Starting phenix.real_space_refine
on Tue Mar  3 13:02:56 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7swo_25477/03_2026/7swo_25477_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7swo_25477/03_2026/7swo_25477.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7swo_25477/03_2026/7swo_25477.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7swo_25477/03_2026/7swo_25477.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7swo_25477/03_2026/7swo_25477_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7swo_25477/03_2026/7swo_25477_neut.cif"
  }
  resolution = 4.1
  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=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      20      5.16       5
     C    3020      2.51       5
     N     804      2.21       5
     O     940      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 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: 4784
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 1545
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 195, 1545
          Classifications: {'peptide': 195}
          Link IDs: {'PTRANS': 11, 'TRANS': 183}
    Chain: "H"
      Number of atoms: 1616
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 219, 1616
          Classifications: {'peptide': 219}
          Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 207}
    Chain: "L"
      Number of atoms: 1623
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 213, 1623
          Classifications: {'peptide': 213}
          Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 200}
  Time building chain proxies: 1.02, per 1000 atoms: 0.21
  Number of scatterers: 4784
  At special positions: 0
  Unit cell: (81.675, 72.6, 122.925, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      20     16.00
     O     940      8.00
     N     804      7.00
     C    3020      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=8, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 336 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 379 " - pdb=" SG  CYS A 432 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 391 " - pdb=" SG  CYS A 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 480 " - pdb=" SG  CYS A 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  95 " distance=2.04
    Simple disulfide: pdb=" SG  CYS H 144 " - pdb=" SG  CYS H 200 " distance=2.04
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  89 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L 134 " - pdb=" SG  CYS L 194 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.36
  Conformation dependent library (CDL) restraints added in 273.1 milliseconds
  

  1242 Ramachandran restraints generated.
    621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1148

  Finding SS restraints...
    Secondary structure from input PDB file:
      14 helices and 11 sheets defined
      12.4% alpha, 32.9% 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 338 through 343
    Processing helix  chain 'A' and resid 349 through 353
    Processing helix  chain 'A' and resid 386 through 390
      removed outlier: 3.825A  pdb=" N   LEU A 390 " --> pdb=" O   LEU A 387 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 404 through 411
    Processing helix  chain 'A' and resid 416 through 421
      removed outlier: 3.514A  pdb=" N   TYR A 421 " --> pdb=" O   LYS A 417 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 438 through 443
      removed outlier: 3.523A  pdb=" N   SER A 443 " --> pdb=" O   ASN A 439 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 28 through 32
      removed outlier: 3.800A  pdb=" N   ASN H  32 " --> pdb=" O   VAL H  29 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 86 through 90
      removed outlier: 3.607A  pdb=" N   THR H  90 " --> pdb=" O   ALA H  87 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 131 through 135
      removed outlier: 3.655A  pdb=" N   THR H 135 " --> pdb=" O   SER H 132 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 160 through 162
      No H-bonds generated for 'chain 'H' and resid 160 through 162'
    Processing helix  chain 'H' and resid 189 through 194
      removed outlier: 4.149A  pdb=" N   GLY H 194 " --> pdb=" O   SER H 190 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 80 through 84
    Processing helix  chain 'L' and resid 121 through 126
    Processing helix  chain 'L' and resid 183 through 189
      removed outlier: 3.902A  pdb=" N   HIS L 189 " --> pdb=" O   ASP L 185 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 376 through 379
    Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454
    Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 474
    Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 7
      removed outlier: 3.663A  pdb=" N   GLN H   3 " --> pdb=" O   SER H  25 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 12
      removed outlier: 3.890A  pdb=" N   TYR H  33 " --> pdb=" O   ASP H  98 " (cutoff:3.500A)
      removed outlier: 6.731A  pdb=" N   MET H  34 " --> pdb=" O   VAL H  50 " (cutoff:3.500A)
      removed outlier: 4.503A  pdb=" N   VAL H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 6.655A  pdb=" N   TRP H  36 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
      removed outlier: 4.784A  pdb=" N   ALA H  40 " --> pdb=" O   GLY H  44 " (cutoff:3.500A)
      removed outlier: 5.847A  pdb=" N   GLY H  44 " --> pdb=" O   ALA H  40 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'H' and resid 125 through 128
      removed outlier: 5.638A  pdb=" N   TYR H 180 " --> pdb=" O   ASP H 148 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'H' and resid 155 through 158
    Processing sheet with id=AA8, first strand: chain 'L' and resid 4 through 7
      removed outlier: 6.587A  pdb=" N   THR L  70 " --> pdb=" O   ALA L  25 " (cutoff:3.500A)
      removed outlier: 10.917A  pdb=" N   GLN L  27 " --> pdb=" O   SER L  68 " (cutoff:3.500A)
      removed outlier: 10.188A  pdb=" N   SER L  68 " --> pdb=" O   GLN L  27 " (cutoff:3.500A)
      removed outlier: 11.355A  pdb=" N   VAL L  29 " --> pdb=" O   SER L  66 " (cutoff:3.500A)
      removed outlier: 11.926A  pdb=" N   SER L  66 " --> pdb=" O   VAL L  29 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'L' and resid 11 through 13
      removed outlier: 3.557A  pdb=" N   TYR L  87 " --> pdb=" O   THR L 102 " (cutoff:3.500A)
      removed outlier: 7.504A  pdb=" N   LEU L  34 " --> pdb=" O   TYR L  50 " (cutoff:3.500A)
      removed outlier: 5.591A  pdb=" N   TYR L  50 " --> pdb=" O   LEU L  34 " (cutoff:3.500A)
      removed outlier: 6.520A  pdb=" N   TRP L  36 " --> pdb=" O   LEU L  48 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'L' and resid 116 through 118
      removed outlier: 5.228A  pdb=" N   SER L 131 " --> pdb=" O   LEU L 181 " (cutoff:3.500A)
      removed outlier: 7.464A  pdb=" N   LEU L 181 " --> pdb=" O   SER L 131 " (cutoff:3.500A)
      removed outlier: 6.743A  pdb=" N   VAL L 133 " --> pdb=" O   LEU L 179 " (cutoff:3.500A)
      removed outlier: 7.802A  pdb=" N   LEU L 179 " --> pdb=" O   VAL L 133 " (cutoff:3.500A)
      removed outlier: 5.696A  pdb=" N   LEU L 135 " --> pdb=" O   SER L 177 " (cutoff:3.500A)
      removed outlier: 7.255A  pdb=" N   SER L 177 " --> pdb=" O   LEU L 135 " (cutoff:3.500A)
      removed outlier: 5.216A  pdb=" N   ASN L 137 " --> pdb=" O   LEU L 175 " (cutoff:3.500A)
      removed outlier: 6.922A  pdb=" N   LEU L 175 " --> pdb=" O   ASN L 137 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'L' and resid 144 through 150

