Starting phenix.real_space_refine
on Sat May 10 01:36:08 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8tm1_41374/05_2025/8tm1_41374.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8tm1_41374/05_2025/8tm1_41374.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.79
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8tm1_41374/05_2025/8tm1_41374.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8tm1_41374/05_2025/8tm1_41374.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8tm1_41374/05_2025/8tm1_41374.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8tm1_41374/05_2025/8tm1_41374.cif"
  }
  resolution = 2.79
  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=  -0.008 sd=   0.167
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      15      5.16       5
     C    2908      2.51       5
     N     754      2.21       5
     O     859      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 4536
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1407
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 175, 1407
          Classifications: {'peptide': 175}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 8, 'TRANS': 166}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
    Chain: "B"
      Number of atoms: 1282
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 159, 1282
          Classifications: {'peptide': 159}
          Link IDs: {'PTRANS': 7, 'TRANS': 151}
          Chain breaks: 2
    Chain: "H"
      Number of atoms: 1015
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 127, 1015
          Classifications: {'peptide': 127}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 120}
    Chain: "L"
      Number of atoms: 832
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 832
          Classifications: {'peptide': 108}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 101}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
  Time building chain proxies: 4.30, per 1000 atoms: 0.95
  Number of scatterers: 4536
  At special positions: 0
  Unit cell: (96.8, 74.8, 92.4, 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      15     16.00
     O     859      8.00
     N     754      7.00
     C    2908      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 379 " - pdb=" SG  CYS A 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 480 " - pdb=" SG  CYS A 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 379 " - pdb=" SG  CYS B 432 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 480 " - pdb=" SG  CYS B 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  92 " distance=2.04
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  88 " 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: 1.00
  Conformation dependent library (CDL) restraints added in 559.0 milliseconds
  

  1110 Ramachandran restraints generated.
    555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1044

  Finding SS restraints...
    Secondary structure from input PDB file:
      15 helices and 12 sheets defined
      14.8% alpha, 32.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.55
  Creating SS restraints...
    Processing helix  chain 'A' and resid 338 through 343
    Processing helix  chain 'A' and resid 349 through 353
      removed outlier: 3.528A  pdb=" N   TRP A 353 " --> pdb=" O   VAL A 350 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 366 through 370
    Processing helix  chain 'A' and resid 383 through 390
      removed outlier: 4.450A  pdb=" N   ASN A 388 " --> pdb=" O   THR A 385 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   LEU A 390 " --> pdb=" O   LEU A 387 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 405 through 410
      removed outlier: 4.408A  pdb=" N   ARG A 408 " --> pdb=" O   ASP A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 416 through 422
    Processing helix  chain 'A' and resid 502 through 505
    Processing helix  chain 'B' and resid 339 through 343
    Processing helix  chain 'B' and resid 349 through 353
      removed outlier: 3.653A  pdb=" N   TRP B 353 " --> pdb=" O   VAL B 350 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 367 through 371
    Processing helix  chain 'B' and resid 405 through 410
      removed outlier: 4.074A  pdb=" N   ARG B 408 " --> pdb=" O   ASP B 405 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 416 through 422
    Processing helix  chain 'B' and resid 438 through 443
    Processing helix  chain 'B' and resid 502 through 505
    Processing helix  chain 'H' and resid 83 through 87
      removed outlier: 3.703A  pdb=" N   THR H  87 " --> pdb=" O   ALA H  84 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 357
    Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454
    Processing sheet with id=AA3, first strand: chain 'B' and resid 356 through 357
    Processing sheet with id=AA4, first strand: chain 'B' and resid 376 through 379
      removed outlier: 3.522A  pdb=" N   PHE B 400 " --> pdb=" O   VAL B 510 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 452 through 454
    Processing sheet with id=AA6, first strand: chain 'B' and resid 473 through 474
    Processing sheet with id=AA7, first strand: chain 'H' and resid 3 through 7
      removed outlier: 3.715A  pdb=" N   GLN H   3 " --> pdb=" O   SER H  25 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   SER H  70 " --> pdb=" O   SER H  79 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'H' and resid 11 through 12
      removed outlier: 3.500A  pdb=" N   VAL H 109 " --> pdb=" O   ALA H  88 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   ALA H  88 " --> pdb=" O   VAL H 109 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'H' and resid 57 through 59
      removed outlier: 6.909A  pdb=" N   TRP H  36 " --> pdb=" O   ILE H  48 " (cutoff:3.500A)
      removed outlier: 4.543A  pdb=" N   ASN H  50 " --> pdb=" O   TRP H  35A" (cutoff:3.500A)
      removed outlier: 6.884A  pdb=" N   TRP H  35A" --> pdb=" O   ASN H  50 " (cutoff:3.500A)
      removed outlier: 6.119A  pdb=" N   TYR H  52 " --> pdb=" O   TYR H  34 " (cutoff:3.500A)
      removed outlier: 8.953A  pdb=" N   TYR H  34 " --> pdb=" O   TYR H  52 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   TYR H  35 " --> pdb=" O   GLY H  95 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   ARG H  94 " --> pdb=" O   ILE H 102 " (cutoff:3.500A)
      removed outlier: 4.093A  pdb=" N   ILE H 102 " --> pdb=" O   ARG H  94 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'L' and resid 4 through 7
      removed outlier: 3.516A  pdb=" N   SER L   7 " --> pdb=" O   THR L  22 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   THR L  22 " --> pdb=" O   SER L   7 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   VAL L  19 " --> pdb=" O   ILE L  75 " (cutoff:3.500A)
      removed outlier: 6.242A  pdb=" N   THR L  69 " --> pdb=" O   ALA L  25 " (cutoff:3.500A)
      removed outlier: 10.386A  pdb=" N   GLN L  27 " --> pdb=" O   SER L  67 " (cutoff:3.500A)
      removed outlier: 10.177A  pdb=" N   SER L  67 " --> pdb=" O   GLN L  27 " (cutoff:3.500A)
      removed outlier: 12.189A  pdb=" N   ILE L  29 " --> pdb=" O   SER L  65 " (cutoff:3.500A)
      removed outlier: 12.128A  pdb=" N   SER L  65 " --> pdb=" O   ILE L  29 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'L' and resid 10 through 13
      removed outlier: 6.675A  pdb=" N   LEU L  33 " --> pdb=" O   TYR L  49 " (cutoff:3.500A)
      removed outlier: 4.572A  pdb=" N   TYR L  49 " --> pdb=" O   LEU L  33 " (cutoff:3.500A)
      removed outlier: 6.630A  pdb=" N   TRP L  35 " --> pdb=" O   LEU L  47 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'L' and resid 10 through 13
      removed outlier: 3.812A  pdb=" N   THR L  97 " --> pdb=" O   GLN L  90 " (cutoff:3.500A)

