Starting phenix.real_space_refine
on Thu Jul 24 09:40:50 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9kml_62437/07_2025/9kml_62437.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9kml_62437/07_2025/9kml_62437.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.11
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9kml_62437/07_2025/9kml_62437.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9kml_62437/07_2025/9kml_62437.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9kml_62437/07_2025/9kml_62437.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9kml_62437/07_2025/9kml_62437.cif"
  }
  resolution = 3.11
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.021
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
     S      41      5.16       5
     Cl      1      4.86       5
     C    3854      2.51       5
     N     931      2.21       5
     O    1045      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 5872
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "H"
      Number of atoms: 922
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 118, 922
          Classifications: {'peptide': 118}
          Link IDs: {'PTRANS': 2, 'TRANS': 115}
    Chain: "A"
      Number of atoms: 4145
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 520, 4145
          Classifications: {'peptide': 520}
          Link IDs: {'PTRANS': 25, 'TRANS': 494}
          Chain breaks: 1
    Chain: "L"
      Number of atoms: 804
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 804
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 5, 'TRANS': 102}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' CL': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 4.66, per 1000 atoms: 0.79
  Number of scatterers: 5872
  At special positions: 0
  Unit cell: (72.16, 82.82, 113.16, 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)
     Cl      1     17.00
     S      41     16.00
     O    1045      8.00
     N     931      7.00
     C    3854      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 162 " - pdb=" SG  CYS A 171 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  89 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.65
  Conformation dependent library (CDL) restraints added in 985.1 milliseconds
  

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1352

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 7 sheets defined
      54.3% alpha, 13.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.92
  Creating SS restraints...
    Processing helix  chain 'H' and resid 28 through 32
      removed outlier: 3.587A  pdb=" N   SER H  31 " --> pdb=" O   THR H  28 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   TYR H  32 " --> pdb=" O   PHE H  29 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 28 through 32'
    Processing helix  chain 'H' and resid 87 through 91
      removed outlier: 3.852A  pdb=" N   ASP H  90 " --> pdb=" O   ARG H  87 " (cutoff:3.500A)
      removed outlier: 3.873A  pdb=" N   THR H  91 " --> pdb=" O   SER H  88 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 87 through 91'
    Processing helix  chain 'A' and resid 60 through 65
    Processing helix  chain 'A' and resid 65 through 74
      removed outlier: 3.772A  pdb=" N   TYR A  69 " --> pdb=" O   TRP A  65 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 76 through 78
      No H-bonds generated for 'chain 'A' and resid 76 through 78'
    Processing helix  chain 'A' and resid 79 through 90
    Processing helix  chain 'A' and resid 90 through 105
    Processing helix  chain 'A' and resid 117 through 120
    Processing helix  chain 'A' and resid 121 through 151
      removed outlier: 4.184A  pdb=" N   TYR A 125 " --> pdb=" O   SER A 121 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 173 through 177
    Processing helix  chain 'A' and resid 193 through 203
    Processing helix  chain 'A' and resid 219 through 236
      removed outlier: 4.328A  pdb=" N   TRP A 236 " --> pdb=" O   PHE A 232 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 251 through 266
      removed outlier: 3.739A  pdb=" N   THR A 266 " --> pdb=" O   VAL A 262 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 269 through 279
      removed outlier: 4.170A  pdb=" N   GLY A 273 " --> pdb=" O   GLY A 269 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 281 through 286
      removed outlier: 3.551A  pdb=" N   GLY A 286 " --> pdb=" O   SER A 283 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 287 through 302
      removed outlier: 4.293A  pdb=" N   TRP A 291 " --> pdb=" O   ASP A 287 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 315
      removed outlier: 3.574A  pdb=" N   TYR A 315 " --> pdb=" O   SER A 311 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 323 through 356
    Processing helix  chain 'A' and resid 358 through 362
      removed outlier: 3.653A  pdb=" N   VAL A 362 " --> pdb=" O   ILE A 359 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 372 through 380
    Processing helix  chain 'A' and resid 383 through 418
      removed outlier: 3.666A  pdb=" N   TRP A 387 " --> pdb=" O   LEU A 383 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 425 through 444
    Processing helix  chain 'A' and resid 450 through 462
      removed outlier: 3.939A  pdb=" N   VAL A 454 " --> pdb=" O   GLY A 450 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 465 through 482
    Processing helix  chain 'A' and resid 484 through 496
    Processing helix  chain 'A' and resid 501 through 510
    Processing helix  chain 'A' and resid 510 through 526
      removed outlier: 3.612A  pdb=" N   LEU A 524 " --> pdb=" O   PHE A 520 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 539 through 555
      removed outlier: 3.835A  pdb=" N   SER A 553 " --> pdb=" O   LEU A 549 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 555 through 567
    Processing helix  chain 'A' and resid 571 through 581
    Processing helix  chain 'L' and resid 80 through 84
      removed outlier: 3.940A  pdb=" N   ALA L  84 " --> pdb=" O   ALA L  81 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 5
      removed outlier: 3.566A  pdb=" N   SER H  71 " --> pdb=" O   HIS H  80 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12
      removed outlier: 3.859A  pdb=" N   THR H 113 " --> pdb=" O   TYR H  94 " (cutoff:3.500A)
      removed outlier: 6.005A  pdb=" N   ARG H  38 " --> pdb=" O   TRP H  47 " (cutoff:3.500A)
      removed outlier: 4.844A  pdb=" N   TRP H  47 " --> pdb=" O   ARG H  38 " (cutoff:3.500A)
      removed outlier: 6.533A  pdb=" N   SER H  40 " --> pdb=" O   LEU H  45 " (cutoff:3.500A)
      removed outlier: 6.148A  pdb=" N   LEU H  45 " --> pdb=" O   SER H  40 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'H' and resid 11 through 12
      removed outlier: 3.859A  pdb=" N   THR H 113 " --> pdb=" O   TYR H  94 " (cutoff:3.500A)
      removed outlier: 3.962A  pdb=" N   TYR H 108 " --> pdb=" O   ARG H  98 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 531 through 532
    Processing sheet with id=AA5, first strand: chain 'L' and resid 4 through 6
      removed outlier: 12.362A  pdb=" N   CYS L  23 " --> pdb=" O   THR L  75 " (cutoff:3.500A)
      removed outlier: 11.583A  pdb=" N   THR L  75 " --> pdb=" O   CYS L  23 " (cutoff:3.500A)
      removed outlier: 12.000A  pdb=" N   ALA L  25 " --> pdb=" O   SER L  73 " (cutoff:3.500A)
      removed outlier: 11.785A  pdb=" N   SER L  73 " --> pdb=" O   ALA L  25 " (cutoff:3.500A)
      removed outlier: 11.616A  pdb=" N   SER L  27 " --> pdb=" O   SER L  71 " (cutoff:3.500A)
      removed outlier: 6.967A  pdb=" N   SER L  71 " --> pdb=" O   SER L  27 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   GLY L  69 " --> pdb=" O   VAL L  29 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'L' and resid 10 through 12
      removed outlier: 6.469A  pdb=" N   MET L  11 " --> pdb=" O   GLU L 106 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'L' and resid 54 through 55
      removed outlier: 5.793A  pdb=" N   LEU L  47 " --> pdb=" O   GLN L  38 " (cutoff:3.500A)
      removed outlier: 5.734A  pdb=" N   GLN L  38 " --> pdb=" O   LEU L  47 " (cutoff:3.500A)

