Starting phenix.real_space_refine
on Tue Feb  3 14:45:06 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9c7s_45287/02_2026/9c7s_45287.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9c7s_45287/02_2026/9c7s_45287.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9c7s_45287/02_2026/9c7s_45287.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9c7s_45287/02_2026/9c7s_45287.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9c7s_45287/02_2026/9c7s_45287.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9c7s_45287/02_2026/9c7s_45287.cif"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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=   0.015
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      17      5.16       5
     C    2429      2.51       5
     N     654      2.21       5
     O     737      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3837
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "C"
      Number of atoms: 2123
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 268, 2123
          Classifications: {'peptide': 268}
          Link IDs: {'PTRANS': 16, 'TRANS': 251}
    Chain: "H"
      Number of atoms: 889
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 116, 889
          Classifications: {'peptide': 116}
          Link IDs: {'PTRANS': 3, 'TRANS': 112}
    Chain: "L"
      Number of atoms: 797
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 797
          Classifications: {'peptide': 107}
          Link IDs: {'PTRANS': 6, 'TRANS': 100}
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Time building chain proxies: 0.76, per 1000 atoms: 0.20
  Number of scatterers: 3837
  At special positions: 0
  Unit cell: (94.1385, 113.549, 59.2005, 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      17     16.00
     O     737      8.00
     N     654      7.00
     C    2429      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS C 336 " - pdb=" SG  CYS C 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 391 " - pdb=" SG  CYS C 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  22 " - pdb=" SG  CYS L  89 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.18
  Conformation dependent library (CDL) restraints added in 157.7 milliseconds
  

  970 Ramachandran restraints generated.
    485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  894

  Finding SS restraints...
    Secondary structure from input PDB file:
      5 helices and 11 sheets defined
      6.7% alpha, 20.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.08
  Creating SS restraints...
    Processing helix  chain 'C' and resid 337 through 343
    Processing helix  chain 'C' and resid 365 through 371
    Processing helix  chain 'C' and resid 405 through 411
      removed outlier: 4.625A  pdb=" N   SER C 408 " --> pdb=" O   ASN C 405 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   ALA C 411 " --> pdb=" O   SER C 408 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 416 through 421
    Processing helix  chain 'L' and resid 25 through 30
    Processing sheet with id=AA1, first strand: chain 'C' and resid 354 through 358
      removed outlier: 3.814A  pdb=" N   ASN C 354 " --> pdb=" O   SER C 399 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   SER C 399 " --> pdb=" O   ASN C 354 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   LYS C 356 " --> pdb=" O   ALA C 397 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   ALA C 397 " --> pdb=" O   LYS C 356 " (cutoff:3.500A)
      removed outlier: 4.218A  pdb=" N   VAL C 395 " --> pdb=" O   ILE C 358 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   TYR C 396 " --> pdb=" O   SER C 514 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   CYS C 432 " --> pdb=" O   LEU C 513 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   ALA C 376 " --> pdb=" O   ALA C 435 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 361 through 362
      removed outlier: 6.819A  pdb=" N   CYS C 361 " --> pdb=" O   CYS C 525 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'C' and resid 452 through 453
    Processing sheet with id=AA4, first strand: chain 'C' and resid 538 through 543
    Processing sheet with id=AA5, first strand: chain 'C' and resid 575 through 577
    Processing sheet with id=AA6, first strand: chain 'H' and resid 3 through 4
    Processing sheet with id=AA7, first strand: chain 'H' and resid 58 through 60
      removed outlier: 6.649A  pdb=" N   TRP H  36 " --> pdb=" O   MET H  48 " (cutoff:3.500A)
      removed outlier: 5.454A  pdb=" N   ILE H  50 " --> pdb=" O   LEU H  34 " (cutoff:3.500A)
      removed outlier: 7.527A  pdb=" N   LEU H  34 " --> pdb=" O   ILE H  50 " (cutoff:3.500A)
      removed outlier: 5.674A  pdb=" N   CYS H  96 " --> pdb=" O   TRP H 110 " (cutoff:3.500A)
      removed outlier: 4.242A  pdb=" N   TRP H 110 " --> pdb=" O   CYS H  96 " (cutoff:3.500A)
      removed outlier: 6.590A  pdb=" N   ARG H  98 " --> pdb=" O   ASP H 108 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'H' and resid 71 through 73
      removed outlier: 3.672A  pdb=" N   THR H  71 " --> pdb=" O   TYR H  80 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   VAL H  73 " --> pdb=" O   THR H  78 " (cutoff:3.500A)
      removed outlier: 4.054A  pdb=" N   THR H  78 " --> pdb=" O   VAL H  73 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'L' and resid 16 through 21
      removed outlier: 4.640A  pdb=" N   GLN L  16 " --> pdb=" O   GLY L  78 " (cutoff:3.500A)
      removed outlier: 3.873A  pdb=" N   GLY L  78 " --> pdb=" O   GLN L  16 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   SER L  64 " --> pdb=" O   ALA L  75 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'L' and resid 37 through 38
    Processing sheet with id=AB2, first strand: chain 'L' and resid 91 through 95

