residue: 0.4806
  time to fit residues: 69.2257
Evaluate side-chains
  122 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 111
  time to evaluate  : 0.202 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 ASP
Chi-restraints excluded: chain A residue  185 LEU
Chi-restraints excluded: chain A residue  251 ASP
Chi-restraints excluded: chain A residue  300 MET
Chi-restraints excluded: chain A residue  377 TRP
Chi-restraints excluded: chain A residue  467 ILE
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  251 ASP
Chi-restraints excluded: chain B residue  300 MET
Chi-restraints excluded: chain B residue  377 TRP
Chi-restraints excluded: chain B residue  467 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 45 optimal weight:    8.9990
   chunk 75 optimal weight:    6.9990
   chunk 60 optimal weight:    2.9990
   chunk 36 optimal weight:    3.9990
   chunk 12 optimal weight:    4.9990
   chunk 19 optimal weight:    7.9990
   chunk 50 optimal weight:    8.9990
   chunk 28 optimal weight:    0.0980
   chunk 40 optimal weight:    1.9990
   chunk 66 optimal weight:    2.9990
   chunk 16 optimal weight:    7.9990
   overall best weight:    2.4188

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

Flipped N/Q/H residues before XYZ refinement:
A 162 GLN
A 266 ASN
A 292 GLN
B 162 GLN
B 266 ASN
B 292 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.138601 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.106276 restraints weight = 9353.096|
|-----------------------------------------------------------------------------|
r_work (start): 0.3260 rms_B_bonded: 2.13
r_work: 0.3099 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.2948 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.2948
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8328
moved from start:          0.2192

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.039   7128  Z= 0.236
  Angle     :  0.635   7.771   9648  Z= 0.315
  Chirality :  0.041   0.125   1032
  Planarity :  0.005   0.036   1172
  Dihedral  : 16.140 176.195   1082
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 8.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.84 %
    Favored  : 92.16 %
  Rotamer:
    Outliers :  5.18 %
    Allowed  : 16.81 %
    Favored  : 78.01 %
  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:  0.52 (0.31), residues: 804
  helix:  1.37 (0.22), residues: 596
  sheet:  None (None), residues: 0
  loop : -2.78 (0.39), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 358 
 TYR   0.015   0.001   TYR B 417 
 PHE   0.015   0.002   PHE B 338 
 TRP   0.017   0.001   TRP B 340 
 HIS   0.004   0.001   HIS A 382 

Details of bonding type rmsd
  covalent geometry    : bond        0.00560 ( 7126)
  covalent geometry    : angle       0.63477 ( 9648)
  hydrogen bonds       : bond        0.03771 (  438)
  hydrogen bonds       : angle       4.86950 ( 1308)
  Misc. bond           : bond        0.00030 (    2)

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 102
  time to evaluate  : 0.166 
Fit side-chains
REVERT: A  351 GLU cc_start: 0.8824 (tp30) cc_final: 0.8560 (tp30)
REVERT: A  363 ASP cc_start: 0.9054 (p0) cc_final: 0.8679 (p0)
REVERT: A  368 GLU cc_start: 0.8699 (OUTLIER) cc_final: 0.8458 (pt0)
REVERT: A  400 LYS cc_start: 0.7392 (ttmt) cc_final: 0.7067 (ttmt)
REVERT: A  404 ARG cc_start: 0.7172 (mtt-85) cc_final: 0.6195 (mtm110)
REVERT: B  224 LYS cc_start: 0.8679 (ttpp) cc_final: 0.7925 (tmmt)
REVERT: B  368 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.8478 (pt0)
REVERT: B  404 ARG cc_start: 0.7164 (mtt-85) cc_final: 0.6147 (mtm110)
  outliers start: 37
  outliers final: 11
  residues processed: 123
  average time/residue: 0.4770
  time to fit residues: 62.0327
Evaluate side-chains
  102 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 89
  time to evaluate  : 0.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 ASP
Chi-restraints excluded: chain A residue  185 LEU
Chi-restraints excluded: chain A residue  251 ASP
Chi-restraints excluded: chain A residue  295 LEU
Chi-restraints excluded: chain A residue  368 GLU
Chi-restraints excluded: chain A residue  377 TRP
Chi-restraints excluded: chain A residue  467 ILE
Chi-restraints excluded: chain B residue   73 ASP
Chi-restraints excluded: chain B residue  185 LEU
Chi-restraints excluded: chain B residue  251 ASP
Chi-restraints excluded: chain B residue  368 GLU
Chi-restraints excluded: chain B residue  377 TRP
Chi-restraints excluded: chain B residue  467 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 24 optimal weight:    5.9990
   chunk 4 optimal weight:    7.9990
   chunk 74 optimal weight:    0.8980
   chunk 71 optimal weight:    4.9990
   chunk 3 optimal weight:    0.9990
   chunk 18 optimal weight:    0.5980
   chunk 8 optimal weight:    1.9990
   chunk 5 optimal weight:    6.9990
   chunk 31 optimal weight:    3.9990
   chunk 43 optimal weight:    3.9990
   chunk 42 optimal weight:    0.8980
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
A 162 GLN
A 266 ASN
A 292 GLN
B 162 GLN
B 266 ASN
B 292 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.139955 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.108093 restraints weight = 9249.890|
|-----------------------------------------------------------------------------|
r_work (start): 0.3311 rms_B_bonded: 2.12
r_work: 0.3151 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.3000 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.3000
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8316
moved from start:          0.2465

