Starting phenix.real_space_refine
on Wed Jul 23 10:51:03 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7yvh_34127/07_2025/7yvh_34127.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7yvh_34127/07_2025/7yvh_34127.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7yvh_34127/07_2025/7yvh_34127.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7yvh_34127/07_2025/7yvh_34127.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7yvh_34127/07_2025/7yvh_34127.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7yvh_34127/07_2025/7yvh_34127.cif"
  }
  resolution = 3.6
  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=   0.027
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      16      5.16       5
     C    1988      2.51       5
     N     530      2.21       5
     O     590      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 3124
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 818
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 818
          Classifications: {'peptide': 109}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 101}
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 9
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "C"
      Number of atoms: 865
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 118, 865
          Classifications: {'peptide': 118}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 2, 'TRANS': 115}
          Unresolved non-hydrogen bonds: 21
          Unresolved non-hydrogen angles: 26
          Unresolved non-hydrogen dihedrals: 16
          Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 19
    Chain: "B"
      Number of atoms: 1441
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 193, 1441
          Classifications: {'peptide': 193}
          Incomplete info: {'truncation_to_alanine': 25}
          Link IDs: {'PTRANS': 11, 'TRANS': 181}
          Unresolved non-hydrogen bonds: 102
          Unresolved non-hydrogen angles: 129
          Unresolved non-hydrogen dihedrals: 83
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'TYR:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 75
  Time building chain proxies: 4.33, per 1000 atoms: 1.39
  Number of scatterers: 3124
  At special positions: 0
  Unit cell: (60.68, 70.52, 100.86, 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      16     16.00
     O     590      8.00
     N     530      7.00
     C    1988      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  23 " - pdb=" SG  CYS A  88 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  95 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 336 " - pdb=" SG  CYS B 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 379 " - pdb=" SG  CYS B 432 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 391 " - pdb=" SG  CYS B 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 480 " - pdb=" SG  CYS B 488 " 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: 0.75
  Conformation dependent library (CDL) restraints added in 410.8 milliseconds
  

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  762

  Finding SS restraints...
    Secondary structure from input PDB file:
      7 helices and 6 sheets defined
      9.5% alpha, 27.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.38
  Creating SS restraints...
    Processing helix  chain 'A' and resid 79 through 83
      removed outlier: 4.074A  pdb=" N   SER A  83 " --> pdb=" O   SER A  80 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 72 through 75
    Processing helix  chain 'C' and resid 86 through 90
      removed outlier: 4.152A  pdb=" N   THR C  90 " --> pdb=" O   ALA C  87 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 337 through 344
    Processing helix  chain 'B' and resid 383 through 390
    Processing helix  chain 'B' and resid 405 through 410
      removed outlier: 4.910A  pdb=" N   SER B 408 " --> pdb=" O   ASN B 405 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 502 through 505
    Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 7
      removed outlier: 3.817A  pdb=" N   GLU A  70 " --> pdb=" O   SER A  67 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 13
      removed outlier: 6.579A  pdb=" N   LEU A  11 " --> pdb=" O   GLU A 107 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   ALA A  84 " --> pdb=" O   LEU A 106 " (cutoff:3.500A)
      removed outlier: 6.586A  pdb=" N   TRP A  35 " --> pdb=" O   LEU A  47 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 3 through 7
      removed outlier: 3.708A  pdb=" N   GLN C   3 " --> pdb=" O   SER C  25 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 10 through 12
      removed outlier: 5.827A  pdb=" N   GLY C  10 " --> pdb=" O   THR C 115 " (cutoff:3.500A)
      removed outlier: 6.931A  pdb=" N   MET C  34 " --> pdb=" O   VAL C  50 " (cutoff:3.500A)
      removed outlier: 4.455A  pdb=" N   VAL C  50 " --> pdb=" O   MET C  34 " (cutoff:3.500A)
      removed outlier: 6.682A  pdb=" N   TRP C  36 " --> pdb=" O   VAL C  48 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 354 through 358
      removed outlier: 3.589A  pdb=" N   ASN B 394 " --> pdb=" O   GLU B 516 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   ALA B 376 " --> pdb=" O   ALA B 435 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 452 through 454

    97 hydrogen bonds defined for protein.
    243 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.78