    133 hydrogen bonds defined for protein.
    315 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.12

  Time building geometry restraints manager: 1.21 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: 1430
        1.34 -     1.47: 1322
        1.47 -     1.59: 1896
        1.59 -     1.71: 0
        1.71 -     1.83: 17
  Bond restraints: 4665
  Sorted by residual:
  bond pdb=" CB  PRO A 337 "
       pdb=" CG  PRO A 337 "
    ideal  model  delta    sigma   weight residual
    1.492  1.539 -0.047 5.00e-02 4.00e+02 8.83e-01
  bond pdb=" CB  MET L   4 "
       pdb=" CG  MET L   4 "
    ideal  model  delta    sigma   weight residual
    1.520  1.493  0.027 3.00e-02 1.11e+03 8.31e-01
  bond pdb=" SD  MET L   4 "
       pdb=" CE  MET L   4 "
    ideal  model  delta    sigma   weight residual
    1.791  1.769  0.022 2.50e-02 1.60e+03 7.51e-01
  bond pdb=" N   ASN H  65 "
       pdb=" CA  ASN H  65 "
    ideal  model  delta    sigma   weight residual
    1.460  1.472 -0.012 1.54e-02 4.22e+03 5.98e-01
  bond pdb=" N   SER H  54 "
       pdb=" CA  SER H  54 "
    ideal  model  delta    sigma   weight residual
    1.460  1.474 -0.015 1.95e-02 2.63e+03 5.86e-01
  ... (remaining 4660 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.47: 6047
        1.47 -     2.94: 251
        2.94 -     4.41: 37
        4.41 -     5.88: 3
        5.88 -     7.35: 3
  Bond angle restraints: 6341
  Sorted by residual:
  angle pdb=" C   ASN H  64 "
        pdb=" N   ASN H  65 "
        pdb=" CA  ASN H  65 "
      ideal   model   delta    sigma   weight residual
     122.46  126.03   -3.57 1.41e+00 5.03e-01 6.42e+00
  angle pdb=" C   ASP L  50 "
        pdb=" N   ALA L  51 "
        pdb=" CA  ALA L  51 "
      ideal   model   delta    sigma   weight residual
     121.54  126.32   -4.78 1.91e+00 2.74e-01 6.27e+00
  angle pdb=" CB  MET L   4 "
        pdb=" CG  MET L   4 "
        pdb=" SD  MET L   4 "
      ideal   model   delta    sigma   weight residual
     112.70  105.35    7.35 3.00e+00 1.11e-01 6.01e+00
  angle pdb=" C   ASN B 354 "
        pdb=" N   ARG B 355 "
        pdb=" CA  ARG B 355 "
      ideal   model   delta    sigma   weight residual
     122.81  126.20   -3.39 1.57e+00 4.06e-01 4.65e+00
  angle pdb=" N   ASN B 370 "
        pdb=" CA  ASN B 370 "
        pdb=" C   ASN B 370 "
      ideal   model   delta    sigma   weight residual
     112.23  114.67   -2.44 1.26e+00 6.30e-01 3.74e+00
  ... (remaining 6336 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.90: 2475
       16.90 -    33.81: 193
       33.81 -    50.71: 24
       50.71 -    67.61: 5
       67.61 -    84.51: 6
  Dihedral angle restraints: 2703
    sinusoidal: 1053
      harmonic: 1650
  Sorted by residual:
  dihedral pdb=" CD  ARG B 457 "
           pdb=" NE  ARG B 457 "
           pdb=" CZ  ARG B 457 "
           pdb=" NH1 ARG B 457 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -35.01   35.01     1      1.00e+01 1.00e-02 1.74e+01
  dihedral pdb=" CG  ARG B 403 "
           pdb=" CD  ARG B 403 "
           pdb=" NE  ARG B 403 "
           pdb=" CZ  ARG B 403 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00  134.71  -44.71     2      1.50e+01 4.44e-03 1.06e+01
  dihedral pdb=" CD  ARG A 408 "
           pdb=" NE  ARG A 408 "
           pdb=" CZ  ARG A 408 "
           pdb=" NH1 ARG A 408 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -26.31   26.31     1      1.00e+01 1.00e-02 9.95e+00
  ... (remaining 2700 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 365
       0.031 -    0.062: 175
       0.062 -    0.093: 71
       0.093 -    0.124: 33
       0.124 -    0.155: 15
  Chirality restraints: 659
  Sorted by residual:
  chirality pdb=" CA  ILE L  48 "
            pdb=" N   ILE L  48 "
            pdb=" C   ILE L  48 "
            pdb=" CB  ILE L  48 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.15 2.00e-01 2.50e+01 5.99e-01
  chirality pdb=" CA  ILE H  37 "
            pdb=" N   ILE H  37 "
            pdb=" C   ILE H  37 "
            pdb=" CB  ILE H  37 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.15 2.00e-01 2.50e+01 5.93e-01
  chirality pdb=" CA  ILE B 402 "
            pdb=" N   ILE B 402 "
            pdb=" C   ILE B 402 "
            pdb=" CB  ILE B 402 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.73e-01
  ... (remaining 656 not shown)

  Planarity restraints: 820
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 457 "    0.479 9.50e-02 1.11e+02   2.16e-01 3.63e+01
        pdb=" NE  ARG B 457 "   -0.046 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 457 "    0.044 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 457 "   -0.019 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 457 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 408 "    0.369 9.50e-02 1.11e+02   1.67e-01 2.15e+01
        pdb=" NE  ARG A 408 "   -0.035 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 408 "    0.033 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 408 "   -0.015 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 408 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 355 "    0.191 9.50e-02 1.11e+02   8.65e-02 6.00e+00
        pdb=" NE  ARG B 355 "   -0.018 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 355 "    0.019 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 355 "   -0.009 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 355 "   -0.000 2.00e-02 2.50e+03
  ... (remaining 817 not shown)