    153 hydrogen bonds defined for protein.
    363 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.77

  Time building geometry restraints manager: 0.51 seconds

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

  Histogram of bond lengths:
        1.21 -     1.34: 1518
        1.34 -     1.46: 1112
        1.46 -     1.58: 2246
        1.58 -     1.70: 0
        1.70 -     1.82: 23
  Bond restraints: 4899
  Sorted by residual:
  bond pdb=" N   ILE L 106 "
       pdb=" CA  ILE L 106 "
    ideal  model  delta    sigma   weight residual
    1.460  1.494 -0.034 1.10e-02 8.26e+03 9.54e+00
  bond pdb=" N   LYS H 147 "
       pdb=" CA  LYS H 147 "
    ideal  model  delta    sigma   weight residual
    1.456  1.487 -0.031 1.21e-02 6.83e+03 6.53e+00
  bond pdb=" N   ARG L 108 "
       pdb=" CA  ARG L 108 "
    ideal  model  delta    sigma   weight residual
    1.457  1.486 -0.029 1.20e-02 6.94e+03 5.90e+00
  bond pdb=" N   GLU L 123 "
       pdb=" CA  GLU L 123 "
    ideal  model  delta    sigma   weight residual
    1.459  1.488 -0.029 1.23e-02 6.61e+03 5.40e+00
  bond pdb=" N   TYR L  87 "
       pdb=" CA  TYR L  87 "
    ideal  model  delta    sigma   weight residual
    1.456  1.485 -0.028 1.23e-02 6.61e+03 5.35e+00
  ... (remaining 4894 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.93: 6369
        1.93 -     3.86: 243
        3.86 -     5.79: 44
        5.79 -     7.72: 8
        7.72 -     9.65: 1
  Bond angle restraints: 6665
  Sorted by residual:
  angle pdb=" N   THR L 109 "
        pdb=" CA  THR L 109 "
        pdb=" C   THR L 109 "
      ideal   model   delta    sigma   weight residual
     110.35  105.09    5.26 1.40e+00 5.10e-01 1.41e+01
  angle pdb=" C   ASP A 420 "
        pdb=" N   TYR A 421 "
        pdb=" CA  TYR A 421 "
      ideal   model   delta    sigma   weight residual
     122.58  114.99    7.59 2.07e+00 2.33e-01 1.34e+01
  angle pdb=" N   CYS A 525 "
        pdb=" CA  CYS A 525 "
        pdb=" C   CYS A 525 "
      ideal   model   delta    sigma   weight residual
     107.88  112.96   -5.08 1.41e+00 5.03e-01 1.30e+01
  angle pdb=" N   GLU L 123 "
        pdb=" CA  GLU L 123 "
        pdb=" C   GLU L 123 "
      ideal   model   delta    sigma   weight residual
     111.33  107.12    4.21 1.21e+00 6.83e-01 1.21e+01
  angle pdb=" N   LYS L 107 "
        pdb=" CA  LYS L 107 "
        pdb=" C   LYS L 107 "
      ideal   model   delta    sigma   weight residual
     110.24  105.84    4.40 1.47e+00 4.63e-01 8.95e+00
  ... (remaining 6660 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.69: 2604
       17.69 -    35.38: 252
       35.38 -    53.07: 48
       53.07 -    70.75: 7
       70.75 -    88.44: 6
  Dihedral angle restraints: 2917
    sinusoidal: 1111
      harmonic: 1806
  Sorted by residual:
  dihedral pdb=" CB  CYS A 336 "
           pdb=" SG  CYS A 336 "
           pdb=" SG  CYS A 361 "
           pdb=" CB  CYS A 361 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   40.97   52.03     1      1.00e+01 1.00e-02 3.69e+01
  dihedral pdb=" CB  CYS A 379 "
           pdb=" SG  CYS A 379 "
           pdb=" SG  CYS A 432 "
           pdb=" CB  CYS A 432 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -45.72  -40.28     1      1.00e+01 1.00e-02 2.28e+01
  dihedral pdb=" CA  TYR A 365 "
           pdb=" C   TYR A 365 "
           pdb=" N   SER A 366 "
           pdb=" CA  SER A 366 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.92  -22.08     0      5.00e+00 4.00e-02 1.95e+01
  ... (remaining 2914 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 497
       0.046 -    0.091: 176
       0.091 -    0.136: 52
       0.136 -    0.182: 12
       0.182 -    0.227: 4
  Chirality restraints: 741
  Sorted by residual:
  chirality pdb=" CB  VAL H 100 "
            pdb=" CA  VAL H 100 "
            pdb=" CG1 VAL H 100 "
            pdb=" CG2 VAL H 100 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.40   -0.23 2.00e-01 2.50e+01 1.29e+00
  chirality pdb=" CB  ILE H  27 "
            pdb=" CA  ILE H  27 "
            pdb=" CG1 ILE H  27 "
            pdb=" CG2 ILE H  27 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.42    0.22 2.00e-01 2.50e+01 1.24e+00
  chirality pdb=" CA  VAL H 154 "
            pdb=" N   VAL H 154 "
            pdb=" C   VAL H 154 "
            pdb=" CB  VAL H 154 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.63   -0.19 2.00e-01 2.50e+01 8.90e-01
  ... (remaining 738 not shown)