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7128  Z= 0.139
  Angle     :  0.584   8.034   9648  Z= 0.291
  Chirality :  0.038   0.120   1032
  Planarity :  0.004   0.036   1172
  Dihedral  : 15.609 176.739   1082
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 7.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.97 %
    Favored  : 93.03 %
  Rotamer:
    Outliers :  4.20 %
    Allowed  : 18.35 %
    Favored  : 77.45 %
  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:  0.80 (0.31), residues: 804
  helix:  1.57 (0.22), residues: 600
  sheet:  None (None), residues: 0
  loop : -2.78 (0.39), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 358 
 TYR   0.011   0.001   TYR A 417 
 PHE   0.030   0.002   PHE B 443 
 TRP   0.019   0.001   TRP A 340 
 HIS   0.004   0.001   HIS A 474 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 7126)
  covalent geometry    : angle       0.58379 ( 9648)
  hydrogen bonds       : bond        0.03346 (  438)
  hydrogen bonds       : angle       4.77887 ( 1308)
  Misc. bond           : bond        0.00042 (    2)

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 103
  time to evaluate  : 0.268 
Fit side-chains
REVERT: A  224 LYS cc_start: 0.8653 (ttpp) cc_final: 0.7878 (tmmt)
REVERT: A  368 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.8373 (pt0)
REVERT: A  400 LYS cc_start: 0.7370 (ttmt) cc_final: 0.7035 (ttmt)
REVERT: A  404 ARG cc_start: 0.7215 (mtt-85) cc_final: 0.6249 (mtm110)
REVERT: B   73 ASP cc_start: 0.8261 (OUTLIER) cc_final: 0.7989 (t0)
REVERT: B  224 LYS cc_start: 0.8646 (ttpp) cc_final: 0.7851 (tmmt)
REVERT: B  368 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.8394 (pt0)
REVERT: B  404 ARG cc_start: 0.7240 (mtt-85) cc_final: 0.6223 (mtm110)
  outliers start: 30
  outliers final: 13
  residues processed: 122
  average time/residue: 0.5034
  time to fit residues: 64.8244
Evaluate side-chains
  120 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 104
  time to evaluate  : 0.177 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  185 LEU
Chi-restraints excluded: chain A residue  251 ASP
Chi-restraints excluded: chain A residue  300 MET
Chi-restraints excluded: chain A residue  368 GLU
Chi-restraints excluded: chain A residue  377 TRP
Chi-restraints excluded: chain A residue  467 ILE
Chi-restraints excluded: chain B residue   73 ASP
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  251 ASP
Chi-restraints excluded: chain B residue  300 MET
Chi-restraints excluded: chain B residue  368 GLU
Chi-restraints excluded: chain B residue  377 TRP
Chi-restraints excluded: chain B residue  402 MET
Chi-restraints excluded: chain B residue  409 LEU
Chi-restraints excluded: chain B residue  467 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 3 optimal weight:    4.9990
   chunk 1 optimal weight:    2.9990
   chunk 45 optimal weight:   10.0000
   chunk 41 optimal weight:    3.9990
   chunk 34 optimal weight:    0.9980
   chunk 46 optimal weight:   10.0000
   chunk 16 optimal weight:    3.9990
   chunk 77 optimal weight:    3.9990
   chunk 19 optimal weight:    0.6980
   chunk 21 optimal weight:    0.6980
   chunk 14 optimal weight:    2.9990
   overall best weight:    1.6784