  Time building geometry restraints manager: 0.91 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 500
        1.30 -     1.43: 919
        1.43 -     1.56: 1763
        1.56 -     1.69: 0
        1.69 -     1.82: 20
  Bond restraints: 3202
  Sorted by residual:
  bond pdb=" CA  ARG C  97 "
       pdb=" C   ARG C  97 "
    ideal  model  delta    sigma   weight residual
    1.523  1.430  0.094 1.21e-02 6.83e+03 5.98e+01
  bond pdb=" C   ARG C  97 "
       pdb=" O   ARG C  97 "
    ideal  model  delta    sigma   weight residual
    1.236  1.170  0.066 1.14e-02 7.69e+03 3.35e+01
  bond pdb=" CB  TYR B 473 "
       pdb=" CG  TYR B 473 "
    ideal  model  delta    sigma   weight residual
    1.512  1.421  0.091 2.20e-02 2.07e+03 1.70e+01
  bond pdb=" CB  TYR A  98 "
       pdb=" CG  TYR A  98 "
    ideal  model  delta    sigma   weight residual
    1.512  1.425  0.087 2.20e-02 2.07e+03 1.56e+01
  bond pdb=" CA  TYR A  98 "
       pdb=" CB  TYR A  98 "
    ideal  model  delta    sigma   weight residual
    1.533  1.473  0.060 1.72e-02 3.38e+03 1.22e+01
  ... (remaining 3197 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.53: 4292
        3.53 -     7.05: 61
        7.05 -    10.58: 10
       10.58 -    14.11: 0
       14.11 -    17.63: 2
  Bond angle restraints: 4365
  Sorted by residual:
  angle pdb=" N   GLN B 474 "
        pdb=" CA  GLN B 474 "
        pdb=" C   GLN B 474 "
      ideal   model   delta    sigma   weight residual
     108.86  125.29  -16.43 1.41e+00 5.03e-01 1.36e+02
  angle pdb=" C   TYR A  98 "
        pdb=" CA  TYR A  98 "
        pdb=" CB  TYR A  98 "
      ideal   model   delta    sigma   weight residual
     110.43   92.80   17.63 1.68e+00 3.54e-01 1.10e+02
  angle pdb=" O   ILE B 472 "
        pdb=" C   ILE B 472 "
        pdb=" N   TYR B 473 "
      ideal   model   delta    sigma   weight residual
     122.99  117.70    5.29 1.07e+00 8.73e-01 2.45e+01
  angle pdb=" O   TYR A  98 "
        pdb=" C   TYR A  98 "
        pdb=" N   THR A  99 "
      ideal   model   delta    sigma   weight residual
     123.46  118.79    4.67 9.90e-01 1.02e+00 2.23e+01
  angle pdb=" CA  CYS B 391 "
        pdb=" CB  CYS B 391 "
        pdb=" SG  CYS B 391 "
      ideal   model   delta    sigma   weight residual
     114.40  124.75  -10.35 2.30e+00 1.89e-01 2.03e+01
  ... (remaining 4360 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.23: 1763
       23.23 -    46.46: 93
       46.46 -    69.69: 13
       69.69 -    92.92: 1
       92.92 -   116.15: 1
  Dihedral angle restraints: 1871
    sinusoidal: 667
      harmonic: 1204
  Sorted by residual:
  dihedral pdb=" CA  PRO A  95 "
           pdb=" C   PRO A  95 "
           pdb=" N   PRO A  96 "
           pdb=" CA  PRO A  96 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00  -63.85 -116.15     0      5.00e+00 4.00e-02 5.40e+02
  dihedral pdb=" C   TYR A  98 "
           pdb=" N   TYR A  98 "
           pdb=" CA  TYR A  98 "
           pdb=" CB  TYR A  98 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -101.20  -21.40     0      2.50e+00 1.60e-01 7.33e+01
  dihedral pdb=" CB  CYS B 379 "
           pdb=" SG  CYS B 379 "
           pdb=" SG  CYS B 432 "
           pdb=" CB  CYS B 432 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   48.05   44.95     1      1.00e+01 1.00e-02 2.81e+01
  ... (remaining 1868 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.094: 432
       0.094 -    0.187: 40
       0.187 -    0.280: 6
       0.280 -    0.374: 1
       0.374 -    0.467: 1
  Chirality restraints: 480
  Sorted by residual:
  chirality pdb=" CA  GLN B 474 "
            pdb=" N   GLN B 474 "
            pdb=" C   GLN B 474 "
            pdb=" CB  GLN B 474 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.04    0.47 2.00e-01 2.50e+01 5.46e+00
  chirality pdb=" CA  TRP A  94 "
            pdb=" N   TRP A  94 "
            pdb=" C   TRP A  94 "
            pdb=" CB  TRP A  94 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.14    0.37 2.00e-01 2.50e+01 3.34e+00
  chirality pdb=" CB  THR C 112 "
            pdb=" CA  THR C 112 "
            pdb=" OG1 THR C 112 "
            pdb=" CG2 THR C 112 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.30    0.26 2.00e-01 2.50e+01 1.63e+00
  ... (remaining 477 not shown)

  Planarity restraints: 566
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A  94 "   -0.035 2.00e-02 2.50e+03   2.57e-02 1.65e+01
        pdb=" CG  TRP A  94 "    0.068 2.00e-02 2.50e+03
        pdb=" CD1 TRP A  94 "   -0.025 2.00e-02 2.50e+03
        pdb=" CD2 TRP A  94 "   -0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP A  94 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP A  94 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP A  94 "    0.006 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A  94 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A  94 "   -0.006 2.00e-02 2.50e+03
        pdb=" CH2 TRP A  94 "   -0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TRP A  94 "    0.062 5.00e-02 4.00e+02   9.22e-02 1.36e+01
        pdb=" N   PRO A  95 "   -0.159 5.00e-02 4.00e+02
        pdb=" CA  PRO A  95 "    0.046 5.00e-02 4.00e+02
        pdb=" CD  PRO A  95 "    0.051 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A  98 "    0.006 2.00e-02 2.50e+03   1.83e-02 6.68e+00
        pdb=" CG  TYR A  98 "   -0.041 2.00e-02 2.50e+03
        pdb=" CD1 TYR A  98 "    0.006 2.00e-02 2.50e+03
        pdb=" CD2 TYR A  98 "    0.023 2.00e-02 2.50e+03
        pdb=" CE1 TYR A  98 "    0.015 2.00e-02 2.50e+03
        pdb=" CE2 TYR A  98 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ  TYR A  98 "    0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR A  98 "   -0.012 2.00e-02 2.50e+03
  ... (remaining 563 not shown)