  Histogram of nonbonded interaction distances:
        2.31 -     2.83: 1466
        2.83 -     3.35: 3712
        3.35 -     3.87: 6515
        3.87 -     4.38: 7635
        4.38 -     4.90: 13939
  Nonbonded interactions: 33267
  Sorted by model distance:
  nonbonded pdb=" NH2 ARG B 355 "
            pdb=" OD1 ASP B 398 "
     model   vdw
     2.313 3.120
  nonbonded pdb=" NH1 ARG A 357 "
            pdb=" O   ILE A 358 "
     model   vdw
     2.315 3.120
  nonbonded pdb=" N   LYS A 462 "
            pdb=" OE2 GLU A 465 "
     model   vdw
     2.333 3.120
  nonbonded pdb=" OE1 GLU A 406 "
            pdb=" NE2 GLN A 409 "
     model   vdw
     2.350 3.120
  nonbonded pdb=" OG  SER A 349 "
            pdb=" O   LEU A 452 "
     model   vdw
     2.359 3.040
  ... (remaining 33262 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 338 through 358 or resid 366 through 380 or resid 394 thro \ 
ugh 515))
  selection = (chain 'B' and (resid 338 through 358 or resid 366 through 458 or (resid 459 and \ 
 (name N or name CA or name C or name O or name CB )) or resid 460 through 515)) \ 

}

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:             7.980
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     15.810
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:12.580
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.740
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7920
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   4671  Z= 0.116
  Angle     :  0.676   7.352   6353  Z= 0.367
  Chirality :  0.048   0.155    659
  Planarity :  0.012   0.216    820
  Dihedral  : 12.207  84.510   1641
  Min Nonbonded Distance : 2.313

Molprobity Statistics.
  All-atom Clashscore : 2.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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: -1.40 (0.33), residues: 555
  helix: -3.86 (0.58), residues: 32
  sheet:  0.20 (0.41), residues: 170
  loop : -1.27 (0.29), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 353 
 HIS   0.003   0.001   HIS H  77 
 PHE   0.016   0.002   PHE A 377 
 TYR   0.021   0.003   TYR L  49 
 ARG   0.049   0.004   ARG B 457 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.26923 (  128)
  hydrogen bonds       : angle       9.31830 (  315)
  SS BOND              : bond        0.00637 (    6)
  SS BOND              : angle       1.52209 (   12)
  covalent geometry    : bond        0.00261 ( 4665)
  covalent geometry    : angle       0.67382 ( 6341)

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

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

  1110 Ramachandran restraints generated.
    555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1110 Ramachandran restraints generated.
    555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 130
  time to evaluate  : 0.505 
Fit side-chains
REVERT: B  444 LYS cc_start: 0.6749 (ttmm) cc_final: 0.6480 (tppt)
REVERT: L   45 LYS cc_start: 0.8337 (ptmm) cc_final: 0.7931 (pttt)
  outliers start: 0
  outliers final: 1
  residues processed: 130
  average time/residue: 0.9755
  time to fit residues: 132.2547
Evaluate side-chains
  81 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 80
  time to evaluate  : 0.488 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   78 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 45 optimal weight:    0.0170
   chunk 40 optimal weight:    1.9990
   chunk 22 optimal weight:    0.4980
   chunk 13 optimal weight:    0.2980
   chunk 27 optimal weight:    2.9990
   chunk 21 optimal weight:    0.2980
   chunk 42 optimal weight:    0.8980
   chunk 16 optimal weight:    2.9990
   chunk 25 optimal weight:    0.4980
   chunk 31 optimal weight:    0.9980
   chunk 49 optimal weight:    4.9990
   overall best weight:    0.3218

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

Flipped N/Q/H residues before XYZ refinement:
H   6 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.139799 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.117566 restraints weight = 6310.350|
|-----------------------------------------------------------------------------|
r_work (start): 0.3475 rms_B_bonded: 1.94
r_work: 0.3342 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3211 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.3211
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8234
moved from start:          0.2530

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.070   4671  Z= 0.118
  Angle     :  0.594  11.876   6353  Z= 0.309
  Chirality :  0.046   0.164    659
  Planarity :  0.004   0.035    820
  Dihedral  :  4.220  31.153    637
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 2.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  : 12.42 %
    Favored  : 85.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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: -0.94 (0.33), residues: 555
  helix: -3.51 (0.64), residues: 33
  sheet:  0.66 (0.41), residues: 170
  loop : -1.02 (0.29), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 436 
 HIS   0.001   0.000   HIS H 101 
 PHE   0.011   0.001   PHE A 377 
 TYR   0.011   0.001   TYR A 369 
 ARG   0.010   0.001   ARG A 346 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03278 (  128)
  hydrogen bonds       : angle       6.54148 (  315)
  SS BOND              : bond        0.01048 (    6)
  SS BOND              : angle       1.99652 (   12)
  covalent geometry    : bond        0.00271 ( 4665)
  covalent geometry    : angle       0.58830 ( 6341)

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

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

  1110 Ramachandran restraints generated.
    555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1110 Ramachandran restraints generated.
    555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 93
  time to evaluate  : 0.468 
Fit side-chains
REVERT: A  442 ASP cc_start: 0.7261 (m-30) cc_final: 0.6809 (m-30)
REVERT: A  466 ARG cc_start: 0.7597 (ttp-110) cc_final: 0.7165 (ttm110)
REVERT: B  444 LYS cc_start: 0.7196 (ttmm) cc_final: 0.6819 (tppt)
REVERT: B  465 GLU cc_start: 0.8301 (tt0) cc_final: 0.8090 (tt0)
REVERT: L    4 MET cc_start: 0.7333 (mpp) cc_final: 0.7128 (mtm)
REVERT: L   45 LYS cc_start: 0.8600 (ptmm) cc_final: 0.8231 (pttt)
  outliers start: 8
  outliers final: 3
  residues processed: 100
  average time/residue: 1.2218
  time to fit residues: 126.5031
Evaluate side-chains
  84 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 81
  time to evaluate  : 0.480 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain B residue  345 THR
Chi-restraints excluded: chain H residue   78 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 42 optimal weight:    0.5980
   chunk 2 optimal weight:    1.9990
   chunk 13 optimal weight:    0.0470
   chunk 15 optimal weight:    4.9990
   chunk 36 optimal weight:    0.0050
   chunk 50 optimal weight:    0.0050
   chunk 31 optimal weight:    0.4980
   chunk 35 optimal weight:    0.9990
   chunk 26 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   overall best weight:    0.2306

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

Flipped N/Q/H residues before XYZ refinement:
A 440 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.139293 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.116673 restraints weight = 6429.705|
|-----------------------------------------------------------------------------|
r_work (start): 0.3462 rms_B_bonded: 2.01
r_work: 0.3334 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3202 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.3202
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8223
moved from start:          0.3091