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

Flipped N/Q/H residues before XYZ refinement:
A 162 GLN
A 266 ASN
A 292 GLN
B 162 GLN
B 266 ASN
B 292 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.140359 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.108094 restraints weight = 9247.420|
|-----------------------------------------------------------------------------|
r_work (start): 0.3288 rms_B_bonded: 2.14
r_work: 0.3124 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work: 0.2974 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.2974
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8302
moved from start:          0.2417

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   7128  Z= 0.180
  Angle     :  0.604   7.895   9648  Z= 0.300
  Chirality :  0.040   0.121   1032
  Planarity :  0.004   0.033   1172
  Dihedral  : 15.543 172.590   1082
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 8.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.84 %
    Favored  : 92.16 %
  Rotamer:
    Outliers :  4.34 %
    Allowed  : 18.77 %
    Favored  : 76.89 %
  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:  0.75 (0.31), residues: 804
  helix:  1.53 (0.22), residues: 602
  sheet:  None (None), residues: 0
  loop : -2.79 (0.40), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 281 
 TYR   0.013   0.001   TYR B 417 
 PHE   0.017   0.001   PHE B 443 
 TRP   0.022   0.001   TRP B 340 
 HIS   0.004   0.001   HIS A 474 

Details of bonding type rmsd
  covalent geometry    : bond        0.00425 ( 7126)
  covalent geometry    : angle       0.60439 ( 9648)
  hydrogen bonds       : bond        0.03492 (  438)
  hydrogen bonds       : angle       4.79548 ( 1308)
  Misc. bond           : bond        0.00038 (    2)

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 109
  time to evaluate  : 0.256 
Fit side-chains
   revert: symmetry clash
REVERT: A  224 LYS cc_start: 0.8636 (ttpp) cc_final: 0.7847 (tmmt)
REVERT: A  363 ASP cc_start: 0.9020 (p0) cc_final: 0.8677 (p0)
REVERT: A  368 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.8376 (pt0)
REVERT: A  400 LYS cc_start: 0.7335 (ttmt) cc_final: 0.7024 (ttmt)
REVERT: A  404 ARG cc_start: 0.7154 (mtt-85) cc_final: 0.6199 (mtm110)
REVERT: B  224 LYS cc_start: 0.8610 (ttpp) cc_final: 0.7841 (tmmt)
REVERT: B  368 GLU cc_start: 0.8639 (OUTLIER) cc_final: 0.8391 (pt0)
REVERT: B  404 ARG cc_start: 0.7192 (mtt-85) cc_final: 0.6186 (mtm110)
  outliers start: 31
  outliers final: 15
  residues processed: 130
  average time/residue: 0.4839
  time to fit residues: 66.6331
Evaluate side-chains
  117 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 100
  time to evaluate  : 0.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  185 LEU
Chi-restraints excluded: chain A residue  251 ASP
Chi-restraints excluded: chain A residue  266 ASN
Chi-restraints excluded: chain A residue  300 MET
Chi-restraints excluded: chain A residue  368 GLU
Chi-restraints excluded: chain A residue  377 TRP
Chi-restraints excluded: chain A residue  427 ARG
Chi-restraints excluded: chain A residue  467 ILE
Chi-restraints excluded: chain B residue   73 ASP
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  251 ASP
Chi-restraints excluded: chain B residue  266 ASN
Chi-restraints excluded: chain B residue  300 MET
Chi-restraints excluded: chain B residue  368 GLU
Chi-restraints excluded: chain B residue  377 TRP
Chi-restraints excluded: chain B residue  467 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 18 optimal weight:    0.0270
   chunk 75 optimal weight:    0.9980
   chunk 28 optimal weight:    0.6980
   chunk 20 optimal weight:    0.7980
   chunk 48 optimal weight:    0.9990
   chunk 59 optimal weight:    5.9990
   chunk 13 optimal weight:    0.9980
   chunk 7 optimal weight:    1.9990
   chunk 10 optimal weight:    0.7980
   chunk 71 optimal weight:    5.9990
   chunk 16 optimal weight:    0.9990
   overall best weight:    0.6638