  Histogram of nonbonded interaction distances:
        1.94 -     2.53: 22
        2.53 -     3.12: 2487
        3.12 -     3.72: 4482
        3.72 -     4.31: 6260
        4.31 -     4.90: 10416
  Nonbonded interactions: 23667
  Sorted by model distance:
  nonbonded pdb=" CD  ARG B 403 "
            pdb=" OD1 ASN B 405 "
     model   vdw
     1.941 3.440
  nonbonded pdb=" O   ARG C  31 "
            pdb=" OH  TYR B 473 "
     model   vdw
     2.117 3.040
  nonbonded pdb=" OG  SER C  56 "
            pdb=" OG1 THR B 415 "
     model   vdw
     2.271 3.040
  nonbonded pdb=" NZ  LYS B 378 "
            pdb=" O   CYS B 379 "
     model   vdw
     2.291 3.120
  nonbonded pdb=" O   TRP A  94 "
            pdb=" N   GLY A  97 "
     model   vdw
     2.322 3.120
  ... (remaining 23662 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             7.120
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     14.190
  Find NCS groups from input model:        0.030
  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:2.850
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.400
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7388
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.094   3208  Z= 0.347
  Angle     :  1.128  17.632   4377  Z= 0.656
  Chirality :  0.063   0.467    480
  Planarity :  0.006   0.092    566
  Dihedral  : 13.300 116.151   1091
  Min Nonbonded Distance : 1.941

Molprobity Statistics.
  All-atom Clashscore : 15.71
  Ramachandran Plot:
    Outliers :  0.48 %
    Allowed  :  8.94 %
    Favored  : 90.58 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  :  6.94 %
    Favored  : 91.48 %
  Cbeta Deviations :  0.52 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.00 %
    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: -4.17 (0.34), residues: 414
  helix: -4.90 (0.26), residues: 21
  sheet: -1.77 (0.40), residues: 128
  loop : -3.30 (0.31), residues: 265

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.068   0.005   TRP A  94 
 HIS   0.002   0.001   HIS B 505 
 PHE   0.019   0.002   PHE B 371 
 TYR   0.041   0.003   TYR A  98 
 ARG   0.007   0.001   ARG A  61 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.25978 (   97)
  hydrogen bonds       : angle       9.90095 (  243)
  SS BOND              : bond        0.00650 (    6)
  SS BOND              : angle       4.11340 (   12)
  covalent geometry    : bond        0.00627 ( 3202)
  covalent geometry    : angle       1.10913 ( 4365)

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

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

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 109
  time to evaluate  : 0.343 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   78 LEU cc_start: 0.7548 (mp) cc_final: 0.7306 (mp)
REVERT: A   79 GLN cc_start: 0.7702 (mm-40) cc_final: 0.7337 (mt0)
REVERT: C    6 GLU cc_start: 0.8464 (mp0) cc_final: 0.8178 (mp0)
REVERT: C   59 TYR cc_start: 0.8453 (m-80) cc_final: 0.8251 (m-80)
  outliers start: 5
  outliers final: 2
  residues processed: 113
  average time/residue: 0.1756
  time to fit residues: 23.1548
Evaluate side-chains
  64 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 62
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   95 PRO
Chi-restraints excluded: chain B residue  503 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 33 optimal weight:    0.6980
   chunk 30 optimal weight:    0.6980
   chunk 16 optimal weight:    0.7980
   chunk 10 optimal weight:    0.0870
   chunk 20 optimal weight:    0.6980
   chunk 31 optimal weight:    2.9990
   chunk 12 optimal weight:    0.5980
   chunk 19 optimal weight:    0.5980
   chunk 23 optimal weight:    3.9990
   chunk 36 optimal weight:    0.9980
   chunk 11 optimal weight:    2.9990
   overall best weight:    0.5358

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

Flipped N/Q/H residues before XYZ refinement:
** A  92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 493 GLN
B 506 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.121216 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.101272 restraints weight = 8245.082|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.103968 restraints weight = 4447.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.105709 restraints weight = 2984.745|
|-----------------------------------------------------------------------------|
r_work (final): 0.3627
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7541
moved from start:          0.2981

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059   3208  Z= 0.159
  Angle     :  0.818  19.008   4377  Z= 0.415
  Chirality :  0.050   0.329    480
  Planarity :  0.006   0.085    566
  Dihedral  :  5.219  52.318    463
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 10.59
  Ramachandran Plot:
    Outliers :  0.48 %
    Allowed  :  3.38 %
    Favored  : 96.14 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 16.09 %
    Favored  : 79.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.00 %
    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: -2.59 (0.37), residues: 414
  helix: -3.60 (0.67), residues: 23
  sheet: -0.71 (0.44), residues: 122
  loop : -2.15 (0.35), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP C  47 
 HIS   0.002   0.001   HIS B 519 
 PHE   0.010   0.001   PHE B 371 
 TYR   0.017   0.002   TYR A  98 
 ARG   0.005   0.001   ARG A  45 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03907 (   97)
  hydrogen bonds       : angle       6.68822 (  243)
  SS BOND              : bond        0.00678 (    6)
  SS BOND              : angle       4.12958 (   12)
  covalent geometry    : bond        0.00357 ( 3202)
  covalent geometry    : angle       0.78987 ( 4365)

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

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

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 72
  time to evaluate  : 0.316 
Fit side-chains
REVERT: A   36 TYR cc_start: 0.8728 (m-80) cc_final: 0.8379 (m-80)
REVERT: A   89 GLN cc_start: 0.9141 (tt0) cc_final: 0.8916 (tt0)
REVERT: C   46 GLU cc_start: 0.7739 (pt0) cc_final: 0.7510 (tt0)
REVERT: C   59 TYR cc_start: 0.8564 (m-80) cc_final: 0.8354 (m-80)
REVERT: B  390 LEU cc_start: 0.7827 (mt) cc_final: 0.7463 (mt)
REVERT: B  474 GLN cc_start: 0.7251 (OUTLIER) cc_final: 0.6408 (pp30)
  outliers start: 13
  outliers final: 10
  residues processed: 79
  average time/residue: 0.1443
  time to fit residues: 13.8520
Evaluate side-chains
  70 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 59
  time to evaluate  : 0.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 VAL
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue  104 THR
Chi-restraints excluded: chain C residue    2 VAL
Chi-restraints excluded: chain C residue   82 MET
Chi-restraints excluded: chain B residue  387 LEU
Chi-restraints excluded: chain B residue  415 THR
Chi-restraints excluded: chain B residue  432 CYS
Chi-restraints excluded: chain B residue  474 GLN
Chi-restraints excluded: chain B residue  503 VAL
Chi-restraints excluded: chain B residue  512 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 18 optimal weight:    3.9990
   chunk 2 optimal weight:    1.9990
   chunk 13 optimal weight:    2.9990
   chunk 19 optimal weight:    0.5980
   chunk 37 optimal weight:    2.9990
   chunk 36 optimal weight:    2.9990
   chunk 17 optimal weight:    0.6980
   chunk 3 optimal weight:    0.9980
   chunk 30 optimal weight:    4.9990
   chunk 4 optimal weight:    2.9990
   chunk 5 optimal weight:    6.9990
   overall best weight:    1.4584

