Starting phenix.real_space_refine
on Wed Jun  4 17:11:58 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ws6_32748/06_2025/7ws6_32748.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ws6_32748/06_2025/7ws6_32748.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ws6_32748/06_2025/7ws6_32748.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ws6_32748/06_2025/7ws6_32748.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ws6_32748/06_2025/7ws6_32748.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ws6_32748/06_2025/7ws6_32748.cif"
  }
  resolution = 3.8
  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=  -0.002 sd=   0.022
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      15      5.16       5
     C    2245      2.51       5
     N     597      2.21       5
     O     674      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 3531
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "C"
      Number of atoms: 1747
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 218, 1747
          Classifications: {'peptide': 218}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 14, 'TRANS': 203}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 6
          Planarities with less than four sites: {'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "H"
      Number of atoms: 817
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 817
          Classifications: {'peptide': 108}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 100}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "I"
      Number of atoms: 967
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 125, 967
          Classifications: {'peptide': 125}
          Link IDs: {'PTRANS': 3, 'TRANS': 121}
  Time building chain proxies: 3.83, per 1000 atoms: 1.08
  Number of scatterers: 3531
  At special positions: 0
  Unit cell: (59.072, 94.016, 113.152, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      15     16.00
     O     674      8.00
     N     597      7.00
     C    2245      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS C 336 " - pdb=" SG  CYS C 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 379 " - pdb=" SG  CYS C 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 480 " - pdb=" SG  CYS C 488 " distance=2.02
    Simple disulfide: pdb=" SG  CYS H  23 " - pdb=" SG  CYS H  88 " distance=2.03
    Simple disulfide: pdb=" SG  CYS I  22 " - pdb=" SG  CYS I  96 " 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: 0.82
  Conformation dependent library (CDL) restraints added in 434.9 milliseconds
  

  890 Ramachandran restraints generated.
    445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  836

  Finding SS restraints...
    Secondary structure from input PDB file:
      7 helices and 10 sheets defined
      8.9% alpha, 29.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.51
  Creating SS restraints...
    Processing helix  chain 'C' and resid 338 through 343
      removed outlier: 3.527A  pdb=" N   PHE C 342 " --> pdb=" O   PHE C 338 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 365 through 370
      removed outlier: 3.539A  pdb=" N   ASN C 370 " --> pdb=" O   SER C 366 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 383 through 389
      removed outlier: 3.512A  pdb=" N   LEU C 387 " --> pdb=" O   PRO C 384 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   ASN C 388 " --> pdb=" O   THR C 385 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   ASP C 389 " --> pdb=" O   LYS C 386 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 406 through 410
    Processing helix  chain 'C' and resid 416 through 422
    Processing helix  chain 'C' and resid 502 through 506
    Processing helix  chain 'I' and resid 62 through 65
      removed outlier: 3.554A  pdb=" N   LYS I  65 " --> pdb=" O   ASP I  62 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'I' and resid 62 through 65'
    Processing sheet with id=AA1, first strand: chain 'C' and resid 354 through 358
      removed outlier: 3.542A  pdb=" N   ASN C 354 " --> pdb=" O   SER C 399 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 361 through 362
      removed outlier: 6.771A  pdb=" N   CYS C 361 " --> pdb=" O   CYS C 525 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 452 through 454
    Processing sheet with id=AA4, first strand: chain 'H' and resid 4 through 6
    Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 13
      removed outlier: 5.604A  pdb=" N   LEU H  11 " --> pdb=" O   GLU H 106 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'H' and resid 53 through 54
      removed outlier: 6.866A  pdb=" N   TRP H  35 " --> pdb=" O   LEU H  47 " (cutoff:3.500A)
      removed outlier: 5.430A  pdb=" N   TYR H  49 " --> pdb=" O   LEU H  33 " (cutoff:3.500A)
      removed outlier: 7.149A  pdb=" N   LEU H  33 " --> pdb=" O   TYR H  49 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'I' and resid 4 through 7
      removed outlier: 3.680A  pdb=" N   SER I  21 " --> pdb=" O   SER I   7 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'I' and resid 11 through 12
    Processing sheet with id=AA9, first strand: chain 'I' and resid 58 through 60
      removed outlier: 3.952A  pdb=" N   ASP I  59 " --> pdb=" O   GLY I  50 " (cutoff:3.500A)
      removed outlier: 6.741A  pdb=" N   TRP I  36 " --> pdb=" O   VAL I  48 " (cutoff:3.500A)
      removed outlier: 4.646A  pdb=" N   GLY I  50 " --> pdb=" O   MET I  34 " (cutoff:3.500A)
      removed outlier: 6.873A  pdb=" N   MET I  34 " --> pdb=" O   GLY I  50 " (cutoff:3.500A)
      removed outlier: 6.530A  pdb=" N   LYS I  98 " --> pdb=" O   ASP I 111 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'I' and resid 58 through 60
      removed outlier: 3.952A  pdb=" N   ASP I  59 " --> pdb=" O   GLY I  50 " (cutoff:3.500A)
      removed outlier: 6.741A  pdb=" N   TRP I  36 " --> pdb=" O   VAL I  48 " (cutoff:3.500A)
      removed outlier: 4.646A  pdb=" N   GLY I  50 " --> pdb=" O   MET I  34 " (cutoff:3.500A)
      removed outlier: 6.873A  pdb=" N   MET I  34 " --> pdb=" O   GLY I  50 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   TYR I  94 " --> pdb=" O   THR I 117 " (cutoff:3.500A)

    100 hydrogen bonds defined for protein.
    240 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: 0.85

