Starting phenix.real_space_refine
on Wed Jun 11 18:38:51 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9dvk_47209/06_2025/9dvk_47209_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9dvk_47209/06_2025/9dvk_47209.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.06
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9dvk_47209/06_2025/9dvk_47209.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9dvk_47209/06_2025/9dvk_47209.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9dvk_47209/06_2025/9dvk_47209_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9dvk_47209/06_2025/9dvk_47209_trim.cif"
  }
  resolution = 3.06
  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: 6
    Type Number    sf(0)   Gaussians
     P       4      5.49       5
     S      32      5.16       5
     C    4412      2.51       5
     N    1015      2.21       5
     O    1057      1.98       5
     H    6319      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 12839
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 6292
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 378, 6292
          Classifications: {'peptide': 378}
          Link IDs: {'PTRANS': 13, 'TRANS': 364}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 6364
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 382, 6364
          Classifications: {'peptide': 382}
          Link IDs: {'PTRANS': 12, 'TRANS': 369}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 126
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 126
          Unusual residues: {'CLR': 1, 'CPL': 2, 'PO4': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 11
          Unresolved non-hydrogen angles: 17
          Unresolved non-hydrogen dihedrals: 9
    Chain: "B"
      Number of atoms: 57
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 57
          Unusual residues: {'CPL': 1, 'PO4': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 7.79, per 1000 atoms: 0.61
  Number of scatterers: 12839
  At special positions: 0
  Unit cell: (73.4695, 72.644, 118.047, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      32     16.00
     P       4     15.00
     O    1057      8.00
     N    1015      7.00
     C    4412      6.00
     H    6319      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 415 " - pdb=" SG  CYS A 440 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 415 " - pdb=" SG  CYS B 440 " 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: 3.59
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1444

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 0 sheets defined
      80.8% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.85
  Creating SS restraints...
    Processing helix  chain 'A' and resid 230 through 258
    Processing helix  chain 'A' and resid 267 through 296
      removed outlier: 4.401A  pdb=" N   GLY A 274 " --> pdb=" O   ARG A 270 " (cutoff:3.500A)
      removed outlier: 4.575A  pdb=" N   GLY A 275 " --> pdb=" O   ILE A 271 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 298 through 303
    Processing helix  chain 'A' and resid 312 through 337
    Processing helix  chain 'A' and resid 345 through 360
    Processing helix  chain 'A' and resid 367 through 383
    Processing helix  chain 'A' and resid 390 through 403
    Processing helix  chain 'A' and resid 403 through 419
      removed outlier: 4.031A  pdb=" N   LEU A 407 " --> pdb=" O   LEU A 403 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 438 through 443
    Processing helix  chain 'A' and resid 445 through 471
      removed outlier: 3.512A  pdb=" N   ALA A 449 " --> pdb=" O   TYR A 445 " (cutoff:3.500A)
      Proline residue:  A 455  - end of helix
    Processing helix  chain 'A' and resid 472 through 502
      removed outlier: 3.998A  pdb=" N   HIS A 476 " --> pdb=" O   ARG A 472 " (cutoff:3.500A)
      removed outlier: 4.266A  pdb=" N   THR A 486 " --> pdb=" O   LYS A 482 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   PHE A 487 " --> pdb=" O   TYR A 483 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 506 through 532
    Processing helix  chain 'A' and resid 555 through 582
      removed outlier: 4.023A  pdb=" N   TYR A 559 " --> pdb=" O   GLN A 555 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   PHE A 571 " --> pdb=" O   VAL A 567 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 588 through 618
      Proline residue:  A 598  - end of helix
    Processing helix  chain 'B' and resid 231 through 259
    Processing helix  chain 'B' and resid 265 through 296
      removed outlier: 3.932A  pdb=" N   GLY B 274 " --> pdb=" O   ARG B 270 " (cutoff:3.500A)
      removed outlier: 4.394A  pdb=" N   GLY B 275 " --> pdb=" O   ILE B 271 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 298 through 304
    Processing helix  chain 'B' and resid 312 through 337
    Processing helix  chain 'B' and resid 345 through 360
      removed outlier: 4.177A  pdb=" N   LEU B 349 " --> pdb=" O   TYR B 345 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 367 through 383
      removed outlier: 3.603A  pdb=" N   ARG B 371 " --> pdb=" O   TYR B 367 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 390 through 403
    Processing helix  chain 'B' and resid 403 through 420
      removed outlier: 3.598A  pdb=" N   LEU B 407 " --> pdb=" O   LEU B 403 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 438 through 443
      removed outlier: 3.670A  pdb=" N   TYR B 443 " --> pdb=" O   ILE B 439 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 445 through 471
      Proline residue:  B 455  - end of helix
    Processing helix  chain 'B' and resid 472 through 502
      removed outlier: 4.064A  pdb=" N   HIS B 476 " --> pdb=" O   ARG B 472 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   VAL B 478 " --> pdb=" O   PHE B 474 " (cutoff:3.500A)
      removed outlier: 4.631A  pdb=" N   ASN B 479 " --> pdb=" O   PRO B 475 " (cutoff:3.500A)
      removed outlier: 3.980A  pdb=" N   THR B 486 " --> pdb=" O   LYS B 482 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   PHE B 487 " --> pdb=" O   TYR B 483 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 506 through 531
    Processing helix  chain 'B' and resid 555 through 582
      removed outlier: 4.148A  pdb=" N   TYR B 559 " --> pdb=" O   GLN B 555 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 587 through 618
      removed outlier: 4.358A  pdb=" N   ILE B 591 " --> pdb=" O   HIS B 587 " (cutoff:3.500A)
      Proline residue:  B 598  - end of helix

    468 hydrogen bonds defined for protein.
    1404 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: 4.92