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

Flipped N/Q/H residues before XYZ refinement:
** A  92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 422 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.115686 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.095672 restraints weight = 8125.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.098081 restraints weight = 4578.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.099737 restraints weight = 3195.578|
|-----------------------------------------------------------------------------|
r_work (final): 0.3529
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7730
moved from start:          0.3906

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   3208  Z= 0.214
  Angle     :  0.831  18.873   4377  Z= 0.426
  Chirality :  0.049   0.315    480
  Planarity :  0.006   0.082    566
  Dihedral  :  5.801  58.544    460
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 11.58
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  5.56 %
    Favored  : 94.20 %
  Rotamer:
    Outliers :  6.62 %
    Allowed  : 20.50 %
    Favored  : 72.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.00 %
    Twisted General : 0.25 %

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: -2.07 (0.40), residues: 414
  helix: -2.87 (0.86), residues: 23
  sheet: -0.48 (0.44), residues: 134
  loop : -1.80 (0.38), residues: 257

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.003   TRP B 436 
 HIS   0.001   0.000   HIS B 519 
 PHE   0.020   0.002   PHE B 371 
 TYR   0.018   0.002   TYR A  91 
 ARG   0.004   0.001   ARG A  24 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03840 (   97)
  hydrogen bonds       : angle       6.55618 (  243)
  SS BOND              : bond        0.01097 (    6)
  SS BOND              : angle       4.13522 (   12)
  covalent geometry    : bond        0.00490 ( 3202)
  covalent geometry    : angle       0.80306 ( 4365)

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

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

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 65
  time to evaluate  : 0.350 
Fit side-chains
   revert: symmetry clash
REVERT: B  356 LYS cc_start: 0.8361 (mmmt) cc_final: 0.8046 (tptp)
REVERT: B  386 LYS cc_start: 0.9005 (tptt) cc_final: 0.8460 (tppt)
REVERT: B  387 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.8042 (mt)
REVERT: B  390 LEU cc_start: 0.7724 (mt) cc_final: 0.6909 (mt)
  outliers start: 21
  outliers final: 13
  residues processed: 79
  average time/residue: 0.1334
  time to fit residues: 12.9742
Evaluate side-chains
  69 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 55
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue  104 THR
Chi-restraints excluded: chain C residue    2 VAL
Chi-restraints excluded: chain C residue   82 MET
Chi-restraints excluded: chain C residue  112 THR
Chi-restraints excluded: chain B residue  351 TYR
Chi-restraints excluded: chain B residue  387 LEU
Chi-restraints excluded: chain B residue  393 THR
Chi-restraints excluded: chain B residue  415 THR
Chi-restraints excluded: chain B residue  432 CYS
Chi-restraints excluded: chain B residue  436 TRP
Chi-restraints excluded: chain B residue  474 GLN
Chi-restraints excluded: chain B residue  503 VAL
Chi-restraints excluded: chain B residue  512 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 28 optimal weight:    0.0870
   chunk 22 optimal weight:    3.9990
   chunk 8 optimal weight:    0.9980
   chunk 18 optimal weight:    3.9990
   chunk 16 optimal weight:    0.6980
   chunk 21 optimal weight:    3.9990
   chunk 30 optimal weight:    8.9990
   chunk 32 optimal weight:    9.9990
   chunk 19 optimal weight:    2.9990
   chunk 24 optimal weight:    0.0870
   chunk 23 optimal weight:    0.9990
   overall best weight:    0.5738

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

Flipped N/Q/H residues before XYZ refinement:
** A  92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 422 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 = 0.3813 r_free = 0.3813 target = 0.117461 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.096734 restraints weight = 8178.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.099460 restraints weight = 4401.792|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.101246 restraints weight = 2951.453|
|-----------------------------------------------------------------------------|
r_work (final): 0.3552
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7673
moved from start:          0.4316

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   3208  Z= 0.133
  Angle     :  0.765  20.448   4377  Z= 0.387
  Chirality :  0.048   0.300    480
  Planarity :  0.005   0.072    566
  Dihedral  :  5.157  54.185    460
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 7.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 24.29 %
    Favored  : 71.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.00 %
    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: -1.67 (0.40), residues: 414
  helix: -2.44 (0.91), residues: 23
  sheet: -0.00 (0.46), residues: 127
  loop : -1.63 (0.38), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A  94 
 HIS   0.002   0.001   HIS B 519 
 PHE   0.015   0.001   PHE B 371 
 TYR   0.019   0.002   TYR C  59 
 ARG   0.003   0.000   ARG A  24 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03562 (   97)
  hydrogen bonds       : angle       6.02730 (  243)
  SS BOND              : bond        0.00638 (    6)
  SS BOND              : angle       4.02406 (   12)
  covalent geometry    : bond        0.00303 ( 3202)
  covalent geometry    : angle       0.73601 ( 4365)