    320 hydrogen bonds defined for protein.
    915 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.38

  Time building geometry restraints manager: 1.78 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1741
        1.34 -     1.46: 1385
        1.46 -     1.58: 2855
        1.58 -     1.69: 0
        1.69 -     1.81: 60
  Bond restraints: 6041
  Sorted by residual:
  bond pdb=" CB  ILE A 141 "
       pdb=" CG1 ILE A 141 "
    ideal  model  delta    sigma   weight residual
    1.530  1.496  0.034 2.00e-02 2.50e+03 2.91e+00
  bond pdb=" CB  VAL A 140 "
       pdb=" CG1 VAL A 140 "
    ideal  model  delta    sigma   weight residual
    1.521  1.466  0.055 3.30e-02 9.18e+02 2.79e+00
  bond pdb=" N   ASN A 190 "
       pdb=" CA  ASN A 190 "
    ideal  model  delta    sigma   weight residual
    1.457  1.478 -0.021 1.29e-02 6.01e+03 2.65e+00
  bond pdb=" C   THR A 512 "
       pdb=" N   PRO A 513 "
    ideal  model  delta    sigma   weight residual
    1.335  1.357 -0.021 1.36e-02 5.41e+03 2.41e+00
  bond pdb=" CA  PHE A  58 "
       pdb=" CB  PHE A  58 "
    ideal  model  delta    sigma   weight residual
    1.526  1.501  0.026 1.76e-02 3.23e+03 2.10e+00
  ... (remaining 6036 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.23: 7948
        2.23 -     4.46: 228
        4.46 -     6.69: 28
        6.69 -     8.92: 8
        8.92 -    11.15: 1
  Bond angle restraints: 8213
  Sorted by residual:
  angle pdb=" C   SER L  51 "
        pdb=" N   THR L  52 "
        pdb=" CA  THR L  52 "
      ideal   model   delta    sigma   weight residual
     121.54  132.69  -11.15 1.91e+00 2.74e-01 3.41e+01
  angle pdb=" C   TRP A 218 "
        pdb=" N   ASP A 219 "
        pdb=" CA  ASP A 219 "
      ideal   model   delta    sigma   weight residual
     121.54  130.37   -8.83 1.91e+00 2.74e-01 2.14e+01
  angle pdb=" C   PHE A  58 "
        pdb=" N   VAL A  59 "
        pdb=" CA  VAL A  59 "
      ideal   model   delta    sigma   weight residual
     121.97  129.62   -7.65 1.80e+00 3.09e-01 1.81e+01
  angle pdb=" C   VAL A 136 "
        pdb=" N   TYR A 137 "
        pdb=" CA  TYR A 137 "
      ideal   model   delta    sigma   weight residual
     121.14  114.51    6.63 1.75e+00 3.27e-01 1.43e+01
  angle pdb=" C   ILE A 139 "
        pdb=" N   VAL A 140 "
        pdb=" CA  VAL A 140 "
      ideal   model   delta    sigma   weight residual
     120.64  115.00    5.64 1.64e+00 3.72e-01 1.18e+01
  ... (remaining 8208 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.21: 3096
       17.21 -    34.42: 304
       34.42 -    51.63: 49
       51.63 -    68.84: 8
       68.84 -    86.05: 6
  Dihedral angle restraints: 3463
    sinusoidal: 1323
      harmonic: 2140
  Sorted by residual:
  dihedral pdb=" CB  CYS A 162 "
           pdb=" SG  CYS A 162 "
           pdb=" SG  CYS A 171 "
           pdb=" CB  CYS A 171 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -167.10   81.10     1      1.00e+01 1.00e-02 8.12e+01
  dihedral pdb=" CB  CYS H  22 "
           pdb=" SG  CYS H  22 "
           pdb=" SG  CYS H  96 "
           pdb=" CB  CYS H  96 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   51.16   41.84     1      1.00e+01 1.00e-02 2.45e+01
  dihedral pdb=" CA  HIS A 161 "
           pdb=" C   HIS A 161 "
           pdb=" N   CYS A 162 "
           pdb=" CA  CYS A 162 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.35  -24.65     0      5.00e+00 4.00e-02 2.43e+01
  ... (remaining 3460 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 603
       0.045 -    0.090: 210
       0.090 -    0.135: 69
       0.135 -    0.180: 12
       0.180 -    0.224: 5
  Chirality restraints: 899
  Sorted by residual:
  chirality pdb=" CB  THR H  28 "
            pdb=" CA  THR H  28 "
            pdb=" OG1 THR H  28 "
            pdb=" CG2 THR H  28 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.33    0.22 2.00e-01 2.50e+01 1.26e+00
  chirality pdb=" CB  VAL A 357 "
            pdb=" CA  VAL A 357 "
            pdb=" CG1 VAL A 357 "
            pdb=" CG2 VAL A 357 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.41   -0.22 2.00e-01 2.50e+01 1.24e+00
  chirality pdb=" CB  VAL A 140 "
            pdb=" CA  VAL A 140 "
            pdb=" CG1 VAL A 140 "
            pdb=" CG2 VAL A 140 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.43   -0.20 2.00e-01 2.50e+01 1.01e+00
  ... (remaining 896 not shown)