  Time building geometry restraints manager: 4.37 seconds

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

  Histogram of bond lengths:
        0.83 -     1.03: 6303
        1.03 -     1.23: 26
        1.23 -     1.42: 2968
        1.42 -     1.62: 3704
        1.62 -     1.81: 48
  Bond restraints: 13049
  Sorted by residual:
  bond pdb=" O3P CPL A 803 "
       pdb=" P   CPL A 803 "
    ideal  model  delta    sigma   weight residual
    1.633  1.740 -0.107 2.00e-02 2.50e+03 2.88e+01
  bond pdb=" O3P CPL B 802 "
       pdb=" P   CPL B 802 "
    ideal  model  delta    sigma   weight residual
    1.633  1.740 -0.107 2.00e-02 2.50e+03 2.85e+01
  bond pdb=" O4P CPL A 803 "
       pdb=" P   CPL A 803 "
    ideal  model  delta    sigma   weight residual
    1.648  1.714 -0.066 2.00e-02 2.50e+03 1.10e+01
  bond pdb=" O4P CPL B 802 "
       pdb=" P   CPL B 802 "
    ideal  model  delta    sigma   weight residual
    1.648  1.713 -0.065 2.00e-02 2.50e+03 1.07e+01
  bond pdb=" N   TRP B 534 "
       pdb=" H   TRP B 534 "
    ideal  model  delta    sigma   weight residual
    0.860  0.913 -0.053 2.00e-02 2.50e+03 7.04e+00
  ... (remaining 13044 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.05: 23275
        3.05 -     6.09: 72
        6.09 -     9.14: 10
        9.14 -    12.19: 6
       12.19 -    15.24: 2
  Bond angle restraints: 23365
  Sorted by residual:
  angle pdb=" O1P CPL A 803 "
        pdb=" P   CPL A 803 "
        pdb=" O2P CPL A 803 "
      ideal   model   delta    sigma   weight residual
     119.55  134.79  -15.24 3.00e+00 1.11e-01 2.58e+01
  angle pdb=" O1P CPL B 802 "
        pdb=" P   CPL B 802 "
        pdb=" O2P CPL B 802 "
      ideal   model   delta    sigma   weight residual
     119.55  134.72  -15.17 3.00e+00 1.11e-01 2.56e+01
  angle pdb=" CA  TYR B 352 "
        pdb=" C   TYR B 352 "
        pdb=" O   TYR B 352 "
      ideal   model   delta    sigma   weight residual
     119.97  115.46    4.51 1.15e+00 7.56e-01 1.54e+01
  angle pdb=" CA  TRP B 534 "
        pdb=" C   TRP B 534 "
        pdb=" O   TRP B 534 "
      ideal   model   delta    sigma   weight residual
     120.42  116.51    3.91 1.06e+00 8.90e-01 1.36e+01
  angle pdb=" N   TYR A 352 "
        pdb=" CA  TYR A 352 "
        pdb=" C   TYR A 352 "
      ideal   model   delta    sigma   weight residual
     111.71  107.60    4.11 1.15e+00 7.56e-01 1.28e+01
  ... (remaining 23360 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    32.51: 5995
       32.51 -    65.01: 260
       65.01 -    97.52: 16
       97.52 -   130.02: 2
      130.02 -   162.53: 4
  Dihedral angle restraints: 6277
    sinusoidal: 3264
      harmonic: 3013
  Sorted by residual:
  dihedral pdb=" C3  CPL A 803 "
           pdb=" C1  CPL A 803 "
           pdb=" C2  CPL A 803 "
           pdb=" O3P CPL A 803 "
      ideal   model   delta sinusoidal    sigma   weight residual
      72.09  -90.44  162.53     1      3.00e+01 1.11e-03 2.08e+01
  dihedral pdb=" O2  CPL A 803 "
           pdb=" C1  CPL A 803 "
           pdb=" C2  CPL A 803 "
           pdb=" O3P CPL A 803 "
      ideal   model   delta sinusoidal    sigma   weight residual
     309.18  148.89  160.29     1      3.00e+01 1.11e-03 2.07e+01
  dihedral pdb=" C3  CPL B 802 "
           pdb=" C1  CPL B 802 "
           pdb=" C2  CPL B 802 "
           pdb=" O3P CPL B 802 "
      ideal   model   delta sinusoidal    sigma   weight residual
      72.09  -68.45  140.54     1      3.00e+01 1.11e-03 1.89e+01
  ... (remaining 6274 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.073: 908
       0.073 -    0.147: 72
       0.147 -    0.220: 0
       0.220 -    0.294: 1
       0.294 -    0.367: 6
  Chirality restraints: 987
  Sorted by residual:
  chirality pdb=" C17 CLR A 802 "
            pdb=" C13 CLR A 802 "
            pdb=" C16 CLR A 802 "
            pdb=" C20 CLR A 802 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.92   -0.37 2.00e-01 2.50e+01 3.37e+00
  chirality pdb=" C2  CPL B 802 "
            pdb=" C1  CPL B 802 "
            pdb=" C3  CPL B 802 "
            pdb=" O2  CPL B 802 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.65    0.34 2.00e-01 2.50e+01 2.82e+00
  chirality pdb=" C2  CPL A 803 "
            pdb=" C1  CPL A 803 "
            pdb=" C3  CPL A 803 "
            pdb=" O2  CPL A 803 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.65    0.33 2.00e-01 2.50e+01 2.79e+00
  ... (remaining 984 not shown)

  Planarity restraints: 1823
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 479 "    0.095 2.00e-02 2.50e+03   9.73e-02 1.42e+02
        pdb=" CG  ASN A 479 "   -0.014 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 479 "   -0.084 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 479 "   -0.007 2.00e-02 2.50e+03
        pdb="HD21 ASN A 479 "    0.148 2.00e-02 2.50e+03
        pdb="HD22 ASN A 479 "   -0.137 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A 482 "    0.013 2.00e-02 2.50e+03   2.49e-02 6.21e+00
        pdb=" N   TYR A 483 "   -0.043 2.00e-02 2.50e+03
        pdb=" CA  TYR A 483 "    0.011 2.00e-02 2.50e+03
        pdb=" H   TYR A 483 "    0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TRP B 534 "    0.012 2.00e-02 2.50e+03   2.46e-02 6.04e+00
        pdb=" C   TRP B 534 "   -0.042 2.00e-02 2.50e+03
        pdb=" O   TRP B 534 "    0.016 2.00e-02 2.50e+03
        pdb=" N   GLY B 535 "    0.015 2.00e-02 2.50e+03
  ... (remaining 1820 not shown)