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

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

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 64
  time to evaluate  : 0.327 
Fit side-chains
   revert: symmetry clash
REVERT: A   18 ARG cc_start: 0.8122 (mtp-110) cc_final: 0.7875 (mtp-110)
REVERT: C   59 TYR cc_start: 0.8602 (m-80) cc_final: 0.8379 (m-80)
REVERT: B  356 LYS cc_start: 0.8286 (mmmt) cc_final: 0.8031 (tptp)
REVERT: B  386 LYS cc_start: 0.8995 (tptt) cc_final: 0.8375 (tppt)
REVERT: B  390 LEU cc_start: 0.7724 (mt) cc_final: 0.6799 (mt)
REVERT: B  474 GLN cc_start: 0.7794 (OUTLIER) cc_final: 0.7202 (pp30)
  outliers start: 12
  outliers final: 10
  residues processed: 70
  average time/residue: 0.1456
  time to fit residues: 12.6680
Evaluate side-chains
  70 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 59
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain C residue    2 VAL
Chi-restraints excluded: chain C residue   46 GLU
Chi-restraints excluded: chain C residue   82 MET
Chi-restraints excluded: chain B residue  351 TYR
Chi-restraints excluded: chain B residue  387 LEU
Chi-restraints excluded: chain B residue  393 THR
Chi-restraints excluded: chain B residue  415 THR
Chi-restraints excluded: chain B residue  474 GLN
Chi-restraints excluded: chain B residue  503 VAL
Chi-restraints excluded: chain B residue  512 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 39 optimal weight:    0.9990
   chunk 26 optimal weight:    0.9990
   chunk 14 optimal weight:    2.9990
   chunk 0 optimal weight:    8.9990
   chunk 1 optimal weight:    1.9990
   chunk 24 optimal weight:    6.9990
   chunk 10 optimal weight:    0.5980
   chunk 11 optimal weight:    4.9990
   chunk 33 optimal weight:    3.9990
   chunk 17 optimal weight:    2.9990
   chunk 15 optimal weight:    0.6980
   overall best weight:    1.0586

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

Flipped N/Q/H residues before XYZ refinement:
** A  92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 422 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 = 0.3776 r_free = 0.3776 target = 0.115123 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.094525 restraints weight = 8097.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.097136 restraints weight = 4442.946|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.098866 restraints weight = 3004.534|
|-----------------------------------------------------------------------------|
r_work (final): 0.3514
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7735
moved from start:          0.4660

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061   3208  Z= 0.170
  Angle     :  0.716  14.607   4377  Z= 0.366
  Chirality :  0.046   0.161    480
  Planarity :  0.005   0.072    566
  Dihedral  :  5.373  56.377    460
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 8.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.56 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  6.94 %
    Allowed  : 23.03 %
    Favored  : 70.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.00 %
    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: -1.66 (0.40), residues: 414
  helix: -2.33 (0.92), residues: 23
  sheet: -0.10 (0.43), residues: 137
  loop : -1.62 (0.39), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A  94 
 HIS   0.001   0.001   HIS B 505 
 PHE   0.014   0.001   PHE B 371 
 TYR   0.015   0.002   TYR A  49 
 ARG   0.003   0.000   ARG A  24 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03297 (   97)
  hydrogen bonds       : angle       5.93949 (  243)
  SS BOND              : bond        0.00649 (    6)
  SS BOND              : angle       2.47778 (   12)
  covalent geometry    : bond        0.00400 ( 3202)
  covalent geometry    : angle       0.70512 ( 4365)

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

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

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 63
  time to evaluate  : 0.322 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   59 TYR cc_start: 0.8624 (m-80) cc_final: 0.8393 (m-80)
REVERT: B  356 LYS cc_start: 0.8246 (mmmt) cc_final: 0.8006 (tptp)
REVERT: B  474 GLN cc_start: 0.8034 (OUTLIER) cc_final: 0.7572 (pp30)
  outliers start: 22
  outliers final: 16
  residues processed: 75
  average time/residue: 0.1412
  time to fit residues: 12.9153
Evaluate side-chains
  74 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 57
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue   93 ASN
Chi-restraints excluded: chain A residue  104 THR
Chi-restraints excluded: chain C residue    2 VAL
Chi-restraints excluded: chain C residue   46 GLU
Chi-restraints excluded: chain C residue   82 MET
Chi-restraints excluded: chain C residue  112 THR
Chi-restraints excluded: chain B residue  351 TYR
Chi-restraints excluded: chain B residue  353 TRP
Chi-restraints excluded: chain B residue  379 CYS
Chi-restraints excluded: chain B residue  387 LEU
Chi-restraints excluded: chain B residue  393 THR
Chi-restraints excluded: chain B residue  415 THR
Chi-restraints excluded: chain B residue  436 TRP
Chi-restraints excluded: chain B residue  474 GLN
Chi-restraints excluded: chain B residue  503 VAL
Chi-restraints excluded: chain B residue  512 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 30 optimal weight:    0.0970
   chunk 32 optimal weight:    8.9990
   chunk 8 optimal weight:    0.8980
   chunk 23 optimal weight:    4.9990
   chunk 12 optimal weight:    3.9990
   chunk 37 optimal weight:    2.9990
   chunk 13 optimal weight:    0.5980
   chunk 33 optimal weight:    1.9990
   chunk 39 optimal weight:    2.9990
   chunk 5 optimal weight:    0.0370
   chunk 38 optimal weight:    5.9990
   overall best weight:    0.7258

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

Flipped N/Q/H residues before XYZ refinement:
** A  92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 519 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.116226 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.095771 restraints weight = 8346.991|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.098405 restraints weight = 4578.650|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.100131 restraints weight = 3086.904|
|-----------------------------------------------------------------------------|
r_work (final): 0.3532
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7701
moved from start:          0.4935