  Planarity restraints: 1013
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A  92 "   -0.054 5.00e-02 4.00e+02   8.17e-02 1.07e+01
        pdb=" N   PRO A  93 "    0.141 5.00e-02 4.00e+02
        pdb=" CA  PRO A  93 "   -0.041 5.00e-02 4.00e+02
        pdb=" CD  PRO A  93 "   -0.046 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP A 219 "   -0.015 2.00e-02 2.50e+03   2.92e-02 8.55e+00
        pdb=" C   ASP A 219 "    0.051 2.00e-02 2.50e+03
        pdb=" O   ASP A 219 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   LEU A 220 "   -0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 479 "   -0.013 2.00e-02 2.50e+03   2.63e-02 6.91e+00
        pdb=" C   ILE A 479 "    0.045 2.00e-02 2.50e+03
        pdb=" O   ILE A 479 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   ALA A 480 "   -0.015 2.00e-02 2.50e+03
  ... (remaining 1010 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1119
        2.77 -     3.30: 5491
        3.30 -     3.83: 10597
        3.83 -     4.37: 12248
        4.37 -     4.90: 21481
  Nonbonded interactions: 50936
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A  69 "
            pdb=" OD2 ASP A 459 "
     model   vdw
     2.235 3.040
  nonbonded pdb=" O   LYS A 376 "
            pdb=" OG1 THR A 379 "
     model   vdw
     2.312 3.040
  nonbonded pdb=" OD1 ASP A 174 "
            pdb=" OG  SER A 193 "
     model   vdw
     2.328 3.040
  nonbonded pdb=" OH  TYR A  72 "
            pdb=" O   ILE A 359 "
     model   vdw
     2.359 3.040
  nonbonded pdb=" NH1 ARG H  67 "
            pdb=" OD2 ASP H  90 "
     model   vdw
     2.364 3.120
  ... (remaining 50931 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.800
  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:          0.270
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     19.670
  Find NCS groups from input model:        0.310
  Set up NCS constraints:                  0.030
  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:3.180
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.370
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7873
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      :  0.006   0.062   6044  Z= 0.253
  Angle     :  0.884  11.151   8219  Z= 0.488
  Chirality :  0.053   0.224    899
  Planarity :  0.008   0.082   1013
  Dihedral  : 13.751  86.049   2102
  Min Nonbonded Distance : 2.235

Molprobity Statistics.
  All-atom Clashscore : 7.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.88 %
    Favored  : 95.12 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  0.16 %
    Favored  : 99.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.86 (0.28), residues: 738
  helix: -0.90 (0.24), residues: 352
  sheet: -1.22 (0.51), residues: 108
  loop : -1.46 (0.36), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A  65 
 HIS   0.006   0.002   HIS A 164 
 PHE   0.031   0.003   PHE L  92 
 TYR   0.029   0.002   TYR H  57 
 ARG   0.012   0.001   ARG A 201 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15836 (  316)
  hydrogen bonds       : angle       7.35374 (  915)
  SS BOND              : bond        0.00189 (    3)
  SS BOND              : angle       1.22339 (    6)
  covalent geometry    : bond        0.00587 ( 6041)
  covalent geometry    : angle       0.88356 ( 8213)

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

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

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 124
  time to evaluate  : 0.663 
Fit side-chains
REVERT: H   57 TYR cc_start: 0.8511 (m-80) cc_final: 0.7904 (m-80)
REVERT: A   72 TYR cc_start: 0.8511 (t80) cc_final: 0.8076 (t80)
REVERT: A  191 PHE cc_start: 0.7389 (m-80) cc_final: 0.7168 (m-80)
REVERT: A  258 LEU cc_start: 0.7975 (tp) cc_final: 0.7733 (mt)
  outliers start: 1
  outliers final: 0
  residues processed: 124
  average time/residue: 0.2069
  time to fit residues: 32.6519
Evaluate side-chains
  94 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 0.665 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 61 optimal weight:    0.0470
   chunk 55 optimal weight:    0.9980
   chunk 30 optimal weight:    0.6980
   chunk 18 optimal weight:    0.9980
   chunk 37 optimal weight:    0.8980
   chunk 29 optimal weight:    0.0570
   chunk 57 optimal weight:    0.9980
   chunk 22 optimal weight:    0.8980
   chunk 34 optimal weight:    0.6980
   chunk 42 optimal weight:    0.7980
   chunk 66 optimal weight:    1.9990
   overall best weight:    0.4596

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

Flipped N/Q/H residues before XYZ refinement:
A  63 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.163463 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.135648 restraints weight = 6934.863|
|-----------------------------------------------------------------------------|
r_work (start): 0.3512 rms_B_bonded: 1.82
r_work: 0.3392 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3250 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.3250
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8248
moved from start:          0.1517

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6044  Z= 0.152
  Angle     :  0.587   8.428   8219  Z= 0.315
  Chirality :  0.042   0.156    899
  Planarity :  0.006   0.069   1013
  Dihedral  :  4.936  19.091    819
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 8.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  :  8.70 %
    Favored  : 90.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.89 (0.30), residues: 738
  helix:  0.24 (0.26), residues: 359
  sheet: -1.36 (0.49), residues: 113
  loop : -1.22 (0.38), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.001   TRP A 218 
 HIS   0.002   0.001   HIS A 161 
 PHE   0.017   0.002   PHE A 455 
 TYR   0.019   0.001   TYR A 137 
 ARG   0.005   0.001   ARG A 240 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04590 (  316)
  hydrogen bonds       : angle       5.38925 (  915)
  SS BOND              : bond        0.00246 (    3)
  SS BOND              : angle       0.77880 (    6)
  covalent geometry    : bond        0.00341 ( 6041)
  covalent geometry    : angle       0.58720 ( 8213)