  Planarity restraints: 860
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE H 126 "   -0.062 5.00e-02 4.00e+02   9.43e-02 1.42e+01
        pdb=" N   PRO H 127 "    0.163 5.00e-02 4.00e+02
        pdb=" CA  PRO H 127 "   -0.050 5.00e-02 4.00e+02
        pdb=" CD  PRO H 127 "   -0.051 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL L  86 "   -0.012 2.00e-02 2.50e+03   2.43e-02 5.89e+00
        pdb=" C   VAL L  86 "    0.042 2.00e-02 2.50e+03
        pdb=" O   VAL L  86 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   TYR L  87 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 453 "    0.023 2.00e-02 2.50e+03   1.65e-02 5.43e+00
        pdb=" CG  TYR A 453 "   -0.040 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 453 "    0.005 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 453 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 453 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 453 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 453 "    0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR A 453 "    0.003 2.00e-02 2.50e+03
  ... (remaining 857 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 803
        2.75 -     3.29: 4862
        3.29 -     3.83: 7985
        3.83 -     4.36: 9445
        4.36 -     4.90: 15953
  Nonbonded interactions: 39048
  Sorted by model distance:
  nonbonded pdb=" OG  SER L   7 "
            pdb=" OG  SER L  22 "
     model   vdw
     2.215 3.040
  nonbonded pdb=" OG  SER H   7 "
            pdb=" OG  SER H  21 "
     model   vdw
     2.216 3.040
  nonbonded pdb=" OD2 ASP A 398 "
            pdb=" OH  TYR A 423 "
     model   vdw
     2.218 3.040
  nonbonded pdb=" O   GLN H   3 "
            pdb=" OG  SER H  25 "
     model   vdw
     2.227 3.040
  nonbonded pdb=" OG  SER L  66 "
            pdb=" OG1 THR L  73 "
     model   vdw
     2.227 3.040
  ... (remaining 39043 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.860
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     6.500
  Find NCS groups from input model:        0.030
  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:1.380
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.900
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7614
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      :  0.007   0.049   4907  Z= 0.312
  Angle     :  0.897   9.655   6681  Z= 0.487
  Chirality :  0.053   0.227    741
  Planarity :  0.006   0.094    860
  Dihedral  : 14.431  88.441   1745
  Min Nonbonded Distance : 2.215

Molprobity Statistics.
  All-atom Clashscore : 26.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.98 %
    Favored  : 90.02 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  0.93 %
    Favored  : 98.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.76 %
    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 (0.34), residues: 621
  helix: -2.41 (0.88), residues: 25
  sheet: -1.33 (0.34), residues: 229
  loop : -1.97 (0.33), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG H 214 
 TYR   0.040   0.002   TYR A 453 
 PHE   0.022   0.002   PHE L 139 
 TRP   0.019   0.003   TRP A 353 
 HIS   0.003   0.002   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00665 ( 4899)
  covalent geometry    : angle       0.89347 ( 6665)
  SS BOND              : bond        0.00570 (    8)
  SS BOND              : angle       1.76795 (   16)
  hydrogen bonds       : bond        0.13312 (  153)
  hydrogen bonds       : angle       9.48945 (  363)

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

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

  1242 Ramachandran restraints generated.
    621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1242 Ramachandran restraints generated.
    621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 125
  time to evaluate  : 0.143 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  355 ARG cc_start: 0.8149 (mmt90) cc_final: 0.7921 (mmt90)
REVERT: A  444 LYS cc_start: 0.8096 (ttmt) cc_final: 0.7378 (mmtm)
REVERT: A  458 LYS cc_start: 0.8902 (ttmt) cc_final: 0.8417 (tmtt)
REVERT: A  465 GLU cc_start: 0.7893 (mt-10) cc_final: 0.7563 (mt-10)
REVERT: H   20 LEU cc_start: 0.6872 (mp) cc_final: 0.6479 (mp)
REVERT: H   80 LEU cc_start: 0.7629 (tp) cc_final: 0.7052 (tp)
REVERT: L   87 TYR cc_start: 0.8498 (m-80) cc_final: 0.8029 (m-80)
  outliers start: 1
  outliers final: 0
  residues processed: 126
  average time/residue: 0.0997
  time to fit residues: 15.1870
Evaluate side-chains
  103 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.195 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 54 optimal weight:    1.9990
   chunk 24 optimal weight:    0.7980
   chunk 48 optimal weight:    0.9990
   chunk 56 optimal weight:    0.0060
   chunk 26 optimal weight:    3.9990
   chunk 2 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9980
   chunk 32 optimal weight:    0.3980
   chunk 31 optimal weight:    5.9990
   chunk 25 optimal weight:    0.8980
   chunk 58 optimal weight:    9.9990
   overall best weight:    0.6196

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

Flipped N/Q/H residues before XYZ refinement:
A 506 GLN
** H  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 203 ASN
L  39 GLN
** L 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 166 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 = 0.3702 r_free = 0.3702 target = 0.131196 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.106713 restraints weight = 9835.793|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.109679 restraints weight = 5834.282|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.111767 restraints weight = 3997.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.113091 restraints weight = 3020.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.114122 restraints weight = 2479.477|
|-----------------------------------------------------------------------------|
r_work (final): 0.3458
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7503
moved from start:          0.1667

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4907  Z= 0.137
  Angle     :  0.672   8.219   6681  Z= 0.347
  Chirality :  0.046   0.168    741
  Planarity :  0.006   0.069    860
  Dihedral  :  6.069  19.592    682
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 14.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.12 %
    Favored  : 93.88 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.72 %
    Favored  : 93.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.76 %
    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: -2.03 (0.34), residues: 621
  helix: -1.98 (0.85), residues: 32
  sheet: -1.14 (0.33), residues: 232
  loop : -1.40 (0.36), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG H  71 
 TYR   0.012   0.001   TYR L  87 
 PHE   0.009   0.001   PHE H 170 
 TRP   0.015   0.001   TRP A 353 
 HIS   0.002   0.001   HIS L 198 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 4899)
  covalent geometry    : angle       0.67015 ( 6665)
  SS BOND              : bond        0.00404 (    8)
  SS BOND              : angle       1.21432 (   16)
  hydrogen bonds       : bond        0.03655 (  153)
  hydrogen bonds       : angle       7.90011 (  363)