  Histogram of nonbonded interaction distances:
        1.62 -     2.21: 1000
        2.21 -     2.81: 26695
        2.81 -     3.41: 37827
        3.41 -     4.00: 47721
        4.00 -     4.60: 73888
  Nonbonded interactions: 187131
  Sorted by model distance:
  nonbonded pdb=" HB2 GLU B 550 "
            pdb="HD21 LEU B 617 "
     model   vdw
     1.618 2.440
  nonbonded pdb="HH12 ARG A 548 "
            pdb=" OE2 GLU A 613 "
     model   vdw
     1.661 2.450
  nonbonded pdb=" OG  SER A 402 "
            pdb=" HE  ARG A 604 "
     model   vdw
     1.668 2.450
  nonbonded pdb="HH12 ARG B 466 "
            pdb=" O   GLY B 621 "
     model   vdw
     1.692 2.450
  nonbonded pdb="HD21 ASN B 361 "
            pdb=" HG1 THR B 363 "
     model   vdw
     1.717 2.100
  ... (remaining 187126 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 230 through 625 or resid 801))
  selection = (chain 'B' and (resid 230 through 258 or (resid 265 and (name N or name CA or na \ 
me C or name O or name CB or name CG1 or name CG2 or name CD1 or name HA or name \ 
 HB or name HG12 or name HG13 or name HG21 or name HG22 or name HG23 or name HD1 \ 
1 or name HD12 or name HD13)) or resid 266 through 625 or resid 801))
}

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:             4.260
  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:             0.200
  Extract box with map and model:          0.490
  Check model and map are aligned:         0.100
  Set scattering table:                    0.120
  Process input model:                     32.040
  Find NCS groups from input model:        0.380
  Set up NCS constraints:                  0.040
  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:2.790
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   40.420
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7461
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      :  0.004   0.107   6732  Z= 0.224
  Angle     :  0.676  15.237   9132  Z= 0.319
  Chirality :  0.044   0.367    987
  Planarity :  0.003   0.029   1093
  Dihedral  : 17.965 162.531   2437
  Min Nonbonded Distance : 2.258

Molprobity Statistics.
  All-atom Clashscore : 5.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.07 %
    Favored  : 98.93 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  : 15.16 %
    Favored  : 84.10 %
  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:  3.52 (0.30), residues: 750
  helix:  3.29 (0.20), residues: 584
  sheet:  None (None), residues: 0
  loop : -1.53 (0.39), residues: 166

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 573 
 HIS   0.003   0.001   HIS B 616 
 PHE   0.017   0.001   PHE B 322 
 TYR   0.037   0.001   TYR A 352 
 ARG   0.002   0.000   ARG A 472 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.09876 (  468)
  hydrogen bonds       : angle       4.38584 ( 1404)
  SS BOND              : bond        0.00178 (    2)
  SS BOND              : angle       0.36117 (    4)
  covalent geometry    : bond        0.00432 ( 6730)
  covalent geometry    : angle       0.67648 ( 9128)

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

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

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 138
  time to evaluate  : 1.146 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  401 ASN cc_start: 0.7238 (t0) cc_final: 0.6854 (m-40)
REVERT: A  468 ARG cc_start: 0.6795 (ttt180) cc_final: 0.6528 (ttm170)
REVERT: A  471 LYS cc_start: 0.7832 (ttmm) cc_final: 0.7562 (tppt)
REVERT: A  624 ARG cc_start: 0.7524 (mtm110) cc_final: 0.7258 (mtm-85)
REVERT: B  272 TYR cc_start: 0.7642 (m-80) cc_final: 0.7294 (m-80)
REVERT: B  318 GLU cc_start: 0.6568 (mt-10) cc_final: 0.5958 (mm-30)
REVERT: B  347 TYR cc_start: 0.7030 (m-80) cc_final: 0.6725 (m-80)
REVERT: B  354 PHE cc_start: 0.8291 (t80) cc_final: 0.7979 (t80)
REVERT: B  394 PHE cc_start: 0.6584 (OUTLIER) cc_final: 0.5295 (p90)
REVERT: B  465 ARG cc_start: 0.8136 (tpt-90) cc_final: 0.7842 (tpt170)
  outliers start: 5
  outliers final: 4
  residues processed: 143
  average time/residue: 0.3859
  time to fit residues: 73.6077
Evaluate side-chains
  114 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 109
  time to evaluate  : 0.925 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  394 PHE
Chi-restraints excluded: chain A residue  609 PHE
Chi-restraints excluded: chain B residue  394 PHE
Chi-restraints excluded: chain B residue  454 ILE
Chi-restraints excluded: chain B residue  609 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 63 optimal weight:    3.9990
   chunk 56 optimal weight:    0.1980
   chunk 31 optimal weight:    1.9990
   chunk 19 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9980
   chunk 30 optimal weight:    0.8980
   chunk 58 optimal weight:    0.0970
   chunk 22 optimal weight:    0.7980
   chunk 35 optimal weight:    0.5980
   chunk 43 optimal weight:    0.7980
   chunk 68 optimal weight:    0.5980
   overall best weight:    0.4578

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

Flipped N/Q/H residues before XYZ refinement:
** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4137 r_free = 0.4137 target = 0.189143 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.158849 restraints weight = 22622.837|
|-----------------------------------------------------------------------------|
r_work (start): 0.3874 rms_B_bonded: 2.32
r_work: 0.3771 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work (final): 0.3771
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7262
moved from start:          0.1241

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6732  Z= 0.127
  Angle     :  0.467   4.173   9132  Z= 0.255
  Chirality :  0.035   0.135    987
  Planarity :  0.004   0.040   1093
  Dihedral  : 15.271 156.876   1033
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 4.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.20 %
    Favored  : 98.80 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  : 16.79 %
    Favored  : 81.58 %
  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:  3.41 (0.30), residues: 750
  helix:  3.19 (0.20), residues: 592
  sheet:  None (None), residues: 0
  loop : -1.74 (0.38), residues: 158

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 573 
 HIS   0.005   0.001   HIS A 476 
 PHE   0.012   0.001   PHE A 605 
 TYR   0.015   0.001   TYR B 445 
 ARG   0.002   0.000   ARG A 273 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04673 (  468)
  hydrogen bonds       : angle       3.96263 ( 1404)
  SS BOND              : bond        0.00315 (    2)
  SS BOND              : angle       0.91109 (    4)
  covalent geometry    : bond        0.00265 ( 6730)
  covalent geometry    : angle       0.46709 ( 9128)