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   3208  Z= 0.140
  Angle     :  0.682  12.973   4377  Z= 0.349
  Chirality :  0.045   0.161    480
  Planarity :  0.005   0.066    566
  Dihedral  :  5.127  53.254    460
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 7.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.83 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  5.99 %
    Allowed  : 24.92 %
    Favored  : 69.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.00 %
    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: -1.65 (0.40), residues: 414
  helix: -2.25 (0.94), residues: 23
  sheet:  0.03 (0.44), residues: 133
  loop : -1.68 (0.38), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A  94 
 HIS   0.010   0.004   HIS B 519 
 PHE   0.013   0.001   PHE A  71 
 TYR   0.016   0.002   TYR A  49 
 ARG   0.004   0.000   ARG A  61 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03149 (   97)
  hydrogen bonds       : angle       5.66613 (  243)
  SS BOND              : bond        0.00685 (    6)
  SS BOND              : angle       2.19489 (   12)
  covalent geometry    : bond        0.00328 ( 3202)
  covalent geometry    : angle       0.67295 ( 4365)

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

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

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 61
  time to evaluate  : 0.317 
Fit side-chains
   revert: symmetry clash
REVERT: B  356 LYS cc_start: 0.8211 (mmmt) cc_final: 0.8008 (tptp)
REVERT: B  474 GLN cc_start: 0.8052 (OUTLIER) cc_final: 0.7654 (pp30)
  outliers start: 19
  outliers final: 15
  residues processed: 71
  average time/residue: 0.1580
  time to fit residues: 13.5208
Evaluate side-chains
  73 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 57
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue   93 ASN
Chi-restraints excluded: chain C residue    2 VAL
Chi-restraints excluded: chain C residue   46 GLU
Chi-restraints excluded: chain C residue   82 MET
Chi-restraints excluded: chain C residue  112 THR
Chi-restraints excluded: chain B residue  351 TYR
Chi-restraints excluded: chain B residue  353 TRP
Chi-restraints excluded: chain B residue  387 LEU
Chi-restraints excluded: chain B residue  393 THR
Chi-restraints excluded: chain B residue  415 THR
Chi-restraints excluded: chain B residue  436 TRP
Chi-restraints excluded: chain B residue  474 GLN
Chi-restraints excluded: chain B residue  503 VAL
Chi-restraints excluded: chain B residue  512 VAL
Chi-restraints excluded: chain B residue  519 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 36 optimal weight:    2.9990
   chunk 20 optimal weight:    3.9990
   chunk 8 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9990
   chunk 25 optimal weight:    1.9990
   chunk 13 optimal weight:    0.8980
   chunk 27 optimal weight:    3.9990
   chunk 15 optimal weight:    0.6980
   chunk 9 optimal weight:    0.6980
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
** A  92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 519 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.115837 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.095221 restraints weight = 8054.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.097906 restraints weight = 4375.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.099658 restraints weight = 2937.247|
|-----------------------------------------------------------------------------|
r_work (final): 0.3526
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7711
moved from start:          0.5031

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   3208  Z= 0.149
  Angle     :  0.715  12.653   4377  Z= 0.361
  Chirality :  0.045   0.206    480
  Planarity :  0.005   0.067    566
  Dihedral  :  5.070  52.989    460
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 7.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.80 %
    Favored  : 94.20 %
  Rotamer:
    Outliers :  6.94 %
    Allowed  : 24.29 %
    Favored  : 68.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.00 %
    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: -1.55 (0.40), residues: 414
  helix: -2.19 (0.96), residues: 23
  sheet:  0.02 (0.44), residues: 137
  loop : -1.59 (0.38), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A  94 
 HIS   0.010   0.004   HIS B 519 
 PHE   0.014   0.001   PHE A  71 
 TYR   0.013   0.001   TYR A  98 
 ARG   0.002   0.000   ARG A  24 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03290 (   97)
  hydrogen bonds       : angle       5.57979 (  243)
  SS BOND              : bond        0.00590 (    6)
  SS BOND              : angle       2.51717 (   12)
  covalent geometry    : bond        0.00346 ( 3202)
  covalent geometry    : angle       0.70383 ( 4365)

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

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

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 61
  time to evaluate  : 0.344 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   59 TYR cc_start: 0.8558 (m-80) cc_final: 0.8341 (m-80)
REVERT: C   79 TYR cc_start: 0.7247 (m-80) cc_final: 0.6941 (m-80)
REVERT: B  356 LYS cc_start: 0.8186 (mmmt) cc_final: 0.7968 (tptp)
REVERT: B  371 PHE cc_start: 0.5003 (OUTLIER) cc_final: 0.4093 (t80)
REVERT: B  474 GLN cc_start: 0.8023 (OUTLIER) cc_final: 0.7647 (pp30)
  outliers start: 22
  outliers final: 15
  residues processed: 74
  average time/residue: 0.2074
  time to fit residues: 18.2806
Evaluate side-chains
  76 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 59
  time to evaluate  : 0.372 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue   93 ASN
Chi-restraints excluded: chain A residue  104 THR
Chi-restraints excluded: chain C residue    2 VAL
Chi-restraints excluded: chain C residue   46 GLU
Chi-restraints excluded: chain C residue   82 MET
Chi-restraints excluded: chain C residue  112 THR
Chi-restraints excluded: chain B residue  351 TYR
Chi-restraints excluded: chain B residue  353 TRP
Chi-restraints excluded: chain B residue  371 PHE
Chi-restraints excluded: chain B residue  387 LEU
Chi-restraints excluded: chain B residue  393 THR
Chi-restraints excluded: chain B residue  415 THR
Chi-restraints excluded: chain B residue  436 TRP
Chi-restraints excluded: chain B residue  474 GLN
Chi-restraints excluded: chain B residue  503 VAL
Chi-restraints excluded: chain B residue  512 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 19 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9990
   chunk 14 optimal weight:    0.5980
   chunk 0 optimal weight:    7.9990
   chunk 31 optimal weight:    2.9990
   chunk 27 optimal weight:    2.9990
   chunk 11 optimal weight:    4.9990
   chunk 39 optimal weight:    2.9990
   chunk 35 optimal weight:    1.9990
   chunk 29 optimal weight:    0.6980
   chunk 36 optimal weight:    1.9990
   overall best weight:    1.2586