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

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

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 109
  time to evaluate  : 0.625 
Fit side-chains
REVERT: H   46 GLU cc_start: 0.8716 (tt0) cc_final: 0.8358 (tt0)
REVERT: H   57 TYR cc_start: 0.8816 (m-80) cc_final: 0.8390 (m-80)
REVERT: H   78 ILE cc_start: 0.8082 (mp) cc_final: 0.7797 (mp)
REVERT: A  115 LYS cc_start: 0.8304 (mptt) cc_final: 0.7010 (tptt)
REVERT: A  191 PHE cc_start: 0.7553 (m-80) cc_final: 0.7247 (m-80)
REVERT: A  440 TYR cc_start: 0.7986 (t80) cc_final: 0.7658 (t80)
REVERT: L   72 TYR cc_start: 0.7591 (m-80) cc_final: 0.7383 (m-80)
  outliers start: 8
  outliers final: 5
  residues processed: 115
  average time/residue: 0.2020
  time to fit residues: 30.6245
Evaluate side-chains
  102 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 97
  time to evaluate  : 0.661 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   53 SER
Chi-restraints excluded: chain A residue   69 TYR
Chi-restraints excluded: chain A residue  112 CYS
Chi-restraints excluded: chain L residue   77 SER
Chi-restraints excluded: chain L residue  105 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 29 optimal weight:    0.0870
   chunk 26 optimal weight:    2.9990
   chunk 49 optimal weight:    0.5980
   chunk 28 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9990
   chunk 33 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9980
   chunk 18 optimal weight:    0.9990
   chunk 68 optimal weight:    2.9990
   chunk 42 optimal weight:    0.5980
   chunk 46 optimal weight:    0.1980
   overall best weight:    0.4958

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.160100 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.131641 restraints weight = 6988.483|
|-----------------------------------------------------------------------------|
r_work (start): 0.3462 rms_B_bonded: 1.92
r_work: 0.3344 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3197 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.3197
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8116
moved from start:          0.1876

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6044  Z= 0.150
  Angle     :  0.561   8.949   8219  Z= 0.298
  Chirality :  0.042   0.165    899
  Planarity :  0.005   0.064   1013
  Dihedral  :  4.631  17.875    819
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 9.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.74 %
    Favored  : 95.26 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 12.18 %
    Favored  : 85.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.38 (0.31), residues: 738
  helix:  0.77 (0.26), residues: 359
  sheet: -1.36 (0.49), residues: 112
  loop : -1.02 (0.39), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 470 
 HIS   0.002   0.001   HIS H  80 
 PHE   0.018   0.002   PHE A 473 
 TYR   0.022   0.001   TYR A 137 
 ARG   0.003   0.000   ARG A 427 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04376 (  316)
  hydrogen bonds       : angle       5.10458 (  915)
  SS BOND              : bond        0.00205 (    3)
  SS BOND              : angle       0.71251 (    6)
  covalent geometry    : bond        0.00348 ( 6041)
  covalent geometry    : angle       0.56061 ( 8213)

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

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

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 104
  time to evaluate  : 0.627 
Fit side-chains
   revert: symmetry clash
REVERT: H   46 GLU cc_start: 0.8819 (tt0) cc_final: 0.8249 (tt0)
REVERT: H   57 TYR cc_start: 0.8943 (m-80) cc_final: 0.8495 (m-80)
REVERT: H   78 ILE cc_start: 0.7919 (mp) cc_final: 0.7616 (mp)
REVERT: A  191 PHE cc_start: 0.7609 (m-80) cc_final: 0.7232 (m-80)
REVERT: A  429 GLU cc_start: 0.7218 (tt0) cc_final: 0.6959 (mt-10)
REVERT: A  440 TYR cc_start: 0.8219 (t80) cc_final: 0.7723 (t80)
REVERT: A  506 TYR cc_start: 0.8182 (m-80) cc_final: 0.7975 (m-80)
  outliers start: 13
  outliers final: 11
  residues processed: 111
  average time/residue: 0.2003
  time to fit residues: 28.8881
Evaluate side-chains
  111 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 100
  time to evaluate  : 0.616 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   53 SER
Chi-restraints excluded: chain H residue  116 THR
Chi-restraints excluded: chain A residue   69 TYR
Chi-restraints excluded: chain A residue  112 CYS
Chi-restraints excluded: chain A residue  161 HIS
Chi-restraints excluded: chain A residue  292 ILE
Chi-restraints excluded: chain L residue   11 MET
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue   77 SER
Chi-restraints excluded: chain L residue   97 LEU
Chi-restraints excluded: chain L residue  105 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 23 optimal weight:    4.9990
   chunk 24 optimal weight:    0.9980
   chunk 29 optimal weight:    4.9990
   chunk 5 optimal weight:    0.2980
   chunk 12 optimal weight:    0.9990
   chunk 11 optimal weight:    0.9990
   chunk 40 optimal weight:    0.5980
   chunk 49 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9990
   chunk 69 optimal weight:    0.5980
   chunk 53 optimal weight:    0.9980
   overall best weight:    0.6980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.157566 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.126854 restraints weight = 7033.943|
|-----------------------------------------------------------------------------|
r_work (start): 0.3427 rms_B_bonded: 2.13
r_work: 0.3307 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.3152 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.3152
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8111
moved from start:          0.2145

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   6044  Z= 0.181
  Angle     :  0.573   7.337   8219  Z= 0.305
  Chirality :  0.042   0.169    899
  Planarity :  0.005   0.065   1013
  Dihedral  :  4.601  18.050    819
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 9.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.01 %
    Favored  : 94.99 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 12.97 %
    Favored  : 83.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.20 (0.31), residues: 738
  helix:  0.89 (0.27), residues: 360
  sheet: -1.30 (0.50), residues: 112
  loop : -0.88 (0.39), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 470 
 HIS   0.003   0.001   HIS H  80 
 PHE   0.016   0.002   PHE A 455 
 TYR   0.021   0.001   TYR A 137 
 ARG   0.006   0.001   ARG L  62 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04492 (  316)
  hydrogen bonds       : angle       5.09076 (  915)
  SS BOND              : bond        0.00166 (    3)
  SS BOND              : angle       0.59976 (    6)
  covalent geometry    : bond        0.00428 ( 6041)
  covalent geometry    : angle       0.57283 ( 8213)