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

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

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 105
  time to evaluate  : 0.856 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  386 PHE cc_start: 0.7426 (m-10) cc_final: 0.7164 (m-10)
REVERT: A  468 ARG cc_start: 0.6379 (ttt180) cc_final: 0.6063 (ttm170)
REVERT: A  624 ARG cc_start: 0.7650 (mtm110) cc_final: 0.7320 (mtm-85)
REVERT: B  272 TYR cc_start: 0.7473 (m-80) cc_final: 0.7154 (m-80)
REVERT: B  318 GLU cc_start: 0.6554 (mt-10) cc_final: 0.5720 (mm-30)
REVERT: B  354 PHE cc_start: 0.8387 (t80) cc_final: 0.7889 (t80)
REVERT: B  394 PHE cc_start: 0.6864 (OUTLIER) cc_final: 0.5017 (p90)
REVERT: B  538 ASP cc_start: 0.7260 (t0) cc_final: 0.7046 (t70)
  outliers start: 11
  outliers final: 6
  residues processed: 113
  average time/residue: 0.4102
  time to fit residues: 60.9348
Evaluate side-chains
  102 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 95
  time to evaluate  : 0.952 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  394 PHE
Chi-restraints excluded: chain A residue  575 ILE
Chi-restraints excluded: chain A residue  609 PHE
Chi-restraints excluded: chain B residue  304 GLU
Chi-restraints excluded: chain B residue  394 PHE
Chi-restraints excluded: chain B residue  509 VAL
Chi-restraints excluded: chain B residue  609 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 61 optimal weight:    0.9990
   chunk 13 optimal weight:    0.0980
   chunk 58 optimal weight:    0.6980
   chunk 66 optimal weight:    2.9990
   chunk 0 optimal weight:    1.9990
   chunk 15 optimal weight:    0.8980
   chunk 68 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9990
   chunk 34 optimal weight:    1.9990
   chunk 71 optimal weight:    2.9990
   chunk 48 optimal weight:    0.0370
   overall best weight:    0.5460

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

Flipped N/Q/H residues before XYZ refinement:
** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 462 GLN
B 248 ASN
B 310 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.183155 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.152033 restraints weight = 22603.894|
|-----------------------------------------------------------------------------|
r_work (start): 0.3768 rms_B_bonded: 2.36
r_work: 0.3653 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.3653
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7444
moved from start:          0.1894

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6732  Z= 0.128
  Angle     :  0.459   4.564   9132  Z= 0.251
  Chirality :  0.035   0.134    987
  Planarity :  0.004   0.038   1093
  Dihedral  : 14.460 156.415   1031
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 5.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.73 %
    Favored  : 98.27 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 16.20 %
    Favored  : 81.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  3.30 (0.30), residues: 750
  helix:  3.11 (0.20), residues: 592
  sheet:  None (None), residues: 0
  loop : -1.75 (0.39), residues: 158

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 573 
 HIS   0.005   0.001   HIS A 476 
 PHE   0.017   0.001   PHE A 605 
 TYR   0.010   0.001   TYR B 518 
 ARG   0.003   0.000   ARG B 466 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04742 (  468)
  hydrogen bonds       : angle       3.90282 ( 1404)
  SS BOND              : bond        0.00380 (    2)
  SS BOND              : angle       0.94778 (    4)
  covalent geometry    : bond        0.00276 ( 6730)
  covalent geometry    : angle       0.45860 ( 9128)

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

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

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 97
  time to evaluate  : 1.962 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  386 PHE cc_start: 0.7553 (m-10) cc_final: 0.7254 (m-10)
REVERT: A  417 TYR cc_start: 0.7626 (t80) cc_final: 0.7422 (t80)
REVERT: A  468 ARG cc_start: 0.6520 (ttt180) cc_final: 0.6154 (ttm170)
REVERT: A  504 HIS cc_start: 0.6565 (OUTLIER) cc_final: 0.6262 (m-70)
REVERT: A  624 ARG cc_start: 0.7600 (mtm110) cc_final: 0.7351 (mtm-85)
REVERT: B  318 GLU cc_start: 0.6682 (mt-10) cc_final: 0.5934 (mm-30)
REVERT: B  347 TYR cc_start: 0.7210 (m-80) cc_final: 0.6670 (m-80)
  outliers start: 16
  outliers final: 10
  residues processed: 109
  average time/residue: 0.5223
  time to fit residues: 74.9793
Evaluate side-chains
  100 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 89
  time to evaluate  : 1.009 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  367 TYR
Chi-restraints excluded: chain A residue  394 PHE
Chi-restraints excluded: chain A residue  504 HIS
Chi-restraints excluded: chain A residue  575 ILE
Chi-restraints excluded: chain A residue  579 ILE
Chi-restraints excluded: chain A residue  609 PHE
Chi-restraints excluded: chain A residue  620 CYS
Chi-restraints excluded: chain B residue  334 CYS
Chi-restraints excluded: chain B residue  394 PHE
Chi-restraints excluded: chain B residue  509 VAL
Chi-restraints excluded: chain B residue  609 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 37 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9990
   chunk 13 optimal weight:    1.9990
   chunk 3 optimal weight:    0.0270
   chunk 49 optimal weight:    2.9990
   chunk 52 optimal weight:    1.9990
   chunk 68 optimal weight:    0.0770
   chunk 42 optimal weight:    0.9980
   chunk 54 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9980
   chunk 58 optimal weight:    0.9980
   overall best weight:    0.5996

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.178865 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.147674 restraints weight = 22538.321|
|-----------------------------------------------------------------------------|
r_work (start): 0.3758 rms_B_bonded: 2.31
r_work: 0.3649 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.3649
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7528
moved from start:          0.2319

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   6732  Z= 0.130
  Angle     :  0.459   4.218   9132  Z= 0.252
  Chirality :  0.035   0.136    987
  Planarity :  0.004   0.037   1093
  Dihedral  : 13.852 152.671   1031
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 5.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 14.86 %
    Favored  : 82.17 %
  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:  3.17 (0.30), residues: 750
  helix:  3.02 (0.20), residues: 592
  sheet:  None (None), residues: 0
  loop : -1.82 (0.39), residues: 158