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.060   4671  Z= 0.098
  Angle     :  0.518   9.632   6353  Z= 0.271
  Chirality :  0.044   0.154    659
  Planarity :  0.004   0.032    820
  Dihedral  :  3.921  31.533    637
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 2.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 14.46 %
    Favored  : 83.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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: -0.61 (0.33), residues: 555
  helix: -3.32 (0.73), residues: 28
  sheet:  0.89 (0.41), residues: 168
  loop : -0.83 (0.29), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 436 
 HIS   0.001   0.001   HIS H  77 
 PHE   0.011   0.001   PHE A 400 
 TYR   0.010   0.001   TYR A 369 
 ARG   0.005   0.000   ARG A 457 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03196 (  128)
  hydrogen bonds       : angle       5.91358 (  315)
  SS BOND              : bond        0.00676 (    6)
  SS BOND              : angle       1.77624 (   12)
  covalent geometry    : bond        0.00223 ( 4665)
  covalent geometry    : angle       0.51288 ( 6341)

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

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

  1110 Ramachandran restraints generated.
    555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1110 Ramachandran restraints generated.
    555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 82
  time to evaluate  : 0.527 
Fit side-chains
REVERT: A  408 ARG cc_start: 0.8909 (OUTLIER) cc_final: 0.8358 (ttm-80)
REVERT: A  442 ASP cc_start: 0.7303 (m-30) cc_final: 0.6884 (m-30)
REVERT: A  466 ARG cc_start: 0.7676 (ttp-110) cc_final: 0.7248 (ttm110)
REVERT: B  444 LYS cc_start: 0.7181 (ttmm) cc_final: 0.6872 (ttmt)
REVERT: B  498 GLN cc_start: 0.8435 (OUTLIER) cc_final: 0.7871 (mt0)
REVERT: L    4 MET cc_start: 0.7425 (mpp) cc_final: 0.7064 (mtm)
REVERT: L   42 LYS cc_start: 0.7878 (mmtp) cc_final: 0.7565 (mtmt)
REVERT: L   45 LYS cc_start: 0.8681 (ptmm) cc_final: 0.8307 (pttt)
  outliers start: 11
  outliers final: 4
  residues processed: 90
  average time/residue: 1.2306
  time to fit residues: 114.8287
Evaluate side-chains
  86 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 80
  time to evaluate  : 0.533 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  408 ARG
Chi-restraints excluded: chain A residue  510 VAL
Chi-restraints excluded: chain B residue  345 THR
Chi-restraints excluded: chain B residue  498 GLN
Chi-restraints excluded: chain B residue  512 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 13 optimal weight:    0.0170
   chunk 36 optimal weight:    0.4980
   chunk 9 optimal weight:    0.9990
   chunk 11 optimal weight:    2.9990
   chunk 12 optimal weight:    0.6980
   chunk 25 optimal weight:    3.9990
   chunk 28 optimal weight:    0.3980
   chunk 16 optimal weight:    0.8980
   chunk 19 optimal weight:    2.9990
   chunk 7 optimal weight:    0.7980
   chunk 53 optimal weight:    1.9990
   overall best weight:    0.4818

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

Flipped N/Q/H residues before XYZ refinement:
B 474 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.134613 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.111922 restraints weight = 6472.018|
|-----------------------------------------------------------------------------|
r_work (start): 0.3392 rms_B_bonded: 2.00
r_work: 0.3264 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3134 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.3134
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8316
moved from start:          0.3585

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.070   4671  Z= 0.123
  Angle     :  0.566  12.081   6353  Z= 0.298
  Chirality :  0.045   0.166    659
  Planarity :  0.004   0.031    820
  Dihedral  :  4.043  18.197    635
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 2.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 14.26 %
    Favored  : 82.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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: -0.64 (0.33), residues: 555
  helix: -3.13 (0.71), residues: 33
  sheet:  0.99 (0.42), residues: 169
  loop : -0.90 (0.29), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP H  47 
 HIS   0.001   0.001   HIS H  40 
 PHE   0.015   0.001   PHE B 377 
 TYR   0.014   0.001   TYR A 489 
 ARG   0.004   0.001   ARG L  24 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03673 (  128)
  hydrogen bonds       : angle       6.02914 (  315)
  SS BOND              : bond        0.01009 (    6)
  SS BOND              : angle       2.13159 (   12)
  covalent geometry    : bond        0.00289 ( 4665)
  covalent geometry    : angle       0.55915 ( 6341)

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

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

  1110 Ramachandran restraints generated.
    555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1110 Ramachandran restraints generated.
    555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 85
  time to evaluate  : 0.510 
Fit side-chains
REVERT: A  403 ARG cc_start: 0.8646 (ttp-170) cc_final: 0.8301 (ttp-170)
REVERT: A  408 ARG cc_start: 0.9024 (OUTLIER) cc_final: 0.8322 (ttm-80)
REVERT: A  466 ARG cc_start: 0.7677 (ttp-110) cc_final: 0.7437 (ttm110)
REVERT: A  506 GLN cc_start: 0.9139 (OUTLIER) cc_final: 0.8360 (mt0)
REVERT: B  444 LYS cc_start: 0.7161 (ttmm) cc_final: 0.6806 (ttmt)
REVERT: B  498 GLN cc_start: 0.8420 (OUTLIER) cc_final: 0.7879 (mt0)
REVERT: B  512 VAL cc_start: 0.9039 (OUTLIER) cc_final: 0.8758 (t)
REVERT: H    5 GLN cc_start: 0.7921 (mp10) cc_final: 0.7642 (mp10)
REVERT: L    4 MET cc_start: 0.7450 (mpp) cc_final: 0.7159 (mtm)
REVERT: L   42 LYS cc_start: 0.8170 (mmtp) cc_final: 0.7817 (mtmt)
REVERT: L   45 LYS cc_start: 0.8890 (ptmm) cc_final: 0.8599 (pttt)
  outliers start: 18
  outliers final: 7
  residues processed: 97
  average time/residue: 1.2527
  time to fit residues: 125.7951
Evaluate side-chains
  93 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 82
  time to evaluate  : 0.480 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  340 GLU
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  408 ARG
Chi-restraints excluded: chain A residue  465 GLU
Chi-restraints excluded: chain A residue  506 GLN
Chi-restraints excluded: chain A residue  510 VAL
Chi-restraints excluded: chain B residue  345 THR
Chi-restraints excluded: chain B residue  427 ASP
Chi-restraints excluded: chain B residue  498 GLN
Chi-restraints excluded: chain B residue  512 VAL
Chi-restraints excluded: chain H residue   78 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 33 optimal weight:    0.8980
   chunk 46 optimal weight:    2.9990
   chunk 49 optimal weight:    5.9990
   chunk 36 optimal weight:    0.0050
   chunk 16 optimal weight:    2.9990
   chunk 26 optimal weight:    2.9990
   chunk 39 optimal weight:    0.7980
   chunk 4 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 11 optimal weight:    2.9990
   chunk 10 optimal weight:    1.9990
   overall best weight:    1.1398