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

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

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 105
  time to evaluate  : 0.637 
Fit side-chains
   revert: symmetry clash
REVERT: H   46 GLU cc_start: 0.8857 (tt0) cc_final: 0.8283 (tt0)
REVERT: H   57 TYR cc_start: 0.8979 (m-80) cc_final: 0.8476 (m-80)
REVERT: H   78 ILE cc_start: 0.7913 (mp) cc_final: 0.7568 (mp)
REVERT: A  191 PHE cc_start: 0.7684 (m-80) cc_final: 0.7299 (m-80)
REVERT: A  440 TYR cc_start: 0.8403 (t80) cc_final: 0.7832 (t80)
  outliers start: 20
  outliers final: 15
  residues processed: 115
  average time/residue: 0.1963
  time to fit residues: 29.7170
Evaluate side-chains
  118 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 103
  time to evaluate  : 0.629 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   53 SER
Chi-restraints excluded: chain H residue  116 THR
Chi-restraints excluded: chain A residue   69 TYR
Chi-restraints excluded: chain A residue  111 THR
Chi-restraints excluded: chain A residue  112 CYS
Chi-restraints excluded: chain A residue  161 HIS
Chi-restraints excluded: chain A residue  292 ILE
Chi-restraints excluded: chain A residue  422 LEU
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain A residue  543 ILE
Chi-restraints excluded: chain L residue   11 MET
Chi-restraints excluded: chain L residue   14 SER
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue   77 SER
Chi-restraints excluded: chain L residue  105 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 0 optimal weight:    3.9990
   chunk 36 optimal weight:    7.9990
   chunk 39 optimal weight:    0.9990
   chunk 4 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9980
   chunk 10 optimal weight:    0.5980
   chunk 11 optimal weight:    0.8980
   chunk 30 optimal weight:    0.6980
   chunk 22 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   overall best weight:    0.8382

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.154743 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.125610 restraints weight = 7001.956|
|-----------------------------------------------------------------------------|
r_work (start): 0.3420 rms_B_bonded: 1.92
r_work: 0.3297 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3147 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.3147
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8166
moved from start:          0.2351

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   6044  Z= 0.204
  Angle     :  0.591   8.943   8219  Z= 0.313
  Chirality :  0.043   0.168    899
  Planarity :  0.005   0.062   1013
  Dihedral  :  4.646  18.215    819
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 8.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.15 %
    Favored  : 94.85 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 13.29 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.18 (0.31), residues: 738
  helix:  0.90 (0.26), residues: 360
  sheet: -1.31 (0.50), residues: 112
  loop : -0.87 (0.40), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 470 
 HIS   0.003   0.001   HIS H  80 
 PHE   0.016   0.002   PHE A 455 
 TYR   0.021   0.002   TYR A 137 
 ARG   0.004   0.001   ARG H  44 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04591 (  316)
  hydrogen bonds       : angle       5.09775 (  915)
  SS BOND              : bond        0.00198 (    3)
  SS BOND              : angle       0.59575 (    6)
  covalent geometry    : bond        0.00482 ( 6041)
  covalent geometry    : angle       0.59088 ( 8213)

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

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

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 103
  time to evaluate  : 0.634 
Fit side-chains
   revert: symmetry clash
REVERT: H   46 GLU cc_start: 0.8848 (tt0) cc_final: 0.8280 (tt0)
REVERT: H   57 TYR cc_start: 0.8980 (m-80) cc_final: 0.8567 (m-80)
REVERT: H   78 ILE cc_start: 0.7975 (mp) cc_final: 0.7631 (mp)
REVERT: A  191 PHE cc_start: 0.7726 (m-80) cc_final: 0.7323 (m-80)
REVERT: A  225 LEU cc_start: 0.8186 (OUTLIER) cc_final: 0.7736 (tt)
REVERT: A  304 ILE cc_start: 0.7039 (OUTLIER) cc_final: 0.6267 (tp)
REVERT: L   62 ARG cc_start: 0.7125 (OUTLIER) cc_final: 0.5288 (ttm170)
  outliers start: 24
  outliers final: 17
  residues processed: 117
  average time/residue: 0.1969
  time to fit residues: 30.3824
Evaluate side-chains
  121 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 101
  time to evaluate  : 0.692 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   53 SER
Chi-restraints excluded: chain H residue  116 THR
Chi-restraints excluded: chain A residue   69 TYR
Chi-restraints excluded: chain A residue  111 THR
Chi-restraints excluded: chain A residue  112 CYS
Chi-restraints excluded: chain A residue  161 HIS
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  282 ILE
Chi-restraints excluded: chain A residue  292 ILE
Chi-restraints excluded: chain A residue  304 ILE
Chi-restraints excluded: chain A residue  422 LEU
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain A residue  543 ILE
Chi-restraints excluded: chain L residue   11 MET
Chi-restraints excluded: chain L residue   14 SER
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue   62 ARG
Chi-restraints excluded: chain L residue   77 SER
Chi-restraints excluded: chain L residue  105 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 0 optimal weight:    3.9990
   chunk 1 optimal weight:    0.0870
   chunk 12 optimal weight:    0.1980
   chunk 21 optimal weight:    1.9990
   chunk 54 optimal weight:    0.9980
   chunk 15 optimal weight:    0.7980
   chunk 45 optimal weight:    1.9990
   chunk 22 optimal weight:    0.0670
   chunk 14 optimal weight:    0.1980
   chunk 56 optimal weight:    0.9980
   chunk 62 optimal weight:    2.9990
   overall best weight:    0.2696

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.160961 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.130878 restraints weight = 6873.717|
|-----------------------------------------------------------------------------|
r_work (start): 0.3479 rms_B_bonded: 2.11
r_work: 0.3359 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.3205 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.3205
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8056
moved from start:          0.2421

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6044  Z= 0.117
  Angle     :  0.529   7.597   8219  Z= 0.280
  Chirality :  0.040   0.174    899
  Planarity :  0.005   0.057   1013
  Dihedral  :  4.376  16.424    819
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 8.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 14.87 %
    Favored  : 82.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.13 (0.32), residues: 738
  helix:  1.18 (0.27), residues: 360
  sheet: -1.09 (0.50), residues: 112
  loop : -0.79 (0.40), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 470 
 HIS   0.001   0.001   HIS H  80 
 PHE   0.011   0.001   PHE A 455 
 TYR   0.024   0.001   TYR A 137 
 ARG   0.004   0.000   ARG H  44 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03910 (  316)
  hydrogen bonds       : angle       4.88006 (  915)
  SS BOND              : bond        0.00197 (    3)
  SS BOND              : angle       0.75867 (    6)
  covalent geometry    : bond        0.00262 ( 6041)
  covalent geometry    : angle       0.52929 ( 8213)