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 573 
 HIS   0.005   0.001   HIS A 476 
 PHE   0.018   0.001   PHE B 605 
 TYR   0.011   0.001   TYR B 518 
 ARG   0.002   0.000   ARG B 459 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04833 (  468)
  hydrogen bonds       : angle       3.89773 ( 1404)
  SS BOND              : bond        0.00374 (    2)
  SS BOND              : angle       0.91523 (    4)
  covalent geometry    : bond        0.00277 ( 6730)
  covalent geometry    : angle       0.45909 ( 9128)

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

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

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 94
  time to evaluate  : 0.895 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  386 PHE cc_start: 0.7711 (m-10) cc_final: 0.7429 (m-10)
REVERT: A  468 ARG cc_start: 0.6536 (ttt180) cc_final: 0.6209 (ttm170)
REVERT: A  550 GLU cc_start: 0.7165 (mm-30) cc_final: 0.6691 (mt-10)
REVERT: A  624 ARG cc_start: 0.7615 (mtm110) cc_final: 0.7115 (mtm-85)
REVERT: B  318 GLU cc_start: 0.6875 (mt-10) cc_final: 0.6094 (mm-30)
REVERT: B  347 TYR cc_start: 0.7247 (m-80) cc_final: 0.6711 (m-80)
  outliers start: 20
  outliers final: 12
  residues processed: 105
  average time/residue: 0.4252
  time to fit residues: 58.0316
Evaluate side-chains
  101 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 89
  time to evaluate  : 0.884 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  367 TYR
Chi-restraints excluded: chain A residue  394 PHE
Chi-restraints excluded: chain A residue  575 ILE
Chi-restraints excluded: chain A residue  579 ILE
Chi-restraints excluded: chain B residue  334 CYS
Chi-restraints excluded: chain B residue  367 TYR
Chi-restraints excluded: chain B residue  394 PHE
Chi-restraints excluded: chain B residue  454 ILE
Chi-restraints excluded: chain B residue  509 VAL
Chi-restraints excluded: chain B residue  520 ILE
Chi-restraints excluded: chain B residue  538 ASP
Chi-restraints excluded: chain B residue  577 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 52 optimal weight:    1.9990
   chunk 48 optimal weight:    0.6980
   chunk 38 optimal weight:    0.4980
   chunk 5 optimal weight:    0.9990
   chunk 74 optimal weight:    2.9990
   chunk 11 optimal weight:    1.9990
   chunk 28 optimal weight:    0.8980
   chunk 8 optimal weight:    0.9980
   chunk 63 optimal weight:    3.9990
   chunk 18 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.173347 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.142319 restraints weight = 22912.226|
|-----------------------------------------------------------------------------|
r_work (start): 0.3676 rms_B_bonded: 2.25
r_work: 0.3549 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.3549
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7651
moved from start:          0.2789

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6732  Z= 0.156
  Angle     :  0.497   6.393   9132  Z= 0.269
  Chirality :  0.036   0.140    987
  Planarity :  0.004   0.037   1093
  Dihedral  : 13.494 137.009   1027
  Min Nonbonded Distance : 2.376

Molprobity Statistics.
  All-atom Clashscore : 5.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 15.30 %
    Favored  : 82.32 %
  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:  2.99 (0.30), residues: 750
  helix:  2.91 (0.20), residues: 592
  sheet:  None (None), residues: 0
  loop : -1.94 (0.39), residues: 158

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 573 
 HIS   0.005   0.001   HIS A 476 
 PHE   0.023   0.001   PHE B 605 
 TYR   0.012   0.002   TYR B 518 
 ARG   0.003   0.000   ARG B 459 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05181 (  468)
  hydrogen bonds       : angle       3.99563 ( 1404)
  SS BOND              : bond        0.00416 (    2)
  SS BOND              : angle       1.00060 (    4)
  covalent geometry    : bond        0.00351 ( 6730)
  covalent geometry    : angle       0.49687 ( 9128)

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

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

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 97
  time to evaluate  : 0.955 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  386 PHE cc_start: 0.7873 (m-10) cc_final: 0.7615 (m-10)
REVERT: A  468 ARG cc_start: 0.6662 (ttt180) cc_final: 0.6267 (ttm170)
REVERT: A  550 GLU cc_start: 0.7140 (mm-30) cc_final: 0.6784 (mt-10)
REVERT: A  624 ARG cc_start: 0.7687 (mtm110) cc_final: 0.7239 (mtm-85)
REVERT: B  293 ARG cc_start: 0.7731 (mmm-85) cc_final: 0.6539 (ttm170)
  outliers start: 16
  outliers final: 13
  residues processed: 106
  average time/residue: 0.4664
  time to fit residues: 64.2657
Evaluate side-chains
  103 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 90
  time to evaluate  : 0.849 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  367 TYR
Chi-restraints excluded: chain A residue  394 PHE
Chi-restraints excluded: chain A residue  506 ASP
Chi-restraints excluded: chain A residue  552 VAL
Chi-restraints excluded: chain A residue  575 ILE
Chi-restraints excluded: chain A residue  620 CYS
Chi-restraints excluded: chain B residue  334 CYS
Chi-restraints excluded: chain B residue  367 TYR
Chi-restraints excluded: chain B residue  394 PHE
Chi-restraints excluded: chain B residue  509 VAL
Chi-restraints excluded: chain B residue  520 ILE
Chi-restraints excluded: chain B residue  538 ASP
Chi-restraints excluded: chain B residue  577 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 3 optimal weight:    0.0670
   chunk 23 optimal weight:    0.8980
   chunk 66 optimal weight:    0.9990
   chunk 37 optimal weight:    0.9990
   chunk 51 optimal weight:    1.9990
   chunk 67 optimal weight:    0.7980
   chunk 35 optimal weight:    0.9980
   chunk 26 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9990
   chunk 34 optimal weight:    0.9980
   chunk 57 optimal weight:    1.9990
   overall best weight:    0.7518

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

Flipped N/Q/H residues before XYZ refinement:
** A 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.173222 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.142017 restraints weight = 23063.121|
|-----------------------------------------------------------------------------|
r_work (start): 0.3666 rms_B_bonded: 2.32
r_work: 0.3545 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.3545
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7638
moved from start:          0.3040