  Time building geometry restraints manager: 0.99 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1132
        1.34 -     1.46: 899
        1.46 -     1.58: 1573
        1.58 -     1.70: 0
        1.70 -     1.81: 18
  Bond restraints: 3622
  Sorted by residual:
  bond pdb=" N   ASP I  31 "
       pdb=" CA  ASP I  31 "
    ideal  model  delta    sigma   weight residual
    1.458  1.493 -0.036 1.22e-02 6.72e+03 8.47e+00
  bond pdb=" N   ASP C 442 "
       pdb=" CA  ASP C 442 "
    ideal  model  delta    sigma   weight residual
    1.457  1.489 -0.032 1.16e-02 7.43e+03 7.52e+00
  bond pdb=" N   ARG C 346 "
       pdb=" CA  ARG C 346 "
    ideal  model  delta    sigma   weight residual
    1.455  1.486 -0.031 1.25e-02 6.40e+03 6.12e+00
  bond pdb=" N   LYS C 440 "
       pdb=" CA  LYS C 440 "
    ideal  model  delta    sigma   weight residual
    1.456  1.486 -0.031 1.32e-02 5.74e+03 5.37e+00
  bond pdb=" N   ARG C 493 "
       pdb=" CA  ARG C 493 "
    ideal  model  delta    sigma   weight residual
    1.454  1.482 -0.028 1.19e-02 7.06e+03 5.36e+00
  ... (remaining 3617 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.21: 4597
        1.21 -     2.42: 249
        2.42 -     3.64: 61
        3.64 -     4.85: 11
        4.85 -     6.06: 4
  Bond angle restraints: 4922
  Sorted by residual:
  angle pdb=" CA  TYR H  32 "
        pdb=" C   TYR H  32 "
        pdb=" O   TYR H  32 "
      ideal   model   delta    sigma   weight residual
     122.13  118.09    4.04 1.13e+00 7.83e-01 1.28e+01
  angle pdb=" C   SER C 438 "
        pdb=" N   ASN C 439 "
        pdb=" CA  ASN C 439 "
      ideal   model   delta    sigma   weight residual
     121.14  115.95    5.19 1.75e+00 3.27e-01 8.80e+00
  angle pdb=" CA  ARG C 493 "
        pdb=" C   ARG C 493 "
        pdb=" O   ARG C 493 "
      ideal   model   delta    sigma   weight residual
     121.16  118.08    3.08 1.13e+00 7.83e-01 7.43e+00
  angle pdb=" CA  ARG C 346 "
        pdb=" C   ARG C 346 "
        pdb=" O   ARG C 346 "
      ideal   model   delta    sigma   weight residual
     120.66  117.69    2.97 1.15e+00 7.56e-01 6.65e+00
  angle pdb=" CA  LYS H  45 "
        pdb=" C   LYS H  45 "
        pdb=" O   LYS H  45 "
      ideal   model   delta    sigma   weight residual
     121.44  118.43    3.01 1.17e+00 7.31e-01 6.62e+00
  ... (remaining 4917 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.96: 1952
       17.96 -    35.91: 163
       35.91 -    53.87: 24
       53.87 -    71.82: 6
       71.82 -    89.78: 3
  Dihedral angle restraints: 2148
    sinusoidal: 836
      harmonic: 1312
  Sorted by residual:
  dihedral pdb=" CB  CYS C 336 "
           pdb=" SG  CYS C 336 "
           pdb=" SG  CYS C 361 "
           pdb=" CB  CYS C 361 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   35.32   57.68     1      1.00e+01 1.00e-02 4.47e+01
  dihedral pdb=" CA  PRO C 337 "
           pdb=" C   PRO C 337 "
           pdb=" N   PHE C 338 "
           pdb=" CA  PHE C 338 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.69   19.31     0      5.00e+00 4.00e-02 1.49e+01
  dihedral pdb=" CB  CYS H  23 "
           pdb=" SG  CYS H  23 "
           pdb=" SG  CYS H  88 "
           pdb=" CB  CYS H  88 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   63.07   29.93     1      1.00e+01 1.00e-02 1.28e+01
  ... (remaining 2145 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 375
       0.041 -    0.082: 106
       0.082 -    0.124: 43
       0.124 -    0.165: 3
       0.165 -    0.206: 2
  Chirality restraints: 529
  Sorted by residual:
  chirality pdb=" CB  ILE H  75 "
            pdb=" CA  ILE H  75 "
            pdb=" CG1 ILE H  75 "
            pdb=" CG2 ILE H  75 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.44    0.21 2.00e-01 2.50e+01 1.06e+00
  chirality pdb=" CA  THR H  94 "
            pdb=" N   THR H  94 "
            pdb=" C   THR H  94 "
            pdb=" CB  THR H  94 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.34    0.18 2.00e-01 2.50e+01 8.54e-01
  chirality pdb=" CA  ARG C 346 "
            pdb=" N   ARG C 346 "
            pdb=" C   ARG C 346 "
            pdb=" CB  ARG C 346 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.66   -0.15 2.00e-01 2.50e+01 5.60e-01
  ... (remaining 526 not shown)