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

Flipped N/Q/H residues before XYZ refinement:
** A  92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 422 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 = 0.3748 r_free = 0.3748 target = 0.113387 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.092956 restraints weight = 8113.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.095596 restraints weight = 4433.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.097353 restraints weight = 2962.123|
|-----------------------------------------------------------------------------|
r_work (final): 0.3485
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7766
moved from start:          0.5286

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061   3208  Z= 0.191
  Angle     :  0.743  13.274   4377  Z= 0.380
  Chirality :  0.048   0.262    480
  Planarity :  0.005   0.068    566
  Dihedral  :  5.445  55.206    460
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 9.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.28 %
    Favored  : 93.72 %
  Rotamer:
    Outliers :  6.31 %
    Allowed  : 24.92 %
    Favored  : 68.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.00 %
    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: -1.54 (0.40), residues: 414
  helix: -2.36 (0.92), residues: 23
  sheet:  0.11 (0.44), residues: 134
  loop : -1.59 (0.38), residues: 257

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A  94 
 HIS   0.001   0.001   HIS B 519 
 PHE   0.021   0.002   PHE A  71 
 TYR   0.015   0.002   TYR A  49 
 ARG   0.003   0.000   ARG A  61 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03386 (   97)
  hydrogen bonds       : angle       5.91983 (  243)
  SS BOND              : bond        0.00770 (    6)
  SS BOND              : angle       2.28305 (   12)
  covalent geometry    : bond        0.00448 ( 3202)
  covalent geometry    : angle       0.73429 ( 4365)

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

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

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 58
  time to evaluate  : 0.345 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   79 TYR cc_start: 0.7252 (m-80) cc_final: 0.6936 (m-80)
REVERT: B  356 LYS cc_start: 0.8229 (mmmt) cc_final: 0.8011 (tptp)
REVERT: B  371 PHE cc_start: 0.5166 (OUTLIER) cc_final: 0.4197 (t80)
REVERT: B  386 LYS cc_start: 0.9031 (tptp) cc_final: 0.8675 (tppt)
REVERT: B  474 GLN cc_start: 0.8202 (OUTLIER) cc_final: 0.7784 (pp30)
  outliers start: 20
  outliers final: 14
  residues processed: 69
  average time/residue: 0.1743
  time to fit residues: 14.4344
Evaluate side-chains
  68 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 52
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue   93 ASN
Chi-restraints excluded: chain A residue  104 THR
Chi-restraints excluded: chain C residue   21 SER
Chi-restraints excluded: chain C residue   46 GLU
Chi-restraints excluded: chain C residue   82 MET
Chi-restraints excluded: chain C residue  112 THR
Chi-restraints excluded: chain B residue  351 TYR
Chi-restraints excluded: chain B residue  353 TRP
Chi-restraints excluded: chain B residue  371 PHE
Chi-restraints excluded: chain B residue  387 LEU
Chi-restraints excluded: chain B residue  393 THR
Chi-restraints excluded: chain B residue  436 TRP
Chi-restraints excluded: chain B residue  474 GLN
Chi-restraints excluded: chain B residue  503 VAL
Chi-restraints excluded: chain B residue  512 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 35 optimal weight:    0.7980
   chunk 16 optimal weight:    0.0030
   chunk 10 optimal weight:    0.9980
   chunk 29 optimal weight:    3.9990
   chunk 4 optimal weight:    0.5980
   chunk 33 optimal weight:    0.6980
   chunk 0 optimal weight:    7.9990
   chunk 36 optimal weight:    0.9990
   chunk 26 optimal weight:    0.6980
   chunk 2 optimal weight:    3.9990
   chunk 6 optimal weight:    0.7980
   overall best weight:    0.5590

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

Flipped N/Q/H residues before XYZ refinement:
B 422 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.115879 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.095744 restraints weight = 8220.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.098372 restraints weight = 4451.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.100160 restraints weight = 2991.353|
|-----------------------------------------------------------------------------|
r_work (final): 0.3540
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7690
moved from start:          0.5389

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   3208  Z= 0.129
  Angle     :  0.700  12.781   4377  Z= 0.354
  Chirality :  0.046   0.258    480
  Planarity :  0.005   0.067    566
  Dihedral  :  4.988  50.447    460
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 8.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  5.36 %
    Allowed  : 24.92 %
    Favored  : 69.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.00 %
    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 (0.41), residues: 414
  helix: -2.13 (1.01), residues: 23
  sheet:  0.27 (0.45), residues: 134
  loop : -1.56 (0.38), residues: 257

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A  94 
 HIS   0.001   0.001   HIS B 505 
 PHE   0.015   0.001   PHE A  71 
 TYR   0.011   0.001   TYR C 107 
 ARG   0.002   0.000   ARG A  61 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03206 (   97)
  hydrogen bonds       : angle       5.50286 (  243)
  SS BOND              : bond        0.00640 (    6)
  SS BOND              : angle       2.26099 (   12)
  covalent geometry    : bond        0.00302 ( 3202)
  covalent geometry    : angle       0.69078 ( 4365)