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

Flipped N/Q/H residues before XYZ refinement:
A 162 GLN
A 266 ASN
A 292 GLN
B 162 GLN
B 266 ASN
B 292 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.142831 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.111439 restraints weight = 9354.781|
|-----------------------------------------------------------------------------|
r_work (start): 0.3328 rms_B_bonded: 2.15
r_work: 0.3165 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work (final): 0.3165
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8155
moved from start:          0.2647

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7128  Z= 0.121
  Angle     :  0.578   7.896   9648  Z= 0.289
  Chirality :  0.038   0.121   1032
  Planarity :  0.004   0.031   1172
  Dihedral  : 15.130 173.990   1082
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 8.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.72 %
    Favored  : 93.28 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 20.45 %
    Favored  : 76.47 %
  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:  0.96 (0.31), residues: 804
  helix:  1.70 (0.22), residues: 602
  sheet:  None (None), residues: 0
  loop : -2.77 (0.40), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 281 
 TYR   0.010   0.001   TYR A 211 
 PHE   0.031   0.001   PHE B 443 
 TRP   0.027   0.001   TRP A 340 
 HIS   0.004   0.001   HIS B 474 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 7126)
  covalent geometry    : angle       0.57820 ( 9648)
  hydrogen bonds       : bond        0.03238 (  438)
  hydrogen bonds       : angle       4.72804 ( 1308)
  Misc. bond           : bond        0.00047 (    2)

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 112
  time to evaluate  : 0.170 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 ASP cc_start: 0.8093 (m-30) cc_final: 0.7758 (t0)
REVERT: A  224 LYS cc_start: 0.8659 (ttpp) cc_final: 0.7857 (tmmt)
REVERT: A  318 ARG cc_start: 0.7561 (mmp-170) cc_final: 0.7147 (ttm170)
REVERT: A  400 LYS cc_start: 0.7397 (ttmt) cc_final: 0.7089 (ttmt)
REVERT: A  404 ARG cc_start: 0.7192 (mtt-85) cc_final: 0.6236 (mtm110)
REVERT: A  467 ILE cc_start: 0.8452 (OUTLIER) cc_final: 0.8144 (mp)
REVERT: B   73 ASP cc_start: 0.8077 (OUTLIER) cc_final: 0.7787 (t0)
REVERT: B  224 LYS cc_start: 0.8630 (ttpp) cc_final: 0.7828 (tmmt)
REVERT: B  404 ARG cc_start: 0.7165 (mtt-85) cc_final: 0.6174 (mtm110)
REVERT: B  467 ILE cc_start: 0.8468 (OUTLIER) cc_final: 0.8153 (mp)
  outliers start: 22
  outliers final: 10
  residues processed: 126
  average time/residue: 0.5421
  time to fit residues: 71.8080
Evaluate side-chains
  117 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 104
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  251 ASP
Chi-restraints excluded: chain A residue  266 ASN
Chi-restraints excluded: chain A residue  377 TRP
Chi-restraints excluded: chain A residue  427 ARG
Chi-restraints excluded: chain A residue  467 ILE
Chi-restraints excluded: chain B residue   73 ASP
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  251 ASP
Chi-restraints excluded: chain B residue  266 ASN
Chi-restraints excluded: chain B residue  377 TRP
Chi-restraints excluded: chain B residue  409 LEU
Chi-restraints excluded: chain B residue  467 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 19 optimal weight:    4.9990
   chunk 31 optimal weight:    3.9990
   chunk 15 optimal weight:    0.9990
   chunk 56 optimal weight:    3.9990
   chunk 77 optimal weight:    4.9990
   chunk 36 optimal weight:    4.9990
   chunk 11 optimal weight:    0.8980
   chunk 29 optimal weight:    3.9990
   chunk 60 optimal weight:    0.8980
   chunk 73 optimal weight:    3.9990
   chunk 28 optimal weight:    1.9990
   overall best weight:    1.7586

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

Flipped N/Q/H residues before XYZ refinement:
A 162 GLN
A 266 ASN
A 292 GLN
B 162 GLN
B 266 ASN
B 292 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.139873 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.106878 restraints weight = 9367.945|
|-----------------------------------------------------------------------------|
r_work (start): 0.3287 rms_B_bonded: 2.19
r_work: 0.3124 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.3124
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8211
moved from start:          0.2530