  Planarity restraints: 638
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG H  24 "   -0.143 9.50e-02 1.11e+02   6.45e-02 3.09e+00
        pdb=" NE  ARG H  24 "    0.013 2.00e-02 2.50e+03
        pdb=" CZ  ARG H  24 "   -0.011 2.00e-02 2.50e+03
        pdb=" NH1 ARG H  24 "    0.006 2.00e-02 2.50e+03
        pdb=" NH2 ARG H  24 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR I 106 "    0.020 5.00e-02 4.00e+02   2.98e-02 1.42e+00
        pdb=" N   PRO I 107 "   -0.051 5.00e-02 4.00e+02
        pdb=" CA  PRO I 107 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO I 107 "    0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR I  60 "   -0.006 2.00e-02 2.50e+03   8.32e-03 1.39e+00
        pdb=" CG  TYR I  60 "    0.020 2.00e-02 2.50e+03
        pdb=" CD1 TYR I  60 "   -0.004 2.00e-02 2.50e+03
        pdb=" CD2 TYR I  60 "   -0.010 2.00e-02 2.50e+03
        pdb=" CE1 TYR I  60 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE2 TYR I  60 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ  TYR I  60 "    0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR I  60 "    0.000 2.00e-02 2.50e+03
  ... (remaining 635 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.81: 1013
        2.81 -     3.33: 3100
        3.33 -     3.85: 5601
        3.85 -     4.38: 6356
        4.38 -     4.90: 10946
  Nonbonded interactions: 27016
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP C 339 "
            pdb=" N   GLU C 340 "
     model   vdw
     2.282 3.120
  nonbonded pdb=" OD1 ASP I  62 "
            pdb=" N   SER I  63 "
     model   vdw
     2.309 3.120
  nonbonded pdb=" OG1 THR C 393 "
            pdb=" O   GLU C 516 "
     model   vdw
     2.310 3.040
  nonbonded pdb=" OD1 ASN H  34 "
            pdb=" OG  SER I 109 "
     model   vdw
     2.313 3.040
  nonbonded pdb=" OD1 ASP I  99 "
            pdb=" N   ARG I 100 "
     model   vdw
     2.322 3.120
  ... (remaining 27011 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:             5.320
  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:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     14.110
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.760
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.450
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7295
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   0.036   3627  Z= 0.198
  Angle     :  0.685   6.060   4932  Z= 0.391
  Chirality :  0.046   0.206    529
  Planarity :  0.004   0.065    638
  Dihedral  : 13.454  89.776   1297
  Min Nonbonded Distance : 2.282

Molprobity Statistics.
  All-atom Clashscore : 11.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.37 (0.36), residues: 445
  helix: -3.69 (0.62), residues: 26
  sheet:  0.38 (0.45), residues: 133
  loop : -1.33 (0.32), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP I 113 
 HIS   0.003   0.001   HIS I  35 
 PHE   0.016   0.001   PHE C 486 
 TYR   0.020   0.001   TYR I  60 
 ARG   0.013   0.001   ARG H  24 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.27965 (   90)
  hydrogen bonds       : angle      10.33063 (  240)
  SS BOND              : bond        0.00429 (    5)
  SS BOND              : angle       1.38584 (   10)
  covalent geometry    : bond        0.00350 ( 3622)
  covalent geometry    : angle       0.68236 ( 4922)

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

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

  890 Ramachandran restraints generated.
    445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  890 Ramachandran restraints generated.
    445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 0.404 
Fit side-chains
   revert: symmetry clash
REVERT: H   34 ASN cc_start: 0.8518 (m110) cc_final: 0.7462 (m110)
REVERT: H   97 TYR cc_start: 0.8609 (m-80) cc_final: 0.8334 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 107
  average time/residue: 0.1941
  time to fit residues: 24.3562
Evaluate side-chains
  95 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.430 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 36 optimal weight:    0.0060
   chunk 32 optimal weight:    3.9990
   chunk 18 optimal weight:    1.9990
   chunk 11 optimal weight:    0.6980
   chunk 21 optimal weight:    1.9990
   chunk 17 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 20 optimal weight:    3.9990
   chunk 25 optimal weight:    0.9980
   chunk 39 optimal weight:    0.7980
   overall best weight:    0.8998

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

Flipped N/Q/H residues before XYZ refinement:
** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 417 ASN
** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.123756 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.108267 restraints weight = 9391.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.112989 restraints weight = 7025.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.115239 restraints weight = 3785.878|
|-----------------------------------------------------------------------------|
r_work (final): 0.3819
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7359
moved from start:          0.2222

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   3627  Z= 0.197
  Angle     :  0.665   7.964   4932  Z= 0.344
  Chirality :  0.047   0.153    529
  Planarity :  0.004   0.033    638
  Dihedral  :  5.079  18.372    499
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 13.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 13.18 %
    Favored  : 84.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.21 (0.37), residues: 445
  helix: -3.70 (0.60), residues: 24
  sheet:  0.24 (0.44), residues: 141
  loop : -1.12 (0.34), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP I  36 
 HIS   0.002   0.001   HIS I  35 
 PHE   0.020   0.002   PHE C 486 
 TYR   0.018   0.002   TYR I 102 
 ARG   0.005   0.001   ARG H  61 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04522 (   90)
  hydrogen bonds       : angle       6.93091 (  240)
  SS BOND              : bond        0.00282 (    5)
  SS BOND              : angle       1.21429 (   10)
  covalent geometry    : bond        0.00436 ( 3622)
  covalent geometry    : angle       0.66352 ( 4922)

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

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

  890 Ramachandran restraints generated.
    445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  890 Ramachandran restraints generated.
    445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 98
  time to evaluate  : 0.431 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   49 TYR cc_start: 0.7693 (p90) cc_final: 0.7421 (p90)
REVERT: I   31 ASP cc_start: 0.8538 (p0) cc_final: 0.8111 (p0)
REVERT: I   59 ASP cc_start: 0.8146 (t0) cc_final: 0.7886 (t0)
  outliers start: 9
  outliers final: 6
  residues processed: 101
  average time/residue: 0.1628
  time to fit residues: 19.9951
Evaluate side-chains
  95 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 89
  time to evaluate  : 0.374 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  361 CYS
Chi-restraints excluded: chain H residue   22 THR
Chi-restraints excluded: chain H residue   48 ILE
Chi-restraints excluded: chain H residue   58 VAL
Chi-restraints excluded: chain H residue   65 SER
Chi-restraints excluded: chain H residue   75 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 25 optimal weight:    0.7980
   chunk 8 optimal weight:    1.9990
   chunk 28 optimal weight:    3.9990
   chunk 29 optimal weight:    4.9990
   chunk 11 optimal weight:    0.6980
   chunk 15 optimal weight:    0.7980
   chunk 12 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9980
   chunk 14 optimal weight:    0.8980
   chunk 10 optimal weight:    0.9990
   chunk 35 optimal weight:    3.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  89 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 = 0.3937 r_free = 0.3937 target = 0.122878 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.107501 restraints weight = 9165.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.112363 restraints weight = 6630.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.114379 restraints weight = 3583.889|
|-----------------------------------------------------------------------------|
r_work (final): 0.3808
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7375
moved from start:          0.2524