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

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

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 63
  time to evaluate  : 0.367 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   19 ARG cc_start: 0.8027 (ttt180) cc_final: 0.7816 (ptm160)
REVERT: B  356 LYS cc_start: 0.8205 (mmmt) cc_final: 0.7999 (tptp)
REVERT: B  371 PHE cc_start: 0.5142 (OUTLIER) cc_final: 0.4112 (t80)
  outliers start: 17
  outliers final: 11
  residues processed: 73
  average time/residue: 0.2006
  time to fit residues: 17.1101
Evaluate side-chains
  68 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 56
  time to evaluate  : 0.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 VAL
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain C residue   46 GLU
Chi-restraints excluded: chain C residue  112 THR
Chi-restraints excluded: chain B residue  351 TYR
Chi-restraints excluded: chain B residue  353 TRP
Chi-restraints excluded: chain B residue  371 PHE
Chi-restraints excluded: chain B residue  387 LEU
Chi-restraints excluded: chain B residue  393 THR
Chi-restraints excluded: chain B residue  436 TRP
Chi-restraints excluded: chain B residue  503 VAL
Chi-restraints excluded: chain B residue  512 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 34 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 21 optimal weight:    5.9990
   chunk 1 optimal weight:    1.9990
   chunk 22 optimal weight:    0.0670
   chunk 9 optimal weight:    0.0870
   chunk 3 optimal weight:    0.9990
   chunk 38 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9980
   chunk 23 optimal weight:    1.9990
   chunk 36 optimal weight:    0.8980
   overall best weight:    0.6098

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

Flipped N/Q/H residues before XYZ refinement:
** A  92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 417 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.115374 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.095042 restraints weight = 8150.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.097776 restraints weight = 4363.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.099513 restraints weight = 2911.947|
|-----------------------------------------------------------------------------|
r_work (final): 0.3530
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7693
moved from start:          0.5572

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060   3208  Z= 0.138
  Angle     :  0.704  12.882   4377  Z= 0.357
  Chirality :  0.046   0.268    480
  Planarity :  0.005   0.067    566
  Dihedral  :  5.025  49.358    460
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 9.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.28 %
    Favored  : 93.72 %
  Rotamer:
    Outliers :  4.73 %
    Allowed  : 25.24 %
    Favored  : 70.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.00 %
    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: -1.32 (0.41), residues: 414
  helix: -2.13 (0.99), residues: 23
  sheet:  0.47 (0.46), residues: 130
  loop : -1.56 (0.38), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A  94 
 HIS   0.001   0.001   HIS B 505 
 PHE   0.019   0.002   PHE A  71 
 TYR   0.042   0.002   TYR C  79 
 ARG   0.004   0.001   ARG A  18 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03254 (   97)
  hydrogen bonds       : angle       5.84019 (  243)
  SS BOND              : bond        0.00734 (    6)
  SS BOND              : angle       1.95557 (   12)
  covalent geometry    : bond        0.00334 ( 3202)
  covalent geometry    : angle       0.69760 ( 4365)

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

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

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 58
  time to evaluate  : 0.324 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  371 PHE cc_start: 0.5190 (OUTLIER) cc_final: 0.4130 (t80)
REVERT: B  386 LYS cc_start: 0.9063 (tptp) cc_final: 0.8825 (tppt)
  outliers start: 15
  outliers final: 12
  residues processed: 65
  average time/residue: 0.1735
  time to fit residues: 13.3774
Evaluate side-chains
  67 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 54
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 VAL
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain C residue   46 GLU
Chi-restraints excluded: chain C residue   82 MET
Chi-restraints excluded: chain C residue  112 THR
Chi-restraints excluded: chain B residue  351 TYR
Chi-restraints excluded: chain B residue  353 TRP
Chi-restraints excluded: chain B residue  371 PHE
Chi-restraints excluded: chain B residue  387 LEU
Chi-restraints excluded: chain B residue  393 THR
Chi-restraints excluded: chain B residue  436 TRP
Chi-restraints excluded: chain B residue  503 VAL
Chi-restraints excluded: chain B residue  512 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 37 optimal weight:    0.0870
   chunk 3 optimal weight:    1.9990
   chunk 5 optimal weight:    6.9990
   chunk 14 optimal weight:    0.6980
   chunk 39 optimal weight:    0.9980
   chunk 15 optimal weight:    0.8980
   chunk 24 optimal weight:    0.0670
   chunk 0 optimal weight:    7.9990
   chunk 22 optimal weight:    3.9990
   chunk 16 optimal weight:    0.6980
   chunk 6 optimal weight:    5.9990
   overall best weight:    0.4896

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

Flipped N/Q/H residues before XYZ refinement:
** A  92 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 = 0.3797 r_free = 0.3797 target = 0.116152 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.096264 restraints weight = 8195.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.098926 restraints weight = 4393.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.100697 restraints weight = 2937.052|
|-----------------------------------------------------------------------------|
r_work (final): 0.3547
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7657
moved from start:          0.5668

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   3208  Z= 0.127
  Angle     :  0.710  12.901   4377  Z= 0.358
  Chirality :  0.046   0.234    480
  Planarity :  0.005   0.061    566
  Dihedral  :  4.724  44.018    460
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 9.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  4.42 %
    Allowed  : 25.55 %
    Favored  : 70.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.00 %
    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: -1.11 (0.41), residues: 414
  helix: -2.04 (1.02), residues: 23
  sheet:  0.58 (0.47), residues: 124
  loop : -1.34 (0.37), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  35 
 HIS   0.001   0.001   HIS B 505 
 PHE   0.016   0.001   PHE A  71 
 TYR   0.044   0.002   TYR C  79 
 ARG   0.003   0.001   ARG A  18 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03158 (   97)
  hydrogen bonds       : angle       5.61474 (  243)
  SS BOND              : bond        0.00518 (    6)
  SS BOND              : angle       2.32724 (   12)
  covalent geometry    : bond        0.00305 ( 3202)
  covalent geometry    : angle       0.70071 ( 4365)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1802.84 seconds
wall clock time: 31 minutes 50.43 seconds (1910.43 seconds total)