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

Flipped N/Q/H residues before XYZ refinement:
B 414 GLN
B 474 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.130336 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.106334 restraints weight = 6853.040|
|-----------------------------------------------------------------------------|
r_work (start): 0.3308 rms_B_bonded: 2.25
r_work: 0.3189 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.3062 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.3062
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8400
moved from start:          0.4186

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.094   4671  Z= 0.208
  Angle     :  0.721  14.941   6353  Z= 0.380
  Chirality :  0.050   0.246    659
  Planarity :  0.005   0.046    820
  Dihedral  :  4.911  19.092    635
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 3.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.50 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  3.87 %
    Allowed  : 15.07 %
    Favored  : 81.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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: -0.81 (0.33), residues: 555
  helix: -3.71 (0.59), residues: 33
  sheet:  1.02 (0.42), residues: 177
  loop : -1.11 (0.28), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP H  47 
 HIS   0.002   0.001   HIS H 101 
 PHE   0.027   0.002   PHE B 338 
 TYR   0.019   0.002   TYR A 369 
 ARG   0.008   0.001   ARG L  24 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05037 (  128)
  hydrogen bonds       : angle       6.55238 (  315)
  SS BOND              : bond        0.01672 (    6)
  SS BOND              : angle       3.11096 (   12)
  covalent geometry    : bond        0.00507 ( 4665)
  covalent geometry    : angle       0.70842 ( 6341)

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

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

  1110 Ramachandran restraints generated.
    555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1110 Ramachandran restraints generated.
    555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 84
  time to evaluate  : 0.530 
Fit side-chains
   revert: symmetry clash
REVERT: A  403 ARG cc_start: 0.8790 (ttp-170) cc_final: 0.8534 (ttp-170)
REVERT: A  408 ARG cc_start: 0.8995 (OUTLIER) cc_final: 0.8272 (ttm-80)
REVERT: A  466 ARG cc_start: 0.7807 (ttp-110) cc_final: 0.7587 (ttm110)
REVERT: A  498 GLN cc_start: 0.8248 (mt0) cc_final: 0.7980 (mm110)
REVERT: A  506 GLN cc_start: 0.9104 (OUTLIER) cc_final: 0.8393 (mt0)
REVERT: B  444 LYS cc_start: 0.7192 (ttmm) cc_final: 0.6743 (tppt)
REVERT: B  498 GLN cc_start: 0.8419 (OUTLIER) cc_final: 0.7879 (mt0)
REVERT: B  512 VAL cc_start: 0.9099 (OUTLIER) cc_final: 0.8842 (t)
REVERT: H    5 GLN cc_start: 0.8009 (mp10) cc_final: 0.7704 (mp10)
REVERT: H   16 GLU cc_start: 0.7926 (tt0) cc_final: 0.7478 (mt-10)
REVERT: L   42 LYS cc_start: 0.8356 (mmtp) cc_final: 0.7956 (mtmt)
  outliers start: 19
  outliers final: 9
  residues processed: 96
  average time/residue: 1.2802
  time to fit residues: 127.1252
Evaluate side-chains
  96 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 83
  time to evaluate  : 0.472 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  408 ARG
Chi-restraints excluded: chain A residue  465 GLU
Chi-restraints excluded: chain A residue  506 GLN
Chi-restraints excluded: chain A residue  510 VAL
Chi-restraints excluded: chain B residue  345 THR
Chi-restraints excluded: chain B residue  427 ASP
Chi-restraints excluded: chain B residue  498 GLN
Chi-restraints excluded: chain B residue  512 VAL
Chi-restraints excluded: chain H residue   65 ASN
Chi-restraints excluded: chain L residue  100 GLN
Chi-restraints excluded: chain L residue  103 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 41 optimal weight:    0.6980
   chunk 11 optimal weight:    1.9990
   chunk 38 optimal weight:    0.4980
   chunk 22 optimal weight:    0.4980
   chunk 9 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9990
   chunk 51 optimal weight:    1.9990
   chunk 27 optimal weight:    2.9990
   chunk 19 optimal weight:    1.9990
   chunk 36 optimal weight:    0.0870
   chunk 48 optimal weight:    0.7980
   overall best weight:    0.5158

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

Flipped N/Q/H residues before XYZ refinement:
H   3 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.131999 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.109989 restraints weight = 6413.871|
|-----------------------------------------------------------------------------|
r_work (start): 0.3366 rms_B_bonded: 1.92
r_work: 0.3235 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3104 rms_B_bonded: 4.28 restraints_weight: 0.2500
r_work (final): 0.3104
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8400
moved from start:          0.4279

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.072   4671  Z= 0.125
  Angle     :  0.577  12.608   6353  Z= 0.306
  Chirality :  0.045   0.185    659
  Planarity :  0.005   0.041    820
  Dihedral  :  4.364  19.808    635
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 2.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 16.90 %
    Favored  : 79.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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: -0.75 (0.33), residues: 555
  helix: -3.61 (0.71), residues: 28
  sheet:  0.95 (0.41), residues: 181
  loop : -1.08 (0.28), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP H  47 
 HIS   0.001   0.001   HIS H 101 
 PHE   0.011   0.001   PHE B 377 
 TYR   0.019   0.001   TYR A 489 
 ARG   0.008   0.001   ARG L  24 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03629 (  128)
  hydrogen bonds       : angle       6.19649 (  315)
  SS BOND              : bond        0.00965 (    6)
  SS BOND              : angle       2.20431 (   12)
  covalent geometry    : bond        0.00293 ( 4665)
  covalent geometry    : angle       0.56926 ( 6341)