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   3627  Z= 0.186
  Angle     :  0.683   9.657   4932  Z= 0.350
  Chirality :  0.047   0.205    529
  Planarity :  0.004   0.033    638
  Dihedral  :  5.053  18.653    499
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 12.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 16.80 %
    Favored  : 80.10 %
  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: -1.26 (0.37), residues: 445
  helix: -3.57 (0.66), residues: 24
  sheet:  0.17 (0.46), residues: 134
  loop : -1.12 (0.33), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP C 436 
 HIS   0.004   0.002   HIS I  35 
 PHE   0.017   0.002   PHE C 486 
 TYR   0.019   0.002   TYR I 102 
 ARG   0.007   0.001   ARG H  24 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04040 (   90)
  hydrogen bonds       : angle       6.36352 (  240)
  SS BOND              : bond        0.00536 (    5)
  SS BOND              : angle       2.35362 (   10)
  covalent geometry    : bond        0.00422 ( 3622)
  covalent geometry    : angle       0.67533 ( 4922)

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

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

  890 Ramachandran restraints generated.
    445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  890 Ramachandran restraints generated.
    445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 96
  time to evaluate  : 0.434 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  339 ASP cc_start: 0.8418 (p0) cc_final: 0.7934 (t0)
REVERT: H   49 TYR cc_start: 0.7711 (p90) cc_final: 0.7413 (p90)
REVERT: H   81 GLU cc_start: 0.7948 (pp20) cc_final: 0.7523 (pp20)
REVERT: I   31 ASP cc_start: 0.8578 (p0) cc_final: 0.8167 (p0)
REVERT: I   59 ASP cc_start: 0.8154 (t0) cc_final: 0.7744 (t0)
REVERT: I  111 ASP cc_start: 0.9207 (t0) cc_final: 0.9005 (t0)
  outliers start: 12
  outliers final: 8
  residues processed: 102
  average time/residue: 0.1732
  time to fit residues: 21.2060
Evaluate side-chains
  96 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 88
  time to evaluate  : 0.444 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  361 CYS
Chi-restraints excluded: chain C residue  379 CYS
Chi-restraints excluded: chain C residue  494 SER
Chi-restraints excluded: chain H residue   22 THR
Chi-restraints excluded: chain H residue   58 VAL
Chi-restraints excluded: chain H residue   65 SER
Chi-restraints excluded: chain H residue   75 ILE
Chi-restraints excluded: chain I residue   37 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 17 optimal weight:    0.0870
   chunk 10 optimal weight:    1.9990
   chunk 29 optimal weight:    0.0470
   chunk 21 optimal weight:    0.7980
   chunk 5 optimal weight:    0.1980
   chunk 11 optimal weight:    0.7980
   chunk 15 optimal weight:    0.6980
   chunk 40 optimal weight:    3.9990
   chunk 9 optimal weight:    0.8980
   chunk 34 optimal weight:    0.9990
   chunk 0 optimal weight:    1.9990
   overall best weight:    0.3656

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

Flipped N/Q/H residues before XYZ refinement:
** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  89 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 = 0.3972 r_free = 0.3972 target = 0.125703 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.110039 restraints weight = 9470.827|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.115084 restraints weight = 6883.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.116267 restraints weight = 3670.122|
|-----------------------------------------------------------------------------|
r_work (final): 0.3820
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7333
moved from start:          0.2829

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   3627  Z= 0.124
  Angle     :  0.663   9.760   4932  Z= 0.331
  Chirality :  0.045   0.177    529
  Planarity :  0.004   0.032    638
  Dihedral  :  4.763  19.355    499
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 12.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 20.93 %
    Favored  : 75.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.15 (0.37), residues: 445
  helix: -3.47 (0.66), residues: 24
  sheet:  0.31 (0.45), residues: 132
  loop : -1.07 (0.33), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP I  53 
 HIS   0.004   0.001   HIS I  35 
 PHE   0.011   0.001   PHE H  62 
 TYR   0.019   0.001   TYR I 102 
 ARG   0.003   0.000   ARG H  24 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03531 (   90)
  hydrogen bonds       : angle       5.96476 (  240)
  SS BOND              : bond        0.00479 (    5)
  SS BOND              : angle       2.20091 (   10)
  covalent geometry    : bond        0.00295 ( 3622)
  covalent geometry    : angle       0.65654 ( 4922)

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

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

  890 Ramachandran restraints generated.
    445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  890 Ramachandran restraints generated.
    445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 101
  time to evaluate  : 0.419 
Fit side-chains
   revert: symmetry clash
REVERT: C  339 ASP cc_start: 0.8407 (p0) cc_final: 0.7918 (t0)
REVERT: C  340 GLU cc_start: 0.8682 (tm-30) cc_final: 0.8335 (tm-30)
REVERT: H   81 GLU cc_start: 0.7716 (pp20) cc_final: 0.7330 (pp20)
REVERT: I   31 ASP cc_start: 0.8496 (p0) cc_final: 0.8096 (p0)
REVERT: I   59 ASP cc_start: 0.8105 (t0) cc_final: 0.7628 (t0)
REVERT: I   60 TYR cc_start: 0.8448 (m-10) cc_final: 0.8217 (m-10)
REVERT: I  111 ASP cc_start: 0.9158 (t0) cc_final: 0.8956 (t0)
  outliers start: 12
  outliers final: 8
  residues processed: 105
  average time/residue: 0.1625
  time to fit residues: 20.7886
Evaluate side-chains
  94 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 86
  time to evaluate  : 0.424 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  350 VAL
Chi-restraints excluded: chain C residue  361 CYS
Chi-restraints excluded: chain C residue  379 CYS
Chi-restraints excluded: chain H residue   22 THR
Chi-restraints excluded: chain H residue   33 LEU
Chi-restraints excluded: chain H residue   58 VAL
Chi-restraints excluded: chain H residue   75 ILE
Chi-restraints excluded: chain I residue   37 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 35 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9980
   chunk 21 optimal weight:    0.5980
   chunk 10 optimal weight:    0.0470
   chunk 38 optimal weight:    1.9990
   chunk 12 optimal weight:    3.9990
   chunk 24 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 22 optimal weight:    1.9990
   chunk 32 optimal weight:    2.9990
   chunk 3 optimal weight:    0.6980
   overall best weight:    0.8680