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   6732  Z= 0.146
  Angle     :  0.481   4.242   9132  Z= 0.265
  Chirality :  0.035   0.133    987
  Planarity :  0.004   0.036   1093
  Dihedral  : 13.278 116.967   1027
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 6.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 14.86 %
    Favored  : 82.32 %
  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:  2.96 (0.30), residues: 750
  helix:  2.89 (0.20), residues: 592
  sheet:  None (None), residues: 0
  loop : -2.01 (0.39), residues: 158

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 573 
 HIS   0.004   0.001   HIS A 476 
 PHE   0.021   0.001   PHE B 605 
 TYR   0.012   0.001   TYR B 518 
 ARG   0.002   0.000   ARG B 273 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05140 (  468)
  hydrogen bonds       : angle       3.98985 ( 1404)
  SS BOND              : bond        0.00420 (    2)
  SS BOND              : angle       1.07958 (    4)
  covalent geometry    : bond        0.00320 ( 6730)
  covalent geometry    : angle       0.48055 ( 9128)

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

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

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 97
  time to evaluate  : 0.900 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  386 PHE cc_start: 0.7877 (m-10) cc_final: 0.7662 (m-10)
REVERT: A  468 ARG cc_start: 0.6571 (ttt180) cc_final: 0.6252 (ttm170)
REVERT: A  544 ASN cc_start: 0.7179 (OUTLIER) cc_final: 0.6885 (m-40)
REVERT: A  550 GLU cc_start: 0.7101 (mm-30) cc_final: 0.6781 (mt-10)
REVERT: A  624 ARG cc_start: 0.7707 (mtm110) cc_final: 0.7284 (mtm-85)
REVERT: B  293 ARG cc_start: 0.7729 (mmm-85) cc_final: 0.6519 (ttm170)
REVERT: B  347 TYR cc_start: 0.7351 (m-80) cc_final: 0.6739 (m-80)
REVERT: B  442 LYS cc_start: 0.8180 (tptm) cc_final: 0.7879 (mptt)
  outliers start: 19
  outliers final: 13
  residues processed: 109
  average time/residue: 0.4536
  time to fit residues: 63.4731
Evaluate side-chains
  107 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 93
  time to evaluate  : 0.879 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  367 TYR
Chi-restraints excluded: chain A residue  394 PHE
Chi-restraints excluded: chain A residue  506 ASP
Chi-restraints excluded: chain A residue  544 ASN
Chi-restraints excluded: chain A residue  552 VAL
Chi-restraints excluded: chain A residue  575 ILE
Chi-restraints excluded: chain A residue  620 CYS
Chi-restraints excluded: chain B residue  334 CYS
Chi-restraints excluded: chain B residue  367 TYR
Chi-restraints excluded: chain B residue  394 PHE
Chi-restraints excluded: chain B residue  454 ILE
Chi-restraints excluded: chain B residue  520 ILE
Chi-restraints excluded: chain B residue  538 ASP
Chi-restraints excluded: chain B residue  577 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 71 optimal weight:    2.9990
   chunk 48 optimal weight:    0.8980
   chunk 43 optimal weight:    1.9990
   chunk 42 optimal weight:    0.7980
   chunk 27 optimal weight:    0.3980
   chunk 56 optimal weight:    0.8980
   chunk 65 optimal weight:    1.9990
   chunk 3 optimal weight:    0.8980
   chunk 34 optimal weight:    0.5980
   chunk 13 optimal weight:    0.9990
   chunk 39 optimal weight:    0.3980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** A 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.173715 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.143013 restraints weight = 22957.868|
|-----------------------------------------------------------------------------|
r_work (start): 0.3648 rms_B_bonded: 2.30
r_work: 0.3527 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work (final): 0.3527
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7635
moved from start:          0.3216

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6732  Z= 0.132
  Angle     :  0.474   5.866   9132  Z= 0.258
  Chirality :  0.035   0.134    987
  Planarity :  0.004   0.049   1093
  Dihedral  : 12.649 100.731   1027
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 5.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 15.01 %
    Favored  : 82.32 %
  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:  3.01 (0.30), residues: 750
  helix:  2.93 (0.20), residues: 592
  sheet:  None (None), residues: 0
  loop : -1.97 (0.39), residues: 158

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 528 
 HIS   0.014   0.001   HIS A 441 
 PHE   0.019   0.001   PHE A 605 
 TYR   0.011   0.001   TYR B 518 
 ARG   0.002   0.000   ARG B 371 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05028 (  468)
  hydrogen bonds       : angle       3.94576 ( 1404)
  SS BOND              : bond        0.00392 (    2)
  SS BOND              : angle       1.01998 (    4)
  covalent geometry    : bond        0.00287 ( 6730)
  covalent geometry    : angle       0.47324 ( 9128)

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

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

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 98
  time to evaluate  : 0.912 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  386 PHE cc_start: 0.7872 (m-10) cc_final: 0.7659 (m-10)
REVERT: A  468 ARG cc_start: 0.6548 (ttt180) cc_final: 0.6232 (ttm170)
REVERT: A  550 GLU cc_start: 0.7103 (mm-30) cc_final: 0.6842 (mt-10)
REVERT: A  624 ARG cc_start: 0.7755 (mtm110) cc_final: 0.7367 (mtm-85)
REVERT: B  314 GLN cc_start: 0.5765 (mt0) cc_final: 0.5311 (mm-40)
REVERT: B  347 TYR cc_start: 0.7338 (m-80) cc_final: 0.6726 (m-80)
REVERT: B  442 LYS cc_start: 0.8179 (tptm) cc_final: 0.7867 (mptt)
  outliers start: 18
  outliers final: 14
  residues processed: 110
  average time/residue: 0.4589
  time to fit residues: 65.8277
Evaluate side-chains
  111 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 97
  time to evaluate  : 0.979 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  367 TYR
Chi-restraints excluded: chain A residue  394 PHE
Chi-restraints excluded: chain A residue  505 SER
Chi-restraints excluded: chain A residue  506 ASP
Chi-restraints excluded: chain A residue  552 VAL
Chi-restraints excluded: chain A residue  575 ILE
Chi-restraints excluded: chain A residue  579 ILE
Chi-restraints excluded: chain B residue  334 CYS
Chi-restraints excluded: chain B residue  367 TYR
Chi-restraints excluded: chain B residue  394 PHE
Chi-restraints excluded: chain B residue  454 ILE
Chi-restraints excluded: chain B residue  520 ILE
Chi-restraints excluded: chain B residue  538 ASP
Chi-restraints excluded: chain B residue  577 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 41 optimal weight:    0.3980
   chunk 28 optimal weight:    1.9990
   chunk 71 optimal weight:    0.7980
   chunk 2 optimal weight:    0.9980
   chunk 70 optimal weight:    0.9990
   chunk 21 optimal weight:    0.9980
   chunk 40 optimal weight:    0.3980
   chunk 18 optimal weight:    4.9990
   chunk 38 optimal weight:    0.2980
   chunk 59 optimal weight:    1.9990
   chunk 20 optimal weight:    0.0980
   overall best weight:    0.3980