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

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

  1242 Ramachandran restraints generated.
    621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1242 Ramachandran restraints generated.
    621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 133
  time to evaluate  : 0.156 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  444 LYS cc_start: 0.8132 (ttmt) cc_final: 0.7403 (mmtm)
REVERT: A  458 LYS cc_start: 0.8831 (ttmt) cc_final: 0.8330 (tmtt)
REVERT: A  465 GLU cc_start: 0.7760 (mt-10) cc_final: 0.7541 (mt-10)
REVERT: A  505 TYR cc_start: 0.7960 (m-80) cc_final: 0.7703 (m-80)
REVERT: H   80 LEU cc_start: 0.7501 (tp) cc_final: 0.7036 (tp)
REVERT: H   81 GLN cc_start: 0.6697 (tm-30) cc_final: 0.6179 (tm-30)
REVERT: L   11 LEU cc_start: 0.8534 (mt) cc_final: 0.8280 (mt)
REVERT: L   37 TYR cc_start: 0.8825 (m-80) cc_final: 0.8391 (m-80)
REVERT: L  150 VAL cc_start: 0.7908 (t) cc_final: 0.7692 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 133
  average time/residue: 0.0964
  time to fit residues: 15.6073
Evaluate side-chains
  105 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 12 optimal weight:    0.9990
   chunk 49 optimal weight:    2.9990
   chunk 4 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   chunk 3 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9980
   chunk 14 optimal weight:    0.8980
   chunk 46 optimal weight:    5.9990
   chunk 11 optimal weight:    7.9990
   chunk 57 optimal weight:    3.9990
   chunk 50 optimal weight:    0.9990
   overall best weight:    1.1786

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

Flipped N/Q/H residues before XYZ refinement:
A 370 ASN
** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  39 GLN
** H 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 203 ASN
** L 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 166 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 = 0.3701 r_free = 0.3701 target = 0.131098 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.106606 restraints weight = 9799.960|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.109559 restraints weight = 5869.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.111600 restraints weight = 4056.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.113075 restraints weight = 3059.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.113945 restraints weight = 2480.722|
|-----------------------------------------------------------------------------|
r_work (final): 0.3456
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7520
moved from start:          0.2063

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   4907  Z= 0.157
  Angle     :  0.679  10.908   6681  Z= 0.346
  Chirality :  0.046   0.179    741
  Planarity :  0.005   0.056    860
  Dihedral  :  5.903  18.840    682
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 14.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.09 %
    Favored  : 92.91 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.53 %
    Favored  : 93.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.76 %
    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: -1.73 (0.35), residues: 621
  helix: -1.40 (1.10), residues: 25
  sheet: -1.05 (0.32), residues: 253
  loop : -1.13 (0.37), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG H  71 
 TYR   0.017   0.002   TYR A 453 
 PHE   0.012   0.001   PHE H 126 
 TRP   0.015   0.002   TRP A 353 
 HIS   0.002   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 4899)
  covalent geometry    : angle       0.67659 ( 6665)
  SS BOND              : bond        0.00436 (    8)
  SS BOND              : angle       1.32391 (   16)
  hydrogen bonds       : bond        0.03450 (  153)
  hydrogen bonds       : angle       7.70762 (  363)

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

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

  1242 Ramachandran restraints generated.
    621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1242 Ramachandran restraints generated.
    621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 121
  time to evaluate  : 0.123 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  335 LEU cc_start: 0.8472 (pp) cc_final: 0.8214 (tp)
REVERT: A  444 LYS cc_start: 0.8054 (ttpt) cc_final: 0.7399 (mmtm)
REVERT: A  458 LYS cc_start: 0.8794 (ttmt) cc_final: 0.8292 (tmtt)
REVERT: A  465 GLU cc_start: 0.7700 (mt-10) cc_final: 0.7463 (mt-10)
REVERT: H   88 GLU cc_start: 0.8356 (pm20) cc_final: 0.8079 (pm20)
REVERT: L   37 TYR cc_start: 0.8929 (m-80) cc_final: 0.8457 (m-80)
REVERT: L  150 VAL cc_start: 0.7943 (t) cc_final: 0.7670 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 121
  average time/residue: 0.0764
  time to fit residues: 11.7144
Evaluate side-chains
  95 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 54 optimal weight:    6.9990
   chunk 46 optimal weight:    8.9990
   chunk 55 optimal weight:    6.9990
   chunk 12 optimal weight:    2.9990
   chunk 3 optimal weight:    7.9990
   chunk 2 optimal weight:    0.3980
   chunk 17 optimal weight:    0.0040
   chunk 56 optimal weight:    5.9990
   chunk 22 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9990
   chunk 39 optimal weight:    5.9990
   overall best weight:    1.2798

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

Flipped N/Q/H residues before XYZ refinement:
A 370 ASN
** H  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 203 ASN
L 124 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.131470 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.106952 restraints weight = 9662.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.109951 restraints weight = 5732.367|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.111969 restraints weight = 3918.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.113379 restraints weight = 2975.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.114356 restraints weight = 2430.330|
|-----------------------------------------------------------------------------|
r_work (final): 0.3461
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7503
moved from start:          0.2282

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   4907  Z= 0.159
  Angle     :  0.666   9.920   6681  Z= 0.342
  Chirality :  0.046   0.197    741
  Planarity :  0.006   0.051    860
  Dihedral  :  5.756  18.056    682
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 14.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.76 %
    Favored  : 93.24 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  4.10 %
    Favored  : 95.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.76 %
    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: -1.48 (0.36), residues: 621
  helix: -1.90 (0.95), residues: 26
  sheet: -0.77 (0.33), residues: 248
  loop : -1.00 (0.37), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG H  71 
 TYR   0.015   0.002   TYR A 453 
 PHE   0.021   0.002   PHE H 150 
 TRP   0.014   0.002   TRP A 353 
 HIS   0.002   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 ( 4899)
  covalent geometry    : angle       0.66456 ( 6665)
  SS BOND              : bond        0.00432 (    8)
  SS BOND              : angle       1.16359 (   16)
  hydrogen bonds       : bond        0.03329 (  153)
  hydrogen bonds       : angle       7.55281 (  363)