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

Flipped N/Q/H residues before XYZ refinement:
** H  89 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 = 0.3937 r_free = 0.3937 target = 0.122892 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.107921 restraints weight = 9752.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.113256 restraints weight = 7392.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.114542 restraints weight = 3676.529|
|-----------------------------------------------------------------------------|
r_work (final): 0.3794
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7378
moved from start:          0.3063

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   3627  Z= 0.187
  Angle     :  0.677   8.280   4932  Z= 0.346
  Chirality :  0.046   0.182    529
  Planarity :  0.004   0.032    638
  Dihedral  :  5.043  22.521    499
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 14.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.94 %
    Favored  : 95.06 %
  Rotamer:
    Outliers :  4.13 %
    Allowed  : 20.93 %
    Favored  : 74.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.22 (0.37), residues: 445
  helix: -2.72 (0.85), residues: 18
  sheet:  0.02 (0.43), residues: 141
  loop : -1.15 (0.33), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C 436 
 HIS   0.004   0.002   HIS I  35 
 PHE   0.016   0.002   PHE C 486 
 TYR   0.020   0.002   TYR I 102 
 ARG   0.006   0.001   ARG H  24 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03699 (   90)
  hydrogen bonds       : angle       5.98720 (  240)
  SS BOND              : bond        0.00516 (    5)
  SS BOND              : angle       2.28673 (   10)
  covalent geometry    : bond        0.00422 ( 3622)
  covalent geometry    : angle       0.67007 ( 4922)

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

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

  890 Ramachandran restraints generated.
    445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  890 Ramachandran restraints generated.
    445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 92
  time to evaluate  : 0.384 
Fit side-chains
   revert: symmetry clash
REVERT: C  339 ASP cc_start: 0.8422 (p0) cc_final: 0.8034 (t70)
REVERT: C  340 GLU cc_start: 0.8662 (tm-30) cc_final: 0.8223 (tm-30)
REVERT: H   81 GLU cc_start: 0.7638 (pp20) cc_final: 0.7269 (pp20)
REVERT: I   31 ASP cc_start: 0.8535 (p0) cc_final: 0.8109 (p0)
REVERT: I   46 GLU cc_start: 0.8126 (mm-30) cc_final: 0.7911 (mm-30)
REVERT: I   59 ASP cc_start: 0.8137 (t0) cc_final: 0.7668 (t0)
REVERT: I   68 PHE cc_start: 0.7414 (OUTLIER) cc_final: 0.7213 (m-10)
REVERT: I   83 MET cc_start: 0.8462 (mmm) cc_final: 0.7382 (mmm)
  outliers start: 16
  outliers final: 11
  residues processed: 101
  average time/residue: 0.1789
  time to fit residues: 21.8519
Evaluate side-chains
  97 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 85
  time to evaluate  : 0.397 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  350 VAL
Chi-restraints excluded: chain C residue  361 CYS
Chi-restraints excluded: chain C residue  379 CYS
Chi-restraints excluded: chain C residue  425 LEU
Chi-restraints excluded: chain H residue   22 THR
Chi-restraints excluded: chain H residue   33 LEU
Chi-restraints excluded: chain H residue   58 VAL
Chi-restraints excluded: chain H residue   65 SER
Chi-restraints excluded: chain H residue   75 ILE
Chi-restraints excluded: chain I residue    5 VAL
Chi-restraints excluded: chain I residue   37 VAL
Chi-restraints excluded: chain I residue   68 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 15 optimal weight:    0.6980
   chunk 1 optimal weight:    0.8980
   chunk 25 optimal weight:    0.9980
   chunk 32 optimal weight:    1.9990
   chunk 21 optimal weight:    0.3980
   chunk 11 optimal weight:    1.9990
   chunk 20 optimal weight:    0.6980
   chunk 41 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9990
   chunk 39 optimal weight:    0.1980
   chunk 29 optimal weight:    0.8980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
** H  89 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 = 0.3949 r_free = 0.3949 target = 0.124265 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.108920 restraints weight = 9708.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.113557 restraints weight = 7036.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.115147 restraints weight = 3870.906|
|-----------------------------------------------------------------------------|
r_work (final): 0.3804
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7357
moved from start:          0.3278

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   3627  Z= 0.146
  Angle     :  0.668   9.905   4932  Z= 0.336
  Chirality :  0.045   0.173    529
  Planarity :  0.004   0.032    638
  Dihedral  :  4.928  21.829    499
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 12.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  4.13 %
    Allowed  : 21.71 %
    Favored  : 74.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.19 (0.37), residues: 445
  helix: -2.48 (0.90), residues: 18
  sheet:  0.16 (0.44), residues: 139
  loop : -1.20 (0.33), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 436 
 HIS   0.004   0.002   HIS I  35 
 PHE   0.010   0.001   PHE C 490 
 TYR   0.020   0.001   TYR I 102 
 ARG   0.006   0.001   ARG H  24 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03426 (   90)
  hydrogen bonds       : angle       5.85182 (  240)
  SS BOND              : bond        0.00474 (    5)
  SS BOND              : angle       2.22995 (   10)
  covalent geometry    : bond        0.00343 ( 3622)
  covalent geometry    : angle       0.66067 ( 4922)