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

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

  1110 Ramachandran restraints generated.
    555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1110 Ramachandran restraints generated.
    555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 86
  time to evaluate  : 0.532 
Fit side-chains
REVERT: A  403 ARG cc_start: 0.8671 (ttp-170) cc_final: 0.8458 (ttp-170)
REVERT: A  408 ARG cc_start: 0.9005 (OUTLIER) cc_final: 0.8280 (ttm-80)
REVERT: A  466 ARG cc_start: 0.7797 (ttp-110) cc_final: 0.7542 (ttm110)
REVERT: A  506 GLN cc_start: 0.9154 (OUTLIER) cc_final: 0.8364 (mt0)
REVERT: B  444 LYS cc_start: 0.7259 (ttmm) cc_final: 0.6881 (tppt)
REVERT: B  498 GLN cc_start: 0.8454 (OUTLIER) cc_final: 0.7944 (mt0)
REVERT: H   81 LYS cc_start: 0.8880 (OUTLIER) cc_final: 0.8463 (mppt)
REVERT: L   42 LYS cc_start: 0.8364 (mmtp) cc_final: 0.8063 (mtmt)
REVERT: L   70 GLU cc_start: 0.8234 (mm-30) cc_final: 0.7973 (tp30)
  outliers start: 16
  outliers final: 9
  residues processed: 97
  average time/residue: 1.2447
  time to fit residues: 125.1092
Evaluate side-chains
  95 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 82
  time to evaluate  : 0.511 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  408 ARG
Chi-restraints excluded: chain A residue  465 GLU
Chi-restraints excluded: chain A residue  506 GLN
Chi-restraints excluded: chain A residue  510 VAL
Chi-restraints excluded: chain B residue  345 THR
Chi-restraints excluded: chain B residue  427 ASP
Chi-restraints excluded: chain B residue  498 GLN
Chi-restraints excluded: chain B residue  512 VAL
Chi-restraints excluded: chain H residue   65 ASN
Chi-restraints excluded: chain H residue   81 LYS
Chi-restraints excluded: chain L residue  103 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 27 optimal weight:    2.9990
   chunk 21 optimal weight:    2.9990
   chunk 23 optimal weight:    0.8980
   chunk 46 optimal weight:    5.9990
   chunk 32 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   chunk 31 optimal weight:    0.0670
   chunk 25 optimal weight:    0.9980
   chunk 9 optimal weight:    2.9990
   chunk 7 optimal weight:    1.9990
   chunk 28 optimal weight:    0.0670
   overall best weight:    0.8058

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

Flipped N/Q/H residues before XYZ refinement:
H   5 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.130004 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.108034 restraints weight = 6373.196|
|-----------------------------------------------------------------------------|
r_work (start): 0.3338 rms_B_bonded: 1.91
r_work: 0.3205 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3072 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.3072
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8438
moved from start:          0.4410

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.077   4671  Z= 0.161
  Angle     :  0.634  13.157   6353  Z= 0.336
  Chirality :  0.047   0.199    659
  Planarity :  0.005   0.042    820
  Dihedral  :  4.593  20.598    635
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 3.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 17.11 %
    Favored  : 79.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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: -0.78 (0.34), residues: 555
  helix: -3.75 (0.69), residues: 28
  sheet:  1.01 (0.42), residues: 177
  loop : -1.12 (0.28), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP H  47 
 HIS   0.002   0.001   HIS H 101 
 PHE   0.016   0.002   PHE B 338 
 TYR   0.016   0.002   TYR A 489 
 ARG   0.007   0.001   ARG L  24 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04366 (  128)
  hydrogen bonds       : angle       6.37082 (  315)
  SS BOND              : bond        0.01220 (    6)
  SS BOND              : angle       2.58011 (   12)
  covalent geometry    : bond        0.00387 ( 4665)
  covalent geometry    : angle       0.62461 ( 6341)

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

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

  1110 Ramachandran restraints generated.
    555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1110 Ramachandran restraints generated.
    555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 84
  time to evaluate  : 0.514 
Fit side-chains
REVERT: A  340 GLU cc_start: 0.7961 (mp0) cc_final: 0.7653 (mp0)
REVERT: A  403 ARG cc_start: 0.8733 (ttp-170) cc_final: 0.8388 (ttp-170)
REVERT: A  408 ARG cc_start: 0.9018 (OUTLIER) cc_final: 0.8273 (ttm-80)
REVERT: A  466 ARG cc_start: 0.7819 (ttp-110) cc_final: 0.7506 (ttm110)
REVERT: A  506 GLN cc_start: 0.9187 (OUTLIER) cc_final: 0.8435 (mt0)
REVERT: B  444 LYS cc_start: 0.7261 (ttmm) cc_final: 0.6880 (tppt)
REVERT: B  498 GLN cc_start: 0.8456 (OUTLIER) cc_final: 0.7948 (mt0)
REVERT: B  512 VAL cc_start: 0.9001 (OUTLIER) cc_final: 0.8757 (t)
REVERT: H   63 LEU cc_start: 0.7467 (OUTLIER) cc_final: 0.6979 (mt)
REVERT: H   81 LYS cc_start: 0.8918 (OUTLIER) cc_final: 0.8479 (mppt)
REVERT: L   42 LYS cc_start: 0.8390 (mmtp) cc_final: 0.8093 (mtmt)
  outliers start: 18
  outliers final: 8
  residues processed: 94
  average time/residue: 1.1842
  time to fit residues: 115.4380
Evaluate side-chains
  94 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 80
  time to evaluate  : 0.468 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  408 ARG
Chi-restraints excluded: chain A residue  465 GLU
Chi-restraints excluded: chain A residue  506 GLN
Chi-restraints excluded: chain A residue  510 VAL
Chi-restraints excluded: chain B residue  345 THR
Chi-restraints excluded: chain B residue  427 ASP
Chi-restraints excluded: chain B residue  498 GLN
Chi-restraints excluded: chain B residue  512 VAL
Chi-restraints excluded: chain H residue   63 LEU
Chi-restraints excluded: chain H residue   65 ASN
Chi-restraints excluded: chain H residue   81 LYS
Chi-restraints excluded: chain L residue  103 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 25 optimal weight:    0.9980
   chunk 49 optimal weight:    2.9990
   chunk 30 optimal weight:    1.9990
   chunk 45 optimal weight:    0.0570
   chunk 0 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9980
   chunk 46 optimal weight:    0.5980
   chunk 10 optimal weight:    3.9990
   chunk 12 optimal weight:    0.3980
   chunk 32 optimal weight:    1.9990
   chunk 29 optimal weight:    0.0000
   overall best weight:    0.4102