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

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

  1242 Ramachandran restraints generated.
    621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1242 Ramachandran restraints generated.
    621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 123
  time to evaluate  : 0.186 
Fit side-chains
   revert: symmetry clash
REVERT: A  335 LEU cc_start: 0.8384 (pp) cc_final: 0.7994 (tp)
REVERT: A  444 LYS cc_start: 0.8072 (ttpt) cc_final: 0.7403 (mmtm)
REVERT: A  458 LYS cc_start: 0.8828 (ttmt) cc_final: 0.8315 (tmtt)
REVERT: H   19 ARG cc_start: 0.6464 (ttt180) cc_final: 0.6162 (mtp-110)
REVERT: H   34 MET cc_start: 0.8898 (mmm) cc_final: 0.8598 (mmt)
REVERT: H   88 GLU cc_start: 0.8370 (pm20) cc_final: 0.8162 (pm20)
REVERT: L   37 TYR cc_start: 0.8900 (m-80) cc_final: 0.8581 (m-80)
REVERT: L  150 VAL cc_start: 0.8003 (t) cc_final: 0.7703 (t)
  outliers start: 1
  outliers final: 0
  residues processed: 123
  average time/residue: 0.0927
  time to fit residues: 14.0538
Evaluate side-chains
  98 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.188 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 1 optimal weight:    0.8980
   chunk 37 optimal weight:    7.9990
   chunk 59 optimal weight:    5.9990
   chunk 34 optimal weight:    9.9990
   chunk 18 optimal weight:    8.9990
   chunk 41 optimal weight:    2.9990
   chunk 29 optimal weight:    0.5980
   chunk 6 optimal weight:    2.9990
   chunk 55 optimal weight:   10.0000
   chunk 28 optimal weight:    6.9990
   chunk 49 optimal weight:    2.9990
   overall best weight:    2.0986

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

Flipped N/Q/H residues before XYZ refinement:
A 370 ASN
** H  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 203 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.128184 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.104216 restraints weight = 9780.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.107143 restraints weight = 5789.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.109052 restraints weight = 3958.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.110506 restraints weight = 3011.344|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.111498 restraints weight = 2440.342|
|-----------------------------------------------------------------------------|
r_work (final): 0.3413
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7559
moved from start:          0.2307

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   4907  Z= 0.224
  Angle     :  0.724   8.680   6681  Z= 0.374
  Chirality :  0.048   0.200    741
  Planarity :  0.006   0.049    860
  Dihedral  :  6.072  20.763    682
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 17.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.05 %
    Favored  : 91.95 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  3.73 %
    Favored  : 96.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.76 %
    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: -1.40 (0.36), residues: 621
  helix: -1.70 (1.00), residues: 25
  sheet: -0.59 (0.35), residues: 233
  loop : -1.07 (0.36), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG L  24 
 TYR   0.022   0.002   TYR A 453 
 PHE   0.019   0.002   PHE H 150 
 TRP   0.015   0.002   TRP A 353 
 HIS   0.005   0.002   HIS L  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00505 ( 4899)
  covalent geometry    : angle       0.72172 ( 6665)
  SS BOND              : bond        0.00536 (    8)
  SS BOND              : angle       1.45503 (   16)
  hydrogen bonds       : bond        0.03628 (  153)
  hydrogen bonds       : angle       7.76437 (  363)

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

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

  1242 Ramachandran restraints generated.
    621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1242 Ramachandran restraints generated.
    621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 129
  time to evaluate  : 0.130 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  335 LEU cc_start: 0.8424 (pp) cc_final: 0.8199 (tp)
REVERT: A  423 TYR cc_start: 0.8277 (t80) cc_final: 0.7994 (t80)
REVERT: A  444 LYS cc_start: 0.8141 (ttpt) cc_final: 0.7394 (mmtm)
REVERT: H   19 ARG cc_start: 0.6496 (ttt180) cc_final: 0.6078 (mtp85)
REVERT: H   34 MET cc_start: 0.8905 (mmm) cc_final: 0.8500 (mmm)
REVERT: H   88 GLU cc_start: 0.8476 (pm20) cc_final: 0.8171 (pm20)
REVERT: L   37 TYR cc_start: 0.8947 (m-80) cc_final: 0.8685 (m-80)
REVERT: L  103 LYS cc_start: 0.8899 (tttp) cc_final: 0.8530 (tttp)
REVERT: L  150 VAL cc_start: 0.8152 (t) cc_final: 0.7881 (t)
  outliers start: 1
  outliers final: 0
  residues processed: 130
  average time/residue: 0.0888
  time to fit residues: 14.1365
Evaluate side-chains
  103 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.177 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 20 optimal weight:    6.9990
   chunk 36 optimal weight:    0.8980
   chunk 45 optimal weight:    0.0170
   chunk 50 optimal weight:    0.6980
   chunk 24 optimal weight:    0.7980
   chunk 12 optimal weight:    0.0270
   chunk 51 optimal weight:    0.9990
   chunk 22 optimal weight:    0.8980
   chunk 40 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9990
   chunk 2 optimal weight:    0.0870
   overall best weight:    0.3254

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

Flipped N/Q/H residues before XYZ refinement:
A 370 ASN
A 501 ASN
H 201 ASN
H 203 ASN
L 166 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.135054 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.110797 restraints weight = 9750.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.113916 restraints weight = 5664.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.116072 restraints weight = 3812.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.117496 restraints weight = 2840.232|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.118481 restraints weight = 2310.514|
|-----------------------------------------------------------------------------|
r_work (final): 0.3523
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7394
moved from start:          0.3024