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

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

  890 Ramachandran restraints generated.
    445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  890 Ramachandran restraints generated.
    445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 87
  time to evaluate  : 0.404 
Fit side-chains
   revert: symmetry clash
REVERT: C  339 ASP cc_start: 0.8407 (p0) cc_final: 0.7924 (t0)
REVERT: C  340 GLU cc_start: 0.8649 (tm-30) cc_final: 0.8256 (tm-30)
REVERT: H   81 GLU cc_start: 0.7653 (pp20) cc_final: 0.7281 (pp20)
REVERT: I   31 ASP cc_start: 0.8494 (p0) cc_final: 0.8090 (p0)
REVERT: I   59 ASP cc_start: 0.8111 (t0) cc_final: 0.7663 (t0)
REVERT: I   60 TYR cc_start: 0.8414 (m-10) cc_final: 0.8128 (m-10)
  outliers start: 16
  outliers final: 11
  residues processed: 95
  average time/residue: 0.1591
  time to fit residues: 18.4479
Evaluate side-chains
  95 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 84
  time to evaluate  : 0.409 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  350 VAL
Chi-restraints excluded: chain C residue  361 CYS
Chi-restraints excluded: chain C residue  379 CYS
Chi-restraints excluded: chain C residue  425 LEU
Chi-restraints excluded: chain H residue   22 THR
Chi-restraints excluded: chain H residue   33 LEU
Chi-restraints excluded: chain H residue   58 VAL
Chi-restraints excluded: chain H residue   65 SER
Chi-restraints excluded: chain H residue   75 ILE
Chi-restraints excluded: chain H residue   94 THR
Chi-restraints excluded: chain I residue    5 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 40 optimal weight:    0.7980
   chunk 41 optimal weight:    0.8980
   chunk 1 optimal weight:    0.6980
   chunk 27 optimal weight:    0.0050
   chunk 11 optimal weight:    2.9990
   chunk 21 optimal weight:    0.8980
   chunk 9 optimal weight:    2.9990
   chunk 17 optimal weight:    1.9990
   chunk 26 optimal weight:    0.1980
   chunk 34 optimal weight:    0.6980
   chunk 5 optimal weight:    0.0070
   overall best weight:    0.3212

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

Flipped N/Q/H residues before XYZ refinement:
C 414 GLN
H  89 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.126023 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.110606 restraints weight = 9628.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.115906 restraints weight = 6808.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.117362 restraints weight = 3447.251|
|-----------------------------------------------------------------------------|
r_work (final): 0.3839
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7300
moved from start:          0.3448

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   3627  Z= 0.122
  Angle     :  0.660   9.088   4932  Z= 0.331
  Chirality :  0.045   0.163    529
  Planarity :  0.004   0.031    638
  Dihedral  :  4.664  20.423    499
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 11.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  : 23.00 %
    Favored  : 73.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.20 (0.37), residues: 445
  helix: -2.63 (0.85), residues: 18
  sheet:  0.16 (0.44), residues: 139
  loop : -1.21 (0.33), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 436 
 HIS   0.004   0.001   HIS I  35 
 PHE   0.010   0.001   PHE I  29 
 TYR   0.019   0.001   TYR I 102 
 ARG   0.008   0.001   ARG H  24 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03317 (   90)
  hydrogen bonds       : angle       5.71634 (  240)
  SS BOND              : bond        0.00450 (    5)
  SS BOND              : angle       2.18568 (   10)
  covalent geometry    : bond        0.00298 ( 3622)
  covalent geometry    : angle       0.65366 ( 4922)

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

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

  890 Ramachandran restraints generated.
    445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  890 Ramachandran restraints generated.
    445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 87
  time to evaluate  : 0.437 
Fit side-chains
   revert: symmetry clash
REVERT: C  339 ASP cc_start: 0.8425 (p0) cc_final: 0.7894 (t0)
REVERT: C  340 GLU cc_start: 0.8686 (tm-30) cc_final: 0.8339 (tm-30)
REVERT: H   71 PHE cc_start: 0.6533 (m-80) cc_final: 0.6305 (m-80)
REVERT: H   81 GLU cc_start: 0.7649 (pp20) cc_final: 0.7282 (pp20)
REVERT: I   31 ASP cc_start: 0.8474 (p0) cc_final: 0.8086 (p0)
REVERT: I   59 ASP cc_start: 0.8109 (t0) cc_final: 0.7640 (t0)
REVERT: I   60 TYR cc_start: 0.8495 (m-10) cc_final: 0.8129 (m-10)
  outliers start: 14
  outliers final: 12
  residues processed: 95
  average time/residue: 0.1743
  time to fit residues: 19.9975
Evaluate side-chains
  94 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 82
  time to evaluate  : 0.380 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  338 PHE
Chi-restraints excluded: chain C residue  350 VAL
Chi-restraints excluded: chain C residue  361 CYS
Chi-restraints excluded: chain C residue  379 CYS
Chi-restraints excluded: chain H residue   22 THR
Chi-restraints excluded: chain H residue   33 LEU
Chi-restraints excluded: chain H residue   58 VAL
Chi-restraints excluded: chain H residue   65 SER
Chi-restraints excluded: chain H residue   75 ILE
Chi-restraints excluded: chain H residue   89 GLN
Chi-restraints excluded: chain H residue   94 THR
Chi-restraints excluded: chain I residue    5 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 12 optimal weight:    0.9980
   chunk 14 optimal weight:    3.9990
   chunk 31 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9980
   chunk 27 optimal weight:    5.9990
   chunk 23 optimal weight:    1.9990
   chunk 21 optimal weight:    0.0970
   chunk 6 optimal weight:    0.9990
   chunk 3 optimal weight:    0.9990
   chunk 15 optimal weight:    0.8980
   chunk 9 optimal weight:    1.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
H  89 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.123574 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.108513 restraints weight = 9582.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.112627 restraints weight = 6670.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.114063 restraints weight = 4103.633|
|-----------------------------------------------------------------------------|
r_work (final): 0.3787
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7385
moved from start:          0.3619