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

Flipped N/Q/H residues before XYZ refinement:
** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.174866 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.144465 restraints weight = 22972.560|
|-----------------------------------------------------------------------------|
r_work (start): 0.3676 rms_B_bonded: 2.29
r_work: 0.3556 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.3556
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7610
moved from start:          0.3263

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   6732  Z= 0.113
  Angle     :  0.458   7.202   9132  Z= 0.250
  Chirality :  0.035   0.133    987
  Planarity :  0.003   0.035   1093
  Dihedral  : 12.097  95.489   1027
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 5.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 15.60 %
    Favored  : 82.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  3.08 (0.30), residues: 750
  helix:  2.99 (0.20), residues: 592
  sheet:  None (None), residues: 0
  loop : -2.00 (0.39), residues: 158

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 528 
 HIS   0.008   0.001   HIS A 441 
 PHE   0.029   0.001   PHE A 511 
 TYR   0.010   0.001   TYR B 518 
 ARG   0.005   0.000   ARG A 472 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04773 (  468)
  hydrogen bonds       : angle       3.87603 ( 1404)
  SS BOND              : bond        0.00359 (    2)
  SS BOND              : angle       1.04712 (    4)
  covalent geometry    : bond        0.00235 ( 6730)
  covalent geometry    : angle       0.45798 ( 9128)

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

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

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 97
  time to evaluate  : 1.286 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  386 PHE cc_start: 0.7841 (m-10) cc_final: 0.7589 (m-10)
REVERT: A  468 ARG cc_start: 0.6537 (ttt180) cc_final: 0.6216 (ttm170)
REVERT: A  471 LYS cc_start: 0.7998 (ttmm) cc_final: 0.7588 (tppt)
REVERT: A  550 GLU cc_start: 0.7133 (mm-30) cc_final: 0.6904 (mt-10)
REVERT: A  624 ARG cc_start: 0.7779 (mtm110) cc_final: 0.7409 (mtm-85)
REVERT: B  293 ARG cc_start: 0.7758 (mmm-85) cc_final: 0.6544 (ttm170)
REVERT: B  314 GLN cc_start: 0.5802 (mt0) cc_final: 0.5386 (mm-40)
REVERT: B  347 TYR cc_start: 0.7319 (m-80) cc_final: 0.6699 (m-80)
REVERT: B  388 LYS cc_start: 0.7550 (ptmt) cc_final: 0.7350 (ttpt)
REVERT: B  442 LYS cc_start: 0.8164 (tptm) cc_final: 0.7849 (mptt)
  outliers start: 13
  outliers final: 12
  residues processed: 106
  average time/residue: 0.5679
  time to fit residues: 79.1924
Evaluate side-chains
  108 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 96
  time to evaluate  : 1.088 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  367 TYR
Chi-restraints excluded: chain A residue  394 PHE
Chi-restraints excluded: chain A residue  505 SER
Chi-restraints excluded: chain A residue  506 ASP
Chi-restraints excluded: chain A residue  552 VAL
Chi-restraints excluded: chain A residue  575 ILE
Chi-restraints excluded: chain B residue  334 CYS
Chi-restraints excluded: chain B residue  367 TYR
Chi-restraints excluded: chain B residue  394 PHE
Chi-restraints excluded: chain B residue  454 ILE
Chi-restraints excluded: chain B residue  538 ASP
Chi-restraints excluded: chain B residue  577 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 50 optimal weight:    0.6980
   chunk 14 optimal weight:    0.9990
   chunk 62 optimal weight:    3.9990
   chunk 9 optimal weight:    0.9980
   chunk 39 optimal weight:    0.7980
   chunk 47 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9980
   chunk 57 optimal weight:    1.9990
   chunk 36 optimal weight:    0.9980
   chunk 43 optimal weight:    0.5980
   chunk 0 optimal weight:    1.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.172120 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.141566 restraints weight = 22977.794|
|-----------------------------------------------------------------------------|
r_work (start): 0.3578 rms_B_bonded: 2.27
r_work: 0.3452 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.3452
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7655
moved from start:          0.3500

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6732  Z= 0.154
  Angle     :  0.486   4.785   9132  Z= 0.268
  Chirality :  0.035   0.133    987
  Planarity :  0.004   0.036   1093
  Dihedral  : 11.864  98.584   1027
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 6.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 15.60 %
    Favored  : 82.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.86 (0.30), residues: 750
  helix:  2.82 (0.20), residues: 592
  sheet:  None (None), residues: 0
  loop : -2.04 (0.40), residues: 158

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 528 
 HIS   0.009   0.001   HIS A 441 
 PHE   0.022   0.001   PHE A 605 
 TYR   0.011   0.002   TYR B 518 
 ARG   0.004   0.000   ARG A 472 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05196 (  468)
  hydrogen bonds       : angle       4.04201 ( 1404)
  SS BOND              : bond        0.00406 (    2)
  SS BOND              : angle       1.09986 (    4)
  covalent geometry    : bond        0.00345 ( 6730)
  covalent geometry    : angle       0.48578 ( 9128)