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   7128  Z= 0.185
  Angle     :  0.602   7.587   9648  Z= 0.300
  Chirality :  0.040   0.145   1032
  Planarity :  0.004   0.031   1172
  Dihedral  : 15.110 170.712   1082
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 8.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.34 %
    Favored  : 92.66 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 20.59 %
    Favored  : 76.33 %
  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:  0.88 (0.31), residues: 804
  helix:  1.64 (0.22), residues: 600
  sheet:  None (None), residues: 0
  loop : -2.78 (0.39), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 281 
 TYR   0.012   0.001   TYR B 417 
 PHE   0.018   0.002   PHE A 443 
 TRP   0.025   0.001   TRP A 340 
 HIS   0.004   0.001   HIS A 474 

Details of bonding type rmsd
  covalent geometry    : bond        0.00437 ( 7126)
  covalent geometry    : angle       0.60203 ( 9648)
  hydrogen bonds       : bond        0.03457 (  438)
  hydrogen bonds       : angle       4.77703 ( 1308)
  Misc. bond           : bond        0.00042 (    2)

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 108
  time to evaluate  : 0.276 
Fit side-chains
REVERT: A  224 LYS cc_start: 0.8638 (ttpp) cc_final: 0.7858 (tmmt)
REVERT: A  318 ARG cc_start: 0.7495 (mmp-170) cc_final: 0.7171 (ttm170)
REVERT: A  400 LYS cc_start: 0.7415 (ttmt) cc_final: 0.7103 (ttmt)
REVERT: A  404 ARG cc_start: 0.7219 (mtt-85) cc_final: 0.6270 (mtm110)
REVERT: B   73 ASP cc_start: 0.8069 (OUTLIER) cc_final: 0.7748 (t0)
REVERT: B  224 LYS cc_start: 0.8627 (ttpp) cc_final: 0.7849 (tmmt)
REVERT: B  404 ARG cc_start: 0.7187 (mtt-85) cc_final: 0.6191 (mtm110)
  outliers start: 22
  outliers final: 10
  residues processed: 123
  average time/residue: 0.5570
  time to fit residues: 72.1099
Evaluate side-chains
  120 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 109
  time to evaluate  : 0.182 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  251 ASP
Chi-restraints excluded: chain A residue  377 TRP
Chi-restraints excluded: chain A residue  409 LEU
Chi-restraints excluded: chain A residue  467 ILE
Chi-restraints excluded: chain B residue   73 ASP
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  251 ASP
Chi-restraints excluded: chain B residue  377 TRP
Chi-restraints excluded: chain B residue  409 LEU
Chi-restraints excluded: chain B residue  467 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 12 optimal weight:    0.3980
   chunk 59 optimal weight:    6.9990
   chunk 39 optimal weight:    0.6980
   chunk 61 optimal weight:    0.9980
   chunk 44 optimal weight:   10.0000
   chunk 6 optimal weight:    7.9990
   chunk 0 optimal weight:    6.9990
   chunk 5 optimal weight:    0.9990
   chunk 48 optimal weight:    0.6980
   chunk 32 optimal weight:    5.9990
   chunk 57 optimal weight:    0.9990
   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 162 GLN
A 266 ASN
A 292 GLN
B 162 GLN
B 266 ASN
B 292 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.141701 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.109655 restraints weight = 9191.812|
|-----------------------------------------------------------------------------|
r_work (start): 0.3333 rms_B_bonded: 2.13
r_work: 0.3175 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work: 0.3025 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.3025
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8276
moved from start:          0.2794

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7128  Z= 0.124
  Angle     :  0.579   7.728   9648  Z= 0.290
  Chirality :  0.039   0.128   1032
  Planarity :  0.004   0.031   1172
  Dihedral  : 14.701 171.186   1082
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 7.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.97 %
    Favored  : 93.03 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 21.15 %
    Favored  : 75.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.07 (0.31), residues: 804
  helix:  1.77 (0.22), residues: 602
  sheet:  None (None), residues: 0
  loop : -2.71 (0.40), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 281 
 TYR   0.010   0.001   TYR B 211 
 PHE   0.030   0.002   PHE B 443 
 TRP   0.032   0.001   TRP A 340 
 HIS   0.003   0.001   HIS B 474 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 7126)
  covalent geometry    : angle       0.57948 ( 9648)
  hydrogen bonds       : bond        0.03236 (  438)
  hydrogen bonds       : angle       4.73300 ( 1308)
  Misc. bond           : bond        0.00044 (    2)