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   3627  Z= 0.179
  Angle     :  0.691   8.659   4932  Z= 0.350
  Chirality :  0.045   0.176    529
  Planarity :  0.004   0.036    638
  Dihedral  :  5.020  22.156    499
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 12.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.94 %
    Favored  : 95.06 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 21.96 %
    Favored  : 74.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.41 (0.36), residues: 445
  helix: -2.38 (0.94), residues: 18
  sheet: -0.08 (0.42), residues: 141
  loop : -1.34 (0.33), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 436 
 HIS   0.004   0.002   HIS I  35 
 PHE   0.012   0.002   PHE C 486 
 TYR   0.020   0.002   TYR I 102 
 ARG   0.008   0.001   ARG H  24 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03466 (   90)
  hydrogen bonds       : angle       5.86432 (  240)
  SS BOND              : bond        0.00529 (    5)
  SS BOND              : angle       2.21231 (   10)
  covalent geometry    : bond        0.00413 ( 3622)
  covalent geometry    : angle       0.68403 ( 4922)

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

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

  890 Ramachandran restraints generated.
    445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  890 Ramachandran restraints generated.
    445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 84
  time to evaluate  : 0.378 
Fit side-chains
   revert: symmetry clash
REVERT: C  339 ASP cc_start: 0.8441 (p0) cc_final: 0.7949 (t0)
REVERT: C  340 GLU cc_start: 0.8712 (tm-30) cc_final: 0.8363 (tm-30)
REVERT: H   37 GLN cc_start: 0.8479 (OUTLIER) cc_final: 0.8013 (tm-30)
REVERT: H   71 PHE cc_start: 0.6574 (m-80) cc_final: 0.6338 (m-80)
REVERT: H   81 GLU cc_start: 0.7678 (pp20) cc_final: 0.7442 (pp20)
REVERT: I   31 ASP cc_start: 0.8552 (p0) cc_final: 0.8150 (p0)
REVERT: I   59 ASP cc_start: 0.8141 (t0) cc_final: 0.7707 (t0)
REVERT: I   60 TYR cc_start: 0.8527 (m-10) cc_final: 0.8141 (m-10)
  outliers start: 15
  outliers final: 12
  residues processed: 91
  average time/residue: 0.1617
  time to fit residues: 17.9288
Evaluate side-chains
  94 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 81
  time to evaluate  : 0.405 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  350 VAL
Chi-restraints excluded: chain C residue  361 CYS
Chi-restraints excluded: chain C residue  379 CYS
Chi-restraints excluded: chain C residue  418 ILE
Chi-restraints excluded: chain H residue   22 THR
Chi-restraints excluded: chain H residue   33 LEU
Chi-restraints excluded: chain H residue   37 GLN
Chi-restraints excluded: chain H residue   58 VAL
Chi-restraints excluded: chain H residue   65 SER
Chi-restraints excluded: chain H residue   75 ILE
Chi-restraints excluded: chain H residue   89 GLN
Chi-restraints excluded: chain H residue   94 THR
Chi-restraints excluded: chain I residue    5 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 20 optimal weight:    0.8980
   chunk 21 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 31 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9980
   chunk 19 optimal weight:    1.9990
   chunk 39 optimal weight:    3.9990
   chunk 18 optimal weight:    0.0770
   chunk 40 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9980
   overall best weight:    0.7738

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

Flipped N/Q/H residues before XYZ refinement:
** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  89 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 = 0.3937 r_free = 0.3937 target = 0.123263 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.107855 restraints weight = 9464.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.112985 restraints weight = 7089.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.114015 restraints weight = 3672.510|
|-----------------------------------------------------------------------------|
r_work (final): 0.3789
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7389
moved from start:          0.3624

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   3627  Z= 0.179
  Angle     :  0.705   8.433   4932  Z= 0.359
  Chirality :  0.046   0.176    529
  Planarity :  0.004   0.036    638
  Dihedral  :  5.140  22.142    499
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 11.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.29 %
    Favored  : 93.71 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 24.55 %
    Favored  : 72.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.45 (0.36), residues: 445
  helix: -2.65 (0.90), residues: 18
  sheet:  0.01 (0.43), residues: 139
  loop : -1.41 (0.32), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 436 
 HIS   0.004   0.002   HIS I  35 
 PHE   0.012   0.001   PHE C 486 
 TYR   0.020   0.001   TYR I 102 
 ARG   0.008   0.001   ARG H  24 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03417 (   90)
  hydrogen bonds       : angle       5.92401 (  240)
  SS BOND              : bond        0.00505 (    5)
  SS BOND              : angle       2.22670 (   10)
  covalent geometry    : bond        0.00415 ( 3622)
  covalent geometry    : angle       0.69848 ( 4922)