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4907  Z= 0.112
  Angle     :  0.658   8.909   6681  Z= 0.333
  Chirality :  0.046   0.206    741
  Planarity :  0.005   0.047    860
  Dihedral  :  5.545  17.261    682
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 12.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.15 %
    Favored  : 94.85 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.76 %
    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: -1.28 (0.36), residues: 621
  helix: -2.20 (0.79), residues: 32
  sheet: -0.47 (0.34), residues: 233
  loop : -0.92 (0.37), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG L  24 
 TYR   0.013   0.001   TYR H  33 
 PHE   0.012   0.001   PHE H 150 
 TRP   0.016   0.002   TRP A 353 
 HIS   0.002   0.001   HIS L  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 4899)
  covalent geometry    : angle       0.65694 ( 6665)
  SS BOND              : bond        0.00421 (    8)
  SS BOND              : angle       1.11446 (   16)
  hydrogen bonds       : bond        0.03207 (  153)
  hydrogen bonds       : angle       7.12629 (  363)

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

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

  1242 Ramachandran restraints generated.
    621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1242 Ramachandran restraints generated.
    621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 143
  time to evaluate  : 0.192 
Fit side-chains
   revert: symmetry clash
REVERT: A  335 LEU cc_start: 0.8438 (pp) cc_final: 0.8096 (tp)
REVERT: A  420 ASP cc_start: 0.7678 (m-30) cc_final: 0.7474 (m-30)
REVERT: A  444 LYS cc_start: 0.8095 (ttpt) cc_final: 0.7425 (mmtm)
REVERT: A  458 LYS cc_start: 0.8886 (ttmt) cc_final: 0.8420 (tmtt)
REVERT: L    4 LEU cc_start: 0.8406 (mm) cc_final: 0.7929 (tt)
REVERT: L   37 TYR cc_start: 0.8859 (m-80) cc_final: 0.8475 (m-80)
REVERT: L  150 VAL cc_start: 0.8202 (t) cc_final: 0.7802 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 143
  average time/residue: 0.0888
  time to fit residues: 15.8006
Evaluate side-chains
  99 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.213 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 36 optimal weight:    0.8980
   chunk 40 optimal weight:    0.4980
   chunk 60 optimal weight:    0.0270
   chunk 21 optimal weight:    0.0370
   chunk 47 optimal weight:   10.0000
   chunk 25 optimal weight:    0.0770
   chunk 57 optimal weight:    9.9990
   chunk 54 optimal weight:    5.9990
   chunk 43 optimal weight:    0.9980
   chunk 29 optimal weight:    3.9990
   chunk 12 optimal weight:    0.9990
   overall best weight:    0.3074

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

Flipped N/Q/H residues before XYZ refinement:
H 109 GLN
H 203 ASN
** L 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.136334 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.112601 restraints weight = 9687.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.115766 restraints weight = 5600.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.117965 restraints weight = 3741.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.119429 restraints weight = 2758.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.120349 restraints weight = 2217.722|
|-----------------------------------------------------------------------------|
r_work (final): 0.3538
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7353
moved from start:          0.3461

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   4907  Z= 0.118
  Angle     :  0.657   9.419   6681  Z= 0.334
  Chirality :  0.047   0.216    741
  Planarity :  0.005   0.047    860
  Dihedral  :  5.315  17.448    682
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 11.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.15 %
    Favored  : 94.85 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  1.68 %
    Favored  : 98.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.76 %
    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: -1.14 (0.35), residues: 621
  helix: -2.22 (0.80), residues: 32
  sheet: -0.23 (0.34), residues: 227
  loop : -0.94 (0.36), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG L  24 
 TYR   0.012   0.001   TYR H  33 
 PHE   0.018   0.002   PHE L 139 
 TRP   0.021   0.002   TRP H 158 
 HIS   0.002   0.001   HIS H 168 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 4899)
  covalent geometry    : angle       0.65611 ( 6665)
  SS BOND              : bond        0.00532 (    8)
  SS BOND              : angle       1.05616 (   16)
  hydrogen bonds       : bond        0.03073 (  153)
  hydrogen bonds       : angle       6.68192 (  363)

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

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

  1242 Ramachandran restraints generated.
    621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1242 Ramachandran restraints generated.
    621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 146
  time to evaluate  : 0.191 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  335 LEU cc_start: 0.8433 (pp) cc_final: 0.8227 (tp)
REVERT: A  409 GLN cc_start: 0.8208 (pt0) cc_final: 0.7312 (pt0)
REVERT: A  420 ASP cc_start: 0.7427 (m-30) cc_final: 0.7072 (m-30)
REVERT: A  430 THR cc_start: 0.5181 (m) cc_final: 0.4717 (p)
REVERT: A  444 LYS cc_start: 0.7970 (ttpt) cc_final: 0.7445 (mmtm)
REVERT: A  458 LYS cc_start: 0.8852 (ttmt) cc_final: 0.8389 (tmtt)
REVERT: H   19 ARG cc_start: 0.7545 (mmm-85) cc_final: 0.6812 (ttt90)
REVERT: L  150 VAL cc_start: 0.8256 (t) cc_final: 0.7884 (t)
  outliers start: 1
  outliers final: 0
  residues processed: 147
  average time/residue: 0.0768
  time to fit residues: 14.3162
Evaluate side-chains
  111 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 111
  time to evaluate  : 0.110 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 3 optimal weight:    5.9990
   chunk 11 optimal weight:    8.9990
   chunk 0 optimal weight:    5.9990
   chunk 40 optimal weight:    0.7980
   chunk 30 optimal weight:    6.9990
   chunk 39 optimal weight:    0.9980
   chunk 5 optimal weight:    5.9990
   chunk 56 optimal weight:    0.9980
   chunk 24 optimal weight:    0.0060
   chunk 35 optimal weight:   10.0000
   chunk 10 optimal weight:    5.9990
   overall best weight:    1.7598

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

Flipped N/Q/H residues before XYZ refinement:
** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 203 ASN
** L 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.131441 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.107044 restraints weight = 9877.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.110043 restraints weight = 5780.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.112145 restraints weight = 3926.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.113594 restraints weight = 2947.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.114522 restraints weight = 2394.982|
|-----------------------------------------------------------------------------|
r_work (final): 0.3461
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7497
moved from start:          0.3160