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

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

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 94
  time to evaluate  : 0.991 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  386 PHE cc_start: 0.7910 (m-10) cc_final: 0.7706 (m-10)
REVERT: A  468 ARG cc_start: 0.6591 (ttt180) cc_final: 0.6232 (ttm170)
REVERT: A  471 LYS cc_start: 0.8000 (ttmm) cc_final: 0.7585 (tppt)
REVERT: A  504 HIS cc_start: 0.6296 (m-70) cc_final: 0.5699 (m90)
REVERT: A  550 GLU cc_start: 0.7158 (mm-30) cc_final: 0.6881 (mt-10)
REVERT: A  624 ARG cc_start: 0.7820 (mtm110) cc_final: 0.7447 (mtm-85)
REVERT: B  314 GLN cc_start: 0.5844 (mt0) cc_final: 0.5396 (mm-40)
  outliers start: 13
  outliers final: 12
  residues processed: 104
  average time/residue: 0.4651
  time to fit residues: 62.4965
Evaluate side-chains
  105 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 93
  time to evaluate  : 0.889 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  367 TYR
Chi-restraints excluded: chain A residue  505 SER
Chi-restraints excluded: chain A residue  506 ASP
Chi-restraints excluded: chain A residue  552 VAL
Chi-restraints excluded: chain A residue  575 ILE
Chi-restraints excluded: chain A residue  620 CYS
Chi-restraints excluded: chain B residue  334 CYS
Chi-restraints excluded: chain B residue  367 TYR
Chi-restraints excluded: chain B residue  394 PHE
Chi-restraints excluded: chain B residue  454 ILE
Chi-restraints excluded: chain B residue  538 ASP
Chi-restraints excluded: chain B residue  577 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 37 optimal weight:    0.7980
   chunk 60 optimal weight:    0.9980
   chunk 40 optimal weight:    0.6980
   chunk 29 optimal weight:    0.8980
   chunk 65 optimal weight:    0.9990
   chunk 51 optimal weight:    0.6980
   chunk 27 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9980
   chunk 47 optimal weight:    0.6980
   chunk 50 optimal weight:    0.8980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.171699 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.140977 restraints weight = 22732.737|
|-----------------------------------------------------------------------------|
r_work (start): 0.3647 rms_B_bonded: 2.17
r_work: 0.3526 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work (final): 0.3526
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7714
moved from start:          0.3638

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6732  Z= 0.145
  Angle     :  0.476   4.566   9132  Z= 0.264
  Chirality :  0.035   0.133    987
  Planarity :  0.004   0.035   1093
  Dihedral  : 11.676  96.753   1025
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 15.90 %
    Favored  : 82.32 %
  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:  2.79 (0.30), residues: 750
  helix:  2.78 (0.20), residues: 592
  sheet:  None (None), residues: 0
  loop : -2.07 (0.39), residues: 158

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 528 
 HIS   0.009   0.001   HIS A 441 
 PHE   0.024   0.001   PHE A 487 
 TYR   0.018   0.001   TYR B 518 
 ARG   0.004   0.000   ARG A 472 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05171 (  468)
  hydrogen bonds       : angle       4.04527 ( 1404)
  SS BOND              : bond        0.00443 (    2)
  SS BOND              : angle       1.16769 (    4)
  covalent geometry    : bond        0.00323 ( 6730)
  covalent geometry    : angle       0.47593 ( 9128)

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

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

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 94
  time to evaluate  : 0.794 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  468 ARG cc_start: 0.6537 (ttt180) cc_final: 0.6254 (ttm170)
REVERT: A  471 LYS cc_start: 0.7967 (ttmm) cc_final: 0.7576 (tppt)
REVERT: A  504 HIS cc_start: 0.6277 (m-70) cc_final: 0.5703 (m90)
REVERT: A  550 GLU cc_start: 0.7212 (mm-30) cc_final: 0.6979 (mt-10)
REVERT: A  624 ARG cc_start: 0.7821 (mtm110) cc_final: 0.7490 (mtm-85)
  outliers start: 12
  outliers final: 12
  residues processed: 103
  average time/residue: 0.5396
  time to fit residues: 72.4530
Evaluate side-chains
  105 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 93
  time to evaluate  : 0.875 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  367 TYR
Chi-restraints excluded: chain A residue  505 SER
Chi-restraints excluded: chain A residue  506 ASP
Chi-restraints excluded: chain A residue  552 VAL
Chi-restraints excluded: chain A residue  575 ILE
Chi-restraints excluded: chain A residue  620 CYS
Chi-restraints excluded: chain B residue  334 CYS
Chi-restraints excluded: chain B residue  367 TYR
Chi-restraints excluded: chain B residue  394 PHE
Chi-restraints excluded: chain B residue  454 ILE
Chi-restraints excluded: chain B residue  538 ASP
Chi-restraints excluded: chain B residue  577 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 64 optimal weight:    1.9990
   chunk 52 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9980
   chunk 21 optimal weight:    0.1980
   chunk 63 optimal weight:    0.7980
   chunk 23 optimal weight:    0.5980
   chunk 57 optimal weight:    1.9990
   chunk 72 optimal weight:    0.9980
   chunk 39 optimal weight:    0.9990
   chunk 48 optimal weight:    0.6980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.172009 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.140806 restraints weight = 22689.471|
|-----------------------------------------------------------------------------|
r_work (start): 0.3644 rms_B_bonded: 2.24
r_work: 0.3523 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.3523
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7662
moved from start:          0.3744

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6732  Z= 0.138
  Angle     :  0.474   4.474   9132  Z= 0.263
  Chirality :  0.035   0.133    987
  Planarity :  0.004   0.035   1093
  Dihedral  : 11.304  92.885   1025
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 5.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 15.60 %
    Favored  : 82.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.83 (0.30), residues: 750
  helix:  2.81 (0.20), residues: 592
  sheet:  None (None), residues: 0
  loop : -2.06 (0.40), residues: 158

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 528 
 HIS   0.008   0.001   HIS A 441 
 PHE   0.033   0.001   PHE A 487 
 TYR   0.016   0.001   TYR B 518 
 ARG   0.004   0.000   ARG A 472 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05110 (  468)
  hydrogen bonds       : angle       4.02501 ( 1404)
  SS BOND              : bond        0.00428 (    2)
  SS BOND              : angle       1.14571 (    4)
  covalent geometry    : bond        0.00304 ( 6730)
  covalent geometry    : angle       0.47353 ( 9128)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6605.44 seconds
wall clock time: 115 minutes 32.82 seconds (6932.82 seconds total)