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

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

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 111
  time to evaluate  : 0.618 
Fit side-chains
REVERT: H   46 GLU cc_start: 0.8858 (tt0) cc_final: 0.8276 (tt0)
REVERT: H   57 TYR cc_start: 0.8951 (m-80) cc_final: 0.8423 (m-80)
REVERT: H   78 ILE cc_start: 0.7922 (OUTLIER) cc_final: 0.7494 (mp)
REVERT: A  191 PHE cc_start: 0.7593 (m-80) cc_final: 0.7143 (m-80)
REVERT: A  446 MET cc_start: 0.8357 (mtt) cc_final: 0.8140 (mtt)
REVERT: L   17 GLU cc_start: 0.6463 (tm-30) cc_final: 0.6262 (tm-30)
REVERT: L   46 LYS cc_start: 0.8701 (ptpt) cc_final: 0.8501 (ptpp)
REVERT: L   62 ARG cc_start: 0.7075 (OUTLIER) cc_final: 0.5264 (ttm170)
  outliers start: 18
  outliers final: 11
  residues processed: 122
  average time/residue: 0.1914
  time to fit residues: 30.1978
Evaluate side-chains
  112 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 99
  time to evaluate  : 0.606 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   53 SER
Chi-restraints excluded: chain H residue   78 ILE
Chi-restraints excluded: chain H residue  116 THR
Chi-restraints excluded: chain A residue   69 TYR
Chi-restraints excluded: chain A residue  112 CYS
Chi-restraints excluded: chain A residue  161 HIS
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  422 LEU
Chi-restraints excluded: chain A residue  466 VAL
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain L residue   14 SER
Chi-restraints excluded: chain L residue   62 ARG
Chi-restraints excluded: chain L residue  105 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 55 optimal weight:    0.8980
   chunk 9 optimal weight:    2.9990
   chunk 23 optimal weight:    4.9990
   chunk 62 optimal weight:    0.3980
   chunk 43 optimal weight:    0.5980
   chunk 17 optimal weight:    0.9980
   chunk 69 optimal weight:    4.9990
   chunk 12 optimal weight:    0.1980
   chunk 67 optimal weight:    0.7980
   chunk 63 optimal weight:    3.9990
   chunk 71 optimal weight:    0.8980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
H  77 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.156787 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.127848 restraints weight = 6940.849|
|-----------------------------------------------------------------------------|
r_work (start): 0.3424 rms_B_bonded: 2.00
r_work: 0.3301 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3149 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.3149
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8115
moved from start:          0.2548

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6044  Z= 0.161
  Angle     :  0.561   7.910   8219  Z= 0.296
  Chirality :  0.042   0.171    899
  Planarity :  0.005   0.059   1013
  Dihedral  :  4.409  18.161    819
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 8.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.61 %
    Favored  : 95.39 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 15.03 %
    Favored  : 82.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.17 (0.32), residues: 738
  helix:  1.22 (0.27), residues: 359
  sheet: -1.03 (0.50), residues: 112
  loop : -0.79 (0.40), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 470 
 HIS   0.002   0.001   HIS H  80 
 PHE   0.018   0.002   PHE A 473 
 TYR   0.022   0.001   TYR A 137 
 ARG   0.004   0.001   ARG H  44 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04238 (  316)
  hydrogen bonds       : angle       4.90082 (  915)
  SS BOND              : bond        0.00163 (    3)
  SS BOND              : angle       0.80691 (    6)
  covalent geometry    : bond        0.00380 ( 6041)
  covalent geometry    : angle       0.56029 ( 8213)

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

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

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 98
  time to evaluate  : 0.682 
Fit side-chains
REVERT: H   46 GLU cc_start: 0.8852 (tt0) cc_final: 0.8281 (tt0)
REVERT: H   57 TYR cc_start: 0.9011 (m-80) cc_final: 0.8520 (m-80)
REVERT: H   78 ILE cc_start: 0.7925 (OUTLIER) cc_final: 0.7513 (mp)
REVERT: A  191 PHE cc_start: 0.7721 (m-80) cc_final: 0.7453 (m-10)
REVERT: A  304 ILE cc_start: 0.7049 (OUTLIER) cc_final: 0.6264 (tp)
REVERT: L   46 LYS cc_start: 0.8776 (ptpt) cc_final: 0.8573 (ptpp)
REVERT: L   62 ARG cc_start: 0.7169 (OUTLIER) cc_final: 0.5457 (ttm170)
  outliers start: 17
  outliers final: 13
  residues processed: 110
  average time/residue: 0.1901
  time to fit residues: 27.7700
Evaluate side-chains
  114 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 98
  time to evaluate  : 0.631 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   53 SER
Chi-restraints excluded: chain H residue   78 ILE
Chi-restraints excluded: chain H residue  116 THR
Chi-restraints excluded: chain A residue   69 TYR
Chi-restraints excluded: chain A residue  111 THR
Chi-restraints excluded: chain A residue  112 CYS
Chi-restraints excluded: chain A residue  161 HIS
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  292 ILE
Chi-restraints excluded: chain A residue  304 ILE
Chi-restraints excluded: chain A residue  422 LEU
Chi-restraints excluded: chain A residue  466 VAL
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain L residue   14 SER
Chi-restraints excluded: chain L residue   62 ARG
Chi-restraints excluded: chain L residue  105 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 22 optimal weight:    0.2980
   chunk 60 optimal weight:    0.5980
   chunk 4 optimal weight:    1.9990
   chunk 72 optimal weight:    2.9990
   chunk 46 optimal weight:    3.9990
   chunk 35 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9990
   chunk 1 optimal weight:    3.9990
   chunk 15 optimal weight:    0.5980
   chunk 56 optimal weight:    0.9980
   chunk 44 optimal weight:    0.9980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
H  77 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.155382 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.126980 restraints weight = 6932.766|
|-----------------------------------------------------------------------------|
r_work (start): 0.3416 rms_B_bonded: 1.91
r_work: 0.3294 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3143 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.3143
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8170
moved from start:          0.2580