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

Flipped N/Q/H residues before XYZ refinement:
H   5 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.132120 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.110070 restraints weight = 6488.175|
|-----------------------------------------------------------------------------|
r_work (start): 0.3368 rms_B_bonded: 1.97
r_work: 0.3246 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3116 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.3116
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8344
moved from start:          0.4466

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063   4671  Z= 0.114
  Angle     :  0.554  11.233   6353  Z= 0.294
  Chirality :  0.044   0.162    659
  Planarity :  0.004   0.039    820
  Dihedral  :  4.245  20.912    635
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 3.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 18.13 %
    Favored  : 78.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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: -0.71 (0.34), residues: 555
  helix: -3.47 (0.63), residues: 34
  sheet:  0.94 (0.41), residues: 180
  loop : -0.97 (0.29), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP H  47 
 HIS   0.001   0.001   HIS H 101 
 PHE   0.010   0.001   PHE B 377 
 TYR   0.015   0.001   TYR A 489 
 ARG   0.008   0.001   ARG A 346 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03415 (  128)
  hydrogen bonds       : angle       6.13278 (  315)
  SS BOND              : bond        0.00930 (    6)
  SS BOND              : angle       1.95084 (   12)
  covalent geometry    : bond        0.00261 ( 4665)
  covalent geometry    : angle       0.54813 ( 6341)

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

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

  1110 Ramachandran restraints generated.
    555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1110 Ramachandran restraints generated.
    555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 84
  time to evaluate  : 0.478 
Fit side-chains
   revert: symmetry clash
REVERT: A  340 GLU cc_start: 0.7861 (mp0) cc_final: 0.7528 (mp0)
REVERT: A  403 ARG cc_start: 0.8700 (ttp-170) cc_final: 0.8290 (ttp-170)
REVERT: A  408 ARG cc_start: 0.8949 (OUTLIER) cc_final: 0.8203 (ttm-80)
REVERT: A  434 ILE cc_start: 0.9122 (OUTLIER) cc_final: 0.8830 (mp)
REVERT: A  466 ARG cc_start: 0.7699 (ttp-110) cc_final: 0.7466 (ttm110)
REVERT: A  503 VAL cc_start: 0.8474 (p) cc_final: 0.8060 (p)
REVERT: A  506 GLN cc_start: 0.9136 (OUTLIER) cc_final: 0.8313 (mt0)
REVERT: B  444 LYS cc_start: 0.7215 (ttmm) cc_final: 0.6782 (tppt)
REVERT: B  498 GLN cc_start: 0.8424 (OUTLIER) cc_final: 0.7903 (mt0)
REVERT: H   81 LYS cc_start: 0.8937 (OUTLIER) cc_final: 0.8447 (mppt)
REVERT: L   42 LYS cc_start: 0.8320 (mmtp) cc_final: 0.7960 (mtmt)
  outliers start: 15
  outliers final: 9
  residues processed: 95
  average time/residue: 1.1569
  time to fit residues: 114.0903
Evaluate side-chains
  97 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 83
  time to evaluate  : 0.485 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  408 ARG
Chi-restraints excluded: chain A residue  434 ILE
Chi-restraints excluded: chain A residue  465 GLU
Chi-restraints excluded: chain A residue  506 GLN
Chi-restraints excluded: chain A residue  510 VAL
Chi-restraints excluded: chain B residue  345 THR
Chi-restraints excluded: chain B residue  427 ASP
Chi-restraints excluded: chain B residue  498 GLN
Chi-restraints excluded: chain B residue  512 VAL
Chi-restraints excluded: chain H residue   65 ASN
Chi-restraints excluded: chain H residue   81 LYS
Chi-restraints excluded: chain L residue  103 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 49 optimal weight:    0.0170
   chunk 10 optimal weight:    2.9990
   chunk 36 optimal weight:    0.3980
   chunk 43 optimal weight:    0.0570
   chunk 38 optimal weight:    0.7980
   chunk 9 optimal weight:    0.9990
   chunk 40 optimal weight:    0.9990
   chunk 2 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9980
   chunk 35 optimal weight:    0.7980
   chunk 34 optimal weight:    5.9990
   overall best weight:    0.4136

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

Flipped N/Q/H residues before XYZ refinement:
H   3 GLN
H  77 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.132510 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.110392 restraints weight = 6466.955|
|-----------------------------------------------------------------------------|
r_work (start): 0.3373 rms_B_bonded: 1.96
r_work: 0.3248 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3118 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.3118
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8359
moved from start:          0.4500

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061   4671  Z= 0.115
  Angle     :  0.560  10.791   6353  Z= 0.296
  Chirality :  0.044   0.163    659
  Planarity :  0.004   0.037    820
  Dihedral  :  4.167  21.490    635
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 3.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 19.14 %
    Favored  : 78.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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: -0.63 (0.34), residues: 555
  helix: -3.41 (0.64), residues: 34
  sheet:  1.17 (0.42), residues: 170
  loop : -0.96 (0.29), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP H  47 
 HIS   0.001   0.001   HIS H 101 
 PHE   0.010   0.001   PHE B 377 
 TYR   0.016   0.001   TYR A 489 
 ARG   0.008   0.001   ARG A 346 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03469 (  128)
  hydrogen bonds       : angle       6.09468 (  315)
  SS BOND              : bond        0.00944 (    6)
  SS BOND              : angle       1.94051 (   12)
  covalent geometry    : bond        0.00265 ( 4665)
  covalent geometry    : angle       0.55437 ( 6341)