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   4907  Z= 0.192
  Angle     :  0.697   7.943   6681  Z= 0.360
  Chirality :  0.046   0.171    741
  Planarity :  0.006   0.048    860
  Dihedral  :  5.635  18.566    682
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 16.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.44 %
    Favored  : 93.56 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.76 %
    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: -1.18 (0.35), residues: 621
  helix: -1.83 (0.97), residues: 26
  sheet: -0.30 (0.34), residues: 230
  loop : -1.00 (0.35), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 355 
 TYR   0.023   0.002   TYR A 453 
 PHE   0.019   0.002   PHE L 139 
 TRP   0.023   0.003   TRP H 158 
 HIS   0.003   0.001   HIS L 198 

Details of bonding type rmsd
  covalent geometry    : bond        0.00439 ( 4899)
  covalent geometry    : angle       0.69519 ( 6665)
  SS BOND              : bond        0.00645 (    8)
  SS BOND              : angle       1.26164 (   16)
  hydrogen bonds       : bond        0.03330 (  153)
  hydrogen bonds       : angle       6.96999 (  363)

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

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

  1242 Ramachandran restraints generated.
    621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1242 Ramachandran restraints generated.
    621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 129
  time to evaluate  : 0.141 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  335 LEU cc_start: 0.8564 (pp) cc_final: 0.8291 (tp)
REVERT: A  429 PHE cc_start: 0.6554 (t80) cc_final: 0.6344 (t80)
REVERT: A  444 LYS cc_start: 0.8037 (ttpt) cc_final: 0.7331 (mmtm)
REVERT: A  458 LYS cc_start: 0.8852 (ttmt) cc_final: 0.8453 (tmtt)
REVERT: H   19 ARG cc_start: 0.7695 (mmm-85) cc_final: 0.6728 (ttt90)
REVERT: H   34 MET cc_start: 0.8916 (mmm) cc_final: 0.8622 (mmt)
REVERT: H   68 THR cc_start: 0.7334 (p) cc_final: 0.6799 (p)
REVERT: H   81 GLN cc_start: 0.6401 (tm-30) cc_final: 0.6199 (tt0)
REVERT: L   37 TYR cc_start: 0.9003 (m-80) cc_final: 0.8770 (m-80)
REVERT: L  150 VAL cc_start: 0.8286 (t) cc_final: 0.7982 (t)
REVERT: L  207 LYS cc_start: 0.6085 (mmpt) cc_final: 0.5681 (tppt)
  outliers start: 0
  outliers final: 0
  residues processed: 129
  average time/residue: 0.0796
  time to fit residues: 12.8895
Evaluate side-chains
  103 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.178 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 59 optimal weight:    9.9990
   chunk 32 optimal weight:    8.9990
   chunk 13 optimal weight:    0.0970
   chunk 15 optimal weight:    2.9990
   chunk 38 optimal weight:    0.0770
   chunk 46 optimal weight:   10.0000
   chunk 12 optimal weight:    0.6980
   chunk 0 optimal weight:    7.9990
   chunk 49 optimal weight:    0.3980
   chunk 60 optimal weight:    3.9990
   chunk 21 optimal weight:    1.9990
   overall best weight:    0.6538

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

Flipped N/Q/H residues before XYZ refinement:
** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 498 GLN
** H  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 203 ASN
** L 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.135269 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.111436 restraints weight = 9648.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.114557 restraints weight = 5526.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.116711 restraints weight = 3702.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.118175 restraints weight = 2751.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.119198 restraints weight = 2215.438|
|-----------------------------------------------------------------------------|
r_work (final): 0.3529
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7407
moved from start:          0.3543

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4907  Z= 0.128
  Angle     :  0.671   8.243   6681  Z= 0.339
  Chirality :  0.047   0.274    741
  Planarity :  0.005   0.043    860
  Dihedral  :  5.426  18.214    682
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 13.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.48 %
    Favored  : 94.52 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.56 %
    Favored  : 99.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.76 %
    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: -1.08 (0.35), residues: 621
  helix: -2.07 (0.90), residues: 26
  sheet: -0.24 (0.33), residues: 230
  loop : -0.90 (0.36), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG L  24 
 TYR   0.016   0.001   TYR A 453 
 PHE   0.019   0.002   PHE L 139 
 TRP   0.015   0.002   TRP H 158 
 HIS   0.006   0.002   HIS L  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 4899)
  covalent geometry    : angle       0.66938 ( 6665)
  SS BOND              : bond        0.00464 (    8)
  SS BOND              : angle       1.14440 (   16)
  hydrogen bonds       : bond        0.03054 (  153)
  hydrogen bonds       : angle       6.70231 (  363)