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   6044  Z= 0.179
  Angle     :  0.575   7.457   8219  Z= 0.304
  Chirality :  0.042   0.171    899
  Planarity :  0.005   0.059   1013
  Dihedral  :  4.460  18.371    819
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 8.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.28 %
    Favored  : 94.72 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 15.35 %
    Favored  : 81.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.10 (0.32), residues: 738
  helix:  1.15 (0.27), residues: 359
  sheet: -1.08 (0.50), residues: 112
  loop : -0.79 (0.40), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 470 
 HIS   0.002   0.001   HIS H  80 
 PHE   0.016   0.002   PHE A 455 
 TYR   0.021   0.001   TYR A 137 
 ARG   0.004   0.001   ARG H  44 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04364 (  316)
  hydrogen bonds       : angle       4.94366 (  915)
  SS BOND              : bond        0.00151 (    3)
  SS BOND              : angle       0.82300 (    6)
  covalent geometry    : bond        0.00424 ( 6041)
  covalent geometry    : angle       0.57502 ( 8213)

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

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

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 101
  time to evaluate  : 0.756 
Fit side-chains
   revert: symmetry clash
REVERT: H   46 GLU cc_start: 0.8845 (tt0) cc_final: 0.8299 (tt0)
REVERT: H   57 TYR cc_start: 0.8979 (m-80) cc_final: 0.8566 (m-80)
REVERT: H   78 ILE cc_start: 0.7950 (OUTLIER) cc_final: 0.7498 (mp)
REVERT: A  191 PHE cc_start: 0.7796 (m-80) cc_final: 0.7406 (m-80)
REVERT: A  225 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.7977 (tt)
REVERT: A  304 ILE cc_start: 0.7121 (OUTLIER) cc_final: 0.6342 (tp)
REVERT: A  322 SER cc_start: 0.8401 (m) cc_final: 0.8082 (p)
REVERT: L   62 ARG cc_start: 0.7268 (OUTLIER) cc_final: 0.5555 (ttm170)
  outliers start: 18
  outliers final: 14
  residues processed: 111
  average time/residue: 0.2078
  time to fit residues: 30.2854
Evaluate side-chains
  117 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 99
  time to evaluate  : 0.608 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   53 SER
Chi-restraints excluded: chain H residue   78 ILE
Chi-restraints excluded: chain H residue  116 THR
Chi-restraints excluded: chain A residue   69 TYR
Chi-restraints excluded: chain A residue  111 THR
Chi-restraints excluded: chain A residue  112 CYS
Chi-restraints excluded: chain A residue  161 HIS
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  292 ILE
Chi-restraints excluded: chain A residue  304 ILE
Chi-restraints excluded: chain A residue  422 LEU
Chi-restraints excluded: chain A residue  466 VAL
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain L residue   11 MET
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue   62 ARG
Chi-restraints excluded: chain L residue  105 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 10 optimal weight:    1.9990
   chunk 42 optimal weight:    0.1980
   chunk 45 optimal weight:    1.9990
   chunk 62 optimal weight:    0.7980
   chunk 54 optimal weight:    0.5980
   chunk 16 optimal weight:    0.8980
   chunk 37 optimal weight:    2.9990
   chunk 26 optimal weight:    2.9990
   chunk 65 optimal weight:    3.9990
   chunk 46 optimal weight:    0.7980
   chunk 28 optimal weight:    0.9980
   overall best weight:    0.6580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.155470 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.126311 restraints weight = 6954.792|
|-----------------------------------------------------------------------------|
r_work (start): 0.3405 rms_B_bonded: 2.01
r_work: 0.3284 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3129 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.3129
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8132
moved from start:          0.2658

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   6044  Z= 0.172
  Angle     :  0.570   7.740   8219  Z= 0.301
  Chirality :  0.042   0.172    899
  Planarity :  0.005   0.058   1013
  Dihedral  :  4.440  18.400    819
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 8.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.01 %
    Favored  : 94.99 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 14.72 %
    Favored  : 82.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.13 (0.32), residues: 738
  helix:  1.16 (0.27), residues: 359
  sheet: -1.05 (0.50), residues: 112
  loop : -0.77 (0.40), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 470 
 HIS   0.002   0.001   HIS H  80 
 PHE   0.015   0.002   PHE A 391 
 TYR   0.021   0.001   TYR A 137 
 ARG   0.004   0.001   ARG H  44 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04306 (  316)
  hydrogen bonds       : angle       4.92972 (  915)
  SS BOND              : bond        0.00179 (    3)
  SS BOND              : angle       0.85984 (    6)
  covalent geometry    : bond        0.00408 ( 6041)
  covalent geometry    : angle       0.56960 ( 8213)

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

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

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 103
  time to evaluate  : 0.558 
Fit side-chains
   revert: symmetry clash
REVERT: H   46 GLU cc_start: 0.8856 (tt0) cc_final: 0.8285 (tt0)
REVERT: H   57 TYR cc_start: 0.8990 (m-80) cc_final: 0.8566 (m-80)
REVERT: H   78 ILE cc_start: 0.7908 (OUTLIER) cc_final: 0.7431 (mp)
REVERT: A  191 PHE cc_start: 0.7822 (m-80) cc_final: 0.7605 (m-10)
REVERT: A  225 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.7967 (tt)
REVERT: A  304 ILE cc_start: 0.7053 (OUTLIER) cc_final: 0.6274 (tp)
REVERT: A  322 SER cc_start: 0.8311 (m) cc_final: 0.7975 (p)
REVERT: L   62 ARG cc_start: 0.7261 (OUTLIER) cc_final: 0.5608 (ttm170)
  outliers start: 20
  outliers final: 16
  residues processed: 113
  average time/residue: 0.2243
  time to fit residues: 33.3115
Evaluate side-chains
  121 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 101
  time to evaluate  : 0.668 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   53 SER
Chi-restraints excluded: chain H residue   78 ILE
Chi-restraints excluded: chain H residue  116 THR
Chi-restraints excluded: chain A residue   69 TYR
Chi-restraints excluded: chain A residue  111 THR
Chi-restraints excluded: chain A residue  112 CYS
Chi-restraints excluded: chain A residue  161 HIS
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  282 ILE
Chi-restraints excluded: chain A residue  292 ILE
Chi-restraints excluded: chain A residue  304 ILE
Chi-restraints excluded: chain A residue  422 LEU
Chi-restraints excluded: chain A residue  466 VAL
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain A residue  495 MET
Chi-restraints excluded: chain L residue   11 MET
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue   62 ARG
Chi-restraints excluded: chain L residue  105 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 58 optimal weight:    0.1980
   chunk 37 optimal weight:    1.9990
   chunk 13 optimal weight:    0.5980
   chunk 34 optimal weight:    0.6980
   chunk 38 optimal weight:    0.6980
   chunk 24 optimal weight:    0.5980
   chunk 22 optimal weight:    0.0010
   chunk 56 optimal weight:    0.5980
   chunk 66 optimal weight:    1.9990
   chunk 55 optimal weight:    0.5980
   chunk 44 optimal weight:    0.5980
   overall best weight:    0.3986