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

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

  1110 Ramachandran restraints generated.
    555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1110 Ramachandran restraints generated.
    555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 84
  time to evaluate  : 0.524 
Fit side-chains
REVERT: A  340 GLU cc_start: 0.7916 (mp0) cc_final: 0.7599 (mp0)
REVERT: A  408 ARG cc_start: 0.8959 (OUTLIER) cc_final: 0.8220 (ttm-80)
REVERT: A  466 ARG cc_start: 0.7706 (ttp-110) cc_final: 0.7465 (ttm110)
REVERT: A  503 VAL cc_start: 0.8456 (p) cc_final: 0.8057 (p)
REVERT: A  506 GLN cc_start: 0.9137 (OUTLIER) cc_final: 0.8291 (mt0)
REVERT: B  444 LYS cc_start: 0.7238 (ttmm) cc_final: 0.6828 (tppt)
REVERT: B  498 GLN cc_start: 0.8464 (OUTLIER) cc_final: 0.7939 (mt0)
REVERT: H    3 GLN cc_start: 0.8470 (mm110) cc_final: 0.8226 (mm-40)
REVERT: H   81 LYS cc_start: 0.8902 (OUTLIER) cc_final: 0.8459 (mppt)
REVERT: L   42 LYS cc_start: 0.8330 (mmtp) cc_final: 0.7948 (mtmt)
  outliers start: 14
  outliers final: 8
  residues processed: 93
  average time/residue: 1.1965
  time to fit residues: 115.4057
Evaluate side-chains
  92 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 80
  time to evaluate  : 0.499 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  408 ARG
Chi-restraints excluded: chain A residue  465 GLU
Chi-restraints excluded: chain A residue  506 GLN
Chi-restraints excluded: chain A residue  510 VAL
Chi-restraints excluded: chain B residue  345 THR
Chi-restraints excluded: chain B residue  427 ASP
Chi-restraints excluded: chain B residue  498 GLN
Chi-restraints excluded: chain B residue  512 VAL
Chi-restraints excluded: chain H residue   81 LYS
Chi-restraints excluded: chain L residue  103 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 14 optimal weight:    0.0980
   chunk 47 optimal weight:    0.6980
   chunk 20 optimal weight:    0.9990
   chunk 36 optimal weight:    0.3980
   chunk 32 optimal weight:    3.9990
   chunk 41 optimal weight:    1.9990
   chunk 34 optimal weight:    0.0970
   chunk 44 optimal weight:    0.5980
   chunk 13 optimal weight:    0.0970
   chunk 4 optimal weight:    0.0370
   chunk 27 optimal weight:    2.9990
   overall best weight:    0.1454

-------------------------------------------------------------------------------
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 = 0.3729 r_free = 0.3729 target = 0.136667 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.115167 restraints weight = 6424.296|
|-----------------------------------------------------------------------------|
r_work (start): 0.3440 rms_B_bonded: 1.92
r_work: 0.3316 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3187 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.3187
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8305
moved from start:          0.4575

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.048   4671  Z= 0.088
  Angle     :  0.492   8.503   6353  Z= 0.258
  Chirality :  0.042   0.151    659
  Planarity :  0.004   0.038    820
  Dihedral  :  3.816  20.353    635
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 2.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  : 20.57 %
    Favored  : 77.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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: -0.46 (0.34), residues: 555
  helix: -3.23 (0.68), residues: 34
  sheet:  1.17 (0.42), residues: 171
  loop : -0.79 (0.29), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 436 
 HIS   0.001   0.000   HIS H 101 
 PHE   0.011   0.001   PHE A 400 
 TYR   0.011   0.001   TYR A 489 
 ARG   0.008   0.001   ARG L  24 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02704 (  128)
  hydrogen bonds       : angle       5.87776 (  315)
  SS BOND              : bond        0.00721 (    6)
  SS BOND              : angle       1.40751 (   12)
  covalent geometry    : bond        0.00196 ( 4665)
  covalent geometry    : angle       0.48816 ( 6341)

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

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

  1110 Ramachandran restraints generated.
    555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1110 Ramachandran restraints generated.
    555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 83
  time to evaluate  : 0.512 
Fit side-chains
REVERT: A  340 GLU cc_start: 0.7860 (mp0) cc_final: 0.7594 (mp0)
REVERT: A  466 ARG cc_start: 0.7659 (ttp-110) cc_final: 0.7457 (ttm110)
REVERT: A  503 VAL cc_start: 0.8307 (p) cc_final: 0.7887 (p)
REVERT: A  506 GLN cc_start: 0.9077 (OUTLIER) cc_final: 0.8146 (mt0)
REVERT: B  444 LYS cc_start: 0.7234 (ttmm) cc_final: 0.6890 (tppt)
REVERT: H    4 LEU cc_start: 0.8806 (mp) cc_final: 0.8442 (mt)
REVERT: H   81 LYS cc_start: 0.8897 (OUTLIER) cc_final: 0.8532 (mppt)
REVERT: L   42 LYS cc_start: 0.8113 (mmtp) cc_final: 0.7832 (mtmt)
  outliers start: 8
  outliers final: 7
  residues processed: 89
  average time/residue: 1.1304
  time to fit residues: 104.6074
Evaluate side-chains
  91 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 82
  time to evaluate  : 0.455 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  465 GLU
Chi-restraints excluded: chain A residue  506 GLN
Chi-restraints excluded: chain A residue  510 VAL
Chi-restraints excluded: chain B residue  512 VAL
Chi-restraints excluded: chain H residue   65 ASN
Chi-restraints excluded: chain H residue   81 LYS
Chi-restraints excluded: chain L residue  103 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 25 optimal weight:    0.9980
   chunk 11 optimal weight:    1.9990
   chunk 0 optimal weight:    1.9990
   chunk 16 optimal weight:    0.3980
   chunk 40 optimal weight:    0.7980
   chunk 3 optimal weight:    0.9990
   chunk 50 optimal weight:    0.9990
   chunk 41 optimal weight:    0.7980
   chunk 20 optimal weight:    0.3980
   chunk 10 optimal weight:    2.9990
   chunk 18 optimal weight:    1.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
H   3 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.131279 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.109438 restraints weight = 6376.535|
|-----------------------------------------------------------------------------|
r_work (start): 0.3359 rms_B_bonded: 1.91
r_work: 0.3227 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3095 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.3095
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8413
moved from start:          0.4625

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063   4671  Z= 0.143
  Angle     :  0.608  11.082   6353  Z= 0.320
  Chirality :  0.045   0.168    659
  Planarity :  0.005   0.055    820
  Dihedral  :  4.310  21.378    635
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 2.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  : 20.57 %
    Favored  : 77.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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: -0.49 (0.34), residues: 555
  helix: -3.27 (0.72), residues: 34
  sheet:  1.14 (0.42), residues: 174
  loop : -0.82 (0.29), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP H  47 
 HIS   0.001   0.001   HIS H  40 
 PHE   0.012   0.001   PHE B 338 
 TYR   0.018   0.001   TYR A 489 
 ARG   0.015   0.001   ARG A 403 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04045 (  128)
  hydrogen bonds       : angle       6.21612 (  315)
  SS BOND              : bond        0.01100 (    6)
  SS BOND              : angle       2.22575 (   12)
  covalent geometry    : bond        0.00338 ( 4665)
  covalent geometry    : angle       0.60053 ( 6341)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4153.55 seconds
wall clock time: 72 minutes 17.88 seconds (4337.88 seconds total)