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 120
  time to evaluate  : 0.158 
Fit side-chains
REVERT: A   73 ASP cc_start: 0.8314 (m-30) cc_final: 0.7976 (t0)
REVERT: A  318 ARG cc_start: 0.7465 (mmp-170) cc_final: 0.7082 (ttm170)
REVERT: A  363 ASP cc_start: 0.8861 (p0) cc_final: 0.8254 (p0)
REVERT: A  400 LYS cc_start: 0.7334 (ttmt) cc_final: 0.7022 (ttmt)
REVERT: A  404 ARG cc_start: 0.7233 (mtt-85) cc_final: 0.6257 (mtm110)
REVERT: A  467 ILE cc_start: 0.8560 (OUTLIER) cc_final: 0.8295 (mp)
REVERT: B   73 ASP cc_start: 0.8281 (OUTLIER) cc_final: 0.7992 (t0)
REVERT: B  404 ARG cc_start: 0.7149 (mtt-85) cc_final: 0.6767 (mtt90)
REVERT: B  467 ILE cc_start: 0.8576 (OUTLIER) cc_final: 0.8309 (mp)
  outliers start: 21
  outliers final: 12
  residues processed: 135
  average time/residue: 0.5350
  time to fit residues: 76.0140
Evaluate side-chains
  124 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 109
  time to evaluate  : 0.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  251 ASP
Chi-restraints excluded: chain A residue  266 ASN
Chi-restraints excluded: chain A residue  377 TRP
Chi-restraints excluded: chain A residue  467 ILE
Chi-restraints excluded: chain B residue   73 ASP
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  156 VAL
Chi-restraints excluded: chain B residue  251 ASP
Chi-restraints excluded: chain B residue  266 ASN
Chi-restraints excluded: chain B residue  295 LEU
Chi-restraints excluded: chain B residue  300 MET
Chi-restraints excluded: chain B residue  377 TRP
Chi-restraints excluded: chain B residue  409 LEU
Chi-restraints excluded: chain B residue  467 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 14 optimal weight:    1.9990
   chunk 59 optimal weight:    0.2980
   chunk 38 optimal weight:    1.9990
   chunk 70 optimal weight:    2.9990
   chunk 77 optimal weight:    1.9990
   chunk 3 optimal weight:    4.9990
   chunk 56 optimal weight:    0.6980
   chunk 47 optimal weight:    0.8980
   chunk 19 optimal weight:   10.0000
   chunk 7 optimal weight:    0.9990
   chunk 54 optimal weight:    0.6980
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
A 162 GLN
A 292 GLN
B 162 GLN
** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.142775 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.110276 restraints weight = 9214.691|
|-----------------------------------------------------------------------------|
r_work (start): 0.3335 rms_B_bonded: 2.16
r_work: 0.3175 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.3175
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8191
moved from start:          0.2810

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061   7128  Z= 0.213
  Angle     :  1.266  59.199   9648  Z= 0.765
  Chirality :  0.042   0.236   1032
  Planarity :  0.004   0.031   1172
  Dihedral  : 14.702 171.175   1082
  Min Nonbonded Distance : 2.225

Molprobity Statistics.
  All-atom Clashscore : 10.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.72 %
    Favored  : 93.28 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 21.85 %
    Favored  : 76.05 %
  Cbeta Deviations :  0.26 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.11 (0.31), residues: 804
  helix:  1.79 (0.22), residues: 602
  sheet:  None (None), residues: 0
  loop : -2.68 (0.40), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG A 427 
 TYR   0.010   0.001   TYR B 211 
 PHE   0.029   0.002   PHE B 443 
 TRP   0.029   0.001   TRP A 340 
 HIS   0.003   0.001   HIS B 474 

Details of bonding type rmsd
  covalent geometry    : bond        0.00395 ( 7126)
  covalent geometry    : angle       1.26585 ( 9648)
  hydrogen bonds       : bond        0.03227 (  438)
  hydrogen bonds       : angle       4.74417 ( 1308)
  Misc. bond           : bond        0.00046 (    2)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2343.39 seconds
wall clock time: 40 minutes 40.23 seconds (2440.23 seconds total)