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

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

  1242 Ramachandran restraints generated.
    621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1242 Ramachandran restraints generated.
    621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 138
  time to evaluate  : 0.184 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  335 LEU cc_start: 0.8530 (pp) cc_final: 0.8243 (tp)
REVERT: A  429 PHE cc_start: 0.6565 (t80) cc_final: 0.6196 (t80)
REVERT: A  444 LYS cc_start: 0.7961 (ttpt) cc_final: 0.7438 (mmtm)
REVERT: A  458 LYS cc_start: 0.8865 (ttmt) cc_final: 0.8372 (tmtt)
REVERT: A  460 ASN cc_start: 0.8099 (t0) cc_final: 0.6650 (m-40)
REVERT: A  498 GLN cc_start: 0.6756 (mm110) cc_final: 0.6400 (mm-40)
REVERT: H   19 ARG cc_start: 0.7624 (mmm-85) cc_final: 0.6698 (ttt90)
REVERT: H   34 MET cc_start: 0.8870 (mmm) cc_final: 0.8567 (mmt)
REVERT: H   68 THR cc_start: 0.7285 (p) cc_final: 0.6788 (p)
REVERT: H   88 GLU cc_start: 0.8346 (pm20) cc_final: 0.8045 (pm20)
REVERT: L  103 LYS cc_start: 0.8845 (tttp) cc_final: 0.8604 (tttp)
REVERT: L  150 VAL cc_start: 0.8235 (t) cc_final: 0.7853 (t)
REVERT: L  207 LYS cc_start: 0.5765 (mmpt) cc_final: 0.5361 (tppt)
  outliers start: 0
  outliers final: 0
  residues processed: 138
  average time/residue: 0.0849
  time to fit residues: 14.6789
Evaluate side-chains
  107 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 0.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 57 optimal weight:   10.0000
   chunk 28 optimal weight:    5.9990
   chunk 44 optimal weight:    0.6980
   chunk 13 optimal weight:    0.7980
   chunk 51 optimal weight:    6.9990
   chunk 22 optimal weight:    0.7980
   chunk 17 optimal weight:    0.7980
   chunk 58 optimal weight:    7.9990
   chunk 33 optimal weight:   10.0000
   chunk 5 optimal weight:    0.9980
   chunk 15 optimal weight:    0.6980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  32 ASN
** H 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 203 ASN
** L 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.135585 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.111898 restraints weight = 9615.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.114991 restraints weight = 5568.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.117132 restraints weight = 3750.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.118610 restraints weight = 2814.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.119487 restraints weight = 2264.318|
|-----------------------------------------------------------------------------|
r_work (final): 0.3532
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7392
moved from start:          0.3711

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4907  Z= 0.128
  Angle     :  0.651   7.889   6681  Z= 0.331
  Chirality :  0.045   0.169    741
  Planarity :  0.005   0.043    860
  Dihedral  :  5.351  18.021    682
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 13.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.48 %
    Favored  : 94.52 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.76 %
    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: -1.01 (0.35), residues: 621
  helix: -2.03 (0.92), residues: 26
  sheet: -0.21 (0.34), residues: 227
  loop : -0.84 (0.35), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 355 
 TYR   0.014   0.001   TYR A 453 
 PHE   0.026   0.002   PHE A 392 
 TRP   0.015   0.002   TRP A 353 
 HIS   0.006   0.002   HIS L  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 4899)
  covalent geometry    : angle       0.64938 ( 6665)
  SS BOND              : bond        0.00476 (    8)
  SS BOND              : angle       1.15795 (   16)
  hydrogen bonds       : bond        0.03084 (  153)
  hydrogen bonds       : angle       6.59469 (  363)

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

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

  1242 Ramachandran restraints generated.
    621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1242 Ramachandran restraints generated.
    621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 138
  time to evaluate  : 0.196 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  335 LEU cc_start: 0.8506 (pp) cc_final: 0.8213 (tp)
REVERT: A  429 PHE cc_start: 0.6369 (t80) cc_final: 0.6040 (t80)
REVERT: A  430 THR cc_start: 0.5118 (m) cc_final: 0.4571 (p)
REVERT: A  444 LYS cc_start: 0.7890 (ttpt) cc_final: 0.7412 (mmtm)
REVERT: A  458 LYS cc_start: 0.8811 (ttmt) cc_final: 0.8371 (tmtt)
REVERT: A  460 ASN cc_start: 0.8116 (t0) cc_final: 0.6624 (m-40)
REVERT: H   34 MET cc_start: 0.8885 (mmm) cc_final: 0.8625 (mmt)
REVERT: H   68 THR cc_start: 0.6957 (p) cc_final: 0.6718 (p)
REVERT: H   88 GLU cc_start: 0.8345 (pm20) cc_final: 0.8065 (pm20)
REVERT: L  103 LYS cc_start: 0.8818 (tttp) cc_final: 0.8586 (tttp)
REVERT: L  150 VAL cc_start: 0.8260 (t) cc_final: 0.7851 (t)
REVERT: L  207 LYS cc_start: 0.5856 (mmpt) cc_final: 0.5439 (tppt)
  outliers start: 0
  outliers final: 0
  residues processed: 138
  average time/residue: 0.0839
  time to fit residues: 14.6116
Evaluate side-chains
  104 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 3 optimal weight:    5.9990
   chunk 38 optimal weight:    0.5980
   chunk 12 optimal weight:    2.9990
   chunk 54 optimal weight:    0.8980
   chunk 39 optimal weight:    0.8980
   chunk 27 optimal weight:    4.9990
   chunk 2 optimal weight:    9.9990
   chunk 50 optimal weight:    0.9990
   chunk 52 optimal weight:    8.9990
   chunk 25 optimal weight:    0.9980
   chunk 32 optimal weight:    9.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 203 ASN
** L 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.135418 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.111658 restraints weight = 9621.887|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.114721 restraints weight = 5584.326|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.116650 restraints weight = 3755.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.118132 restraints weight = 2837.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.118862 restraints weight = 2286.113|
|-----------------------------------------------------------------------------|
r_work (final): 0.3529
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7410
moved from start:          0.3725

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4907  Z= 0.132
  Angle     :  0.660   7.601   6681  Z= 0.333
  Chirality :  0.046   0.202    741
  Planarity :  0.005   0.044    860
  Dihedral  :  5.325  17.633    682
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 12.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.64 %
    Favored  : 94.36 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.56 %
    Favored  : 99.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.76 %
    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: -0.99 (0.35), residues: 621
  helix: -2.17 (0.90), residues: 26
  sheet: -0.01 (0.34), residues: 216
  loop : -0.93 (0.35), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG L  24 
 TYR   0.015   0.001   TYR A 453 
 PHE   0.021   0.002   PHE A 392 
 TRP   0.013   0.002   TRP H 158 
 HIS   0.005   0.001   HIS L  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 4899)
  covalent geometry    : angle       0.65790 ( 6665)
  SS BOND              : bond        0.00457 (    8)
  SS BOND              : angle       1.19586 (   16)
  hydrogen bonds       : bond        0.03019 (  153)
  hydrogen bonds       : angle       6.65618 (  363)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1082.00 seconds
wall clock time: 19 minutes 21.49 seconds (1161.49 seconds total)