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

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

  890 Ramachandran restraints generated.
    445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  890 Ramachandran restraints generated.
    445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 82
  time to evaluate  : 0.416 
Fit side-chains
   revert: symmetry clash
REVERT: C  339 ASP cc_start: 0.8408 (p0) cc_final: 0.7913 (t0)
REVERT: C  340 GLU cc_start: 0.8717 (tm-30) cc_final: 0.8382 (tm-30)
REVERT: H   37 GLN cc_start: 0.8492 (OUTLIER) cc_final: 0.8034 (tm-30)
REVERT: H   71 PHE cc_start: 0.6615 (m-80) cc_final: 0.6410 (m-80)
REVERT: I   59 ASP cc_start: 0.8126 (t0) cc_final: 0.7703 (t0)
REVERT: I   60 TYR cc_start: 0.8524 (m-10) cc_final: 0.8133 (m-10)
  outliers start: 10
  outliers final: 9
  residues processed: 87
  average time/residue: 0.1715
  time to fit residues: 18.1950
Evaluate side-chains
  90 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 80
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  350 VAL
Chi-restraints excluded: chain C residue  379 CYS
Chi-restraints excluded: chain H residue   22 THR
Chi-restraints excluded: chain H residue   33 LEU
Chi-restraints excluded: chain H residue   37 GLN
Chi-restraints excluded: chain H residue   58 VAL
Chi-restraints excluded: chain H residue   65 SER
Chi-restraints excluded: chain H residue   75 ILE
Chi-restraints excluded: chain H residue   94 THR
Chi-restraints excluded: chain I residue    5 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 30 optimal weight:    1.9990
   chunk 37 optimal weight:    0.0170
   chunk 4 optimal weight:    0.0970
   chunk 25 optimal weight:    0.0020
   chunk 38 optimal weight:    0.5980
   chunk 7 optimal weight:    1.9990
   chunk 20 optimal weight:    0.6980
   chunk 33 optimal weight:    0.6980
   chunk 5 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9990
   chunk 12 optimal weight:    0.4980
   overall best weight:    0.2424

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

Flipped N/Q/H residues before XYZ refinement:
** H  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  89 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 = 0.3982 r_free = 0.3982 target = 0.126473 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.111687 restraints weight = 9641.407|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.115313 restraints weight = 6527.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.117443 restraints weight = 4017.440|
|-----------------------------------------------------------------------------|
r_work (final): 0.3842
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7292
moved from start:          0.3893

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   3627  Z= 0.127
  Angle     :  0.721   8.736   4932  Z= 0.362
  Chirality :  0.046   0.209    529
  Planarity :  0.004   0.037    638
  Dihedral  :  4.737  24.991    499
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 11.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 25.32 %
    Favored  : 72.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.27 (0.36), residues: 445
  helix: -2.73 (0.87), residues: 18
  sheet:  0.25 (0.45), residues: 132
  loop : -1.30 (0.32), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP I  36 
 HIS   0.004   0.001   HIS I  35 
 PHE   0.011   0.001   PHE I  29 
 TYR   0.019   0.001   TYR I 102 
 ARG   0.009   0.001   ARG H  24 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03265 (   90)
  hydrogen bonds       : angle       5.65463 (  240)
  SS BOND              : bond        0.00442 (    5)
  SS BOND              : angle       2.15147 (   10)
  covalent geometry    : bond        0.00313 ( 3622)
  covalent geometry    : angle       0.71508 ( 4922)

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

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

  890 Ramachandran restraints generated.
    445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  890 Ramachandran restraints generated.
    445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 87
  time to evaluate  : 0.430 
Fit side-chains
   revert: symmetry clash
REVERT: C  409 GLN cc_start: 0.6602 (tt0) cc_final: 0.6338 (tt0)
REVERT: I   59 ASP cc_start: 0.8095 (t0) cc_final: 0.7650 (t0)
REVERT: I   60 TYR cc_start: 0.8517 (m-10) cc_final: 0.8153 (m-10)
  outliers start: 7
  outliers final: 6
  residues processed: 90
  average time/residue: 0.1803
  time to fit residues: 19.4969
Evaluate side-chains
  89 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 83
  time to evaluate  : 0.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  338 PHE
Chi-restraints excluded: chain C residue  350 VAL
Chi-restraints excluded: chain C residue  379 CYS
Chi-restraints excluded: chain H residue   75 ILE
Chi-restraints excluded: chain H residue   94 THR
Chi-restraints excluded: chain I residue    5 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 39 optimal weight:    0.4980
   chunk 41 optimal weight:    0.5980
   chunk 32 optimal weight:    0.0020
   chunk 14 optimal weight:    3.9990
   chunk 18 optimal weight:    0.0470
   chunk 35 optimal weight:    0.7980
   chunk 7 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9990
   chunk 1 optimal weight:    3.9990
   chunk 12 optimal weight:    1.9990
   overall best weight:    0.3886

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

Flipped N/Q/H residues before XYZ refinement:
H  34 ASN
H  89 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.125981 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.111399 restraints weight = 9604.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.115178 restraints weight = 6575.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.117188 restraints weight = 3816.140|
|-----------------------------------------------------------------------------|
r_work (final): 0.3837
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7296
moved from start:          0.4133

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   3627  Z= 0.137
  Angle     :  0.742   9.116   4932  Z= 0.376
  Chirality :  0.046   0.203    529
  Planarity :  0.004   0.040    638
  Dihedral  :  4.864  31.355    499
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 11.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.39 %
    Favored  : 94.61 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 25.58 %
    Favored  : 72.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.17 %
    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: -1.30 (0.36), residues: 445
  helix: -2.64 (0.89), residues: 18
  sheet:  0.20 (0.44), residues: 133
  loop : -1.32 (0.32), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP I 113 
 HIS   0.003   0.001   HIS I  35 
 PHE   0.019   0.001   PHE H  71 
 TYR   0.020   0.001   TYR I 112 
 ARG   0.006   0.000   ARG C 493 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03310 (   90)
  hydrogen bonds       : angle       5.64325 (  240)
  SS BOND              : bond        0.00470 (    5)
  SS BOND              : angle       2.11242 (   10)
  covalent geometry    : bond        0.00335 ( 3622)
  covalent geometry    : angle       0.73650 ( 4922)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2023.74 seconds
wall clock time: 35 minutes 27.48 seconds (2127.48 seconds total)