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.158340 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.129451 restraints weight = 6929.911|
|-----------------------------------------------------------------------------|
r_work (start): 0.3443 rms_B_bonded: 2.01
r_work: 0.3322 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3170 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.3170
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8099
moved from start:          0.2672

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6044  Z= 0.133
  Angle     :  0.545   7.445   8219  Z= 0.287
  Chirality :  0.041   0.176    899
  Planarity :  0.005   0.056   1013
  Dihedral  :  4.320  17.934    819
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 9.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 15.82 %
    Favored  : 81.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.30 (0.32), residues: 738
  helix:  1.30 (0.27), residues: 359
  sheet: -0.96 (0.50), residues: 112
  loop : -0.71 (0.41), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 470 
 HIS   0.002   0.001   HIS H  80 
 PHE   0.013   0.001   PHE A 391 
 TYR   0.024   0.001   TYR A 137 
 ARG   0.004   0.001   ARG H  44 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04018 (  316)
  hydrogen bonds       : angle       4.81727 (  915)
  SS BOND              : bond        0.00156 (    3)
  SS BOND              : angle       0.66561 (    6)
  covalent geometry    : bond        0.00307 ( 6041)
  covalent geometry    : angle       0.54494 ( 8213)

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

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

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 103
  time to evaluate  : 0.618 
Fit side-chains
REVERT: H   46 GLU cc_start: 0.8847 (tt0) cc_final: 0.8278 (tt0)
REVERT: H   57 TYR cc_start: 0.8980 (m-80) cc_final: 0.8391 (m-80)
REVERT: H   78 ILE cc_start: 0.7871 (OUTLIER) cc_final: 0.7397 (mp)
REVERT: A  191 PHE cc_start: 0.7756 (m-80) cc_final: 0.7399 (m-80)
REVERT: A  304 ILE cc_start: 0.7041 (OUTLIER) cc_final: 0.6154 (tp)
REVERT: A  322 SER cc_start: 0.8255 (m) cc_final: 0.7956 (p)
REVERT: L   46 LYS cc_start: 0.8780 (ptpt) cc_final: 0.8572 (ptpp)
REVERT: L   62 ARG cc_start: 0.7274 (OUTLIER) cc_final: 0.5620 (ttm170)
  outliers start: 17
  outliers final: 12
  residues processed: 112
  average time/residue: 0.1870
  time to fit residues: 27.1707
Evaluate side-chains
  116 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 101
  time to evaluate  : 0.608 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   53 SER
Chi-restraints excluded: chain H residue   78 ILE
Chi-restraints excluded: chain H residue  116 THR
Chi-restraints excluded: chain A residue   69 TYR
Chi-restraints excluded: chain A residue  111 THR
Chi-restraints excluded: chain A residue  112 CYS
Chi-restraints excluded: chain A residue  161 HIS
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  292 ILE
Chi-restraints excluded: chain A residue  304 ILE
Chi-restraints excluded: chain A residue  422 LEU
Chi-restraints excluded: chain A residue  466 VAL
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain L residue   62 ARG
Chi-restraints excluded: chain L residue  105 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 16 optimal weight:    4.9990
   chunk 33 optimal weight:    0.6980
   chunk 3 optimal weight:    2.9990
   chunk 37 optimal weight:    0.7980
   chunk 53 optimal weight:    0.4980
   chunk 44 optimal weight:    0.7980
   chunk 50 optimal weight:    0.9990
   chunk 25 optimal weight:    0.7980
   chunk 4 optimal weight:    0.9980
   chunk 32 optimal weight:    0.6980
   chunk 61 optimal weight:    2.9990
   overall best weight:    0.6980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.154795 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.126498 restraints weight = 7031.853|
|-----------------------------------------------------------------------------|
r_work (start): 0.3410 rms_B_bonded: 1.91
r_work: 0.3294 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3140 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.3140
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8166
moved from start:          0.2725

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   6044  Z= 0.179
  Angle     :  0.578   8.225   8219  Z= 0.303
  Chirality :  0.042   0.170    899
  Planarity :  0.005   0.058   1013
  Dihedral  :  4.432  18.559    819
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 9.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.42 %
    Favored  : 94.58 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 15.82 %
    Favored  : 81.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.18 (0.32), residues: 738
  helix:  1.17 (0.27), residues: 359
  sheet: -0.95 (0.51), residues: 112
  loop : -0.74 (0.40), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 470 
 HIS   0.002   0.001   HIS H  80 
 PHE   0.014   0.002   PHE A 391 
 TYR   0.021   0.001   TYR A 137 
 ARG   0.007   0.001   ARG A 201 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04364 (  316)
  hydrogen bonds       : angle       4.89268 (  915)
  SS BOND              : bond        0.00175 (    3)
  SS BOND              : angle       0.75813 (    6)
  covalent geometry    : bond        0.00425 ( 6041)
  covalent geometry    : angle       0.57800 ( 8213)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3809.89 seconds
wall clock time: 67 minutes 7.66 seconds (4027.66 seconds total)