    72 hydrogen bonds defined for protein.
    183 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: 0.30

  Time building geometry restraints manager: 0.25 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1244
        1.34 -     1.46: 998
        1.46 -     1.58: 1670
        1.58 -     1.70: 0
        1.70 -     1.82: 21
  Bond restraints: 3933
  Sorted by residual:
  bond pdb=" C   VAL C 382 "
       pdb=" N   SER C 383 "
    ideal  model  delta    sigma   weight residual
    1.331  1.308  0.024 1.59e-02 3.96e+03 2.19e+00
  bond pdb=" C1  NAG C 601 "
       pdb=" O5  NAG C 601 "
    ideal  model  delta    sigma   weight residual
    1.406  1.432 -0.026 2.00e-02 2.50e+03 1.71e+00
  bond pdb=" CA  ASP C 571 "
       pdb=" CB  ASP C 571 "
    ideal  model  delta    sigma   weight residual
    1.532  1.549 -0.017 1.33e-02 5.65e+03 1.58e+00
  bond pdb=" CB  ASP C 571 "
       pdb=" CG  ASP C 571 "
    ideal  model  delta    sigma   weight residual
    1.516  1.547 -0.031 2.50e-02 1.60e+03 1.51e+00
  bond pdb=" CB  LYS C 440 "
       pdb=" CG  LYS C 440 "
    ideal  model  delta    sigma   weight residual
    1.520  1.554 -0.034 3.00e-02 1.11e+03 1.32e+00
  ... (remaining 3928 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.10: 5192
        2.10 -     4.20: 122
        4.20 -     6.29: 23
        6.29 -     8.39: 6
        8.39 -    10.49: 3
  Bond angle restraints: 5346
  Sorted by residual:
  angle pdb=" C   ASP C 420 "
        pdb=" N   TYR C 421 "
        pdb=" CA  TYR C 421 "
      ideal   model   delta    sigma   weight residual
     121.54  114.01    7.53 1.91e+00 2.74e-01 1.55e+01
  angle pdb=" CB  LYS C 440 "
        pdb=" CG  LYS C 440 "
        pdb=" CD  LYS C 440 "
      ideal   model   delta    sigma   weight residual
     111.30  119.84   -8.54 2.30e+00 1.89e-01 1.38e+01
  angle pdb=" CB  MET H  48 "
        pdb=" CG  MET H  48 "
        pdb=" SD  MET H  48 "
      ideal   model   delta    sigma   weight residual
     112.70  123.19  -10.49 3.00e+00 1.11e-01 1.22e+01
  angle pdb=" CA  MET H  81 "
        pdb=" CB  MET H  81 "
        pdb=" CG  MET H  81 "
      ideal   model   delta    sigma   weight residual
     114.10  121.04   -6.94 2.00e+00 2.50e-01 1.21e+01
  angle pdb=" C   TYR H  80 "
        pdb=" N   MET H  81 "
        pdb=" CA  MET H  81 "
      ideal   model   delta    sigma   weight residual
     122.81  117.46    5.35 1.68e+00 3.54e-01 1.01e+01
  ... (remaining 5341 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.19: 1936
       17.19 -    34.37: 306
       34.37 -    51.56: 70
       51.56 -    68.74: 21
       68.74 -    85.93: 7
  Dihedral angle restraints: 2340
    sinusoidal: 933
      harmonic: 1407
  Sorted by residual:
  dihedral pdb=" CB  CYS L  22 "
           pdb=" SG  CYS L  22 "
           pdb=" SG  CYS L  89 "
           pdb=" CB  CYS L  89 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  122.98  -29.98     1      1.00e+01 1.00e-02 1.28e+01
  dihedral pdb=" CB  CYS C 391 "
           pdb=" SG  CYS C 391 "
           pdb=" SG  CYS C 525 "
           pdb=" CB  CYS C 525 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  122.54  -29.54     1      1.00e+01 1.00e-02 1.25e+01
  dihedral pdb=" CA  ASP H 108 "
           pdb=" CB  ASP H 108 "
           pdb=" CG  ASP H 108 "
           pdb=" OD1 ASP H 108 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -86.26   56.26     1      2.00e+01 2.50e-03 1.07e+01
  ... (remaining 2337 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 368
       0.035 -    0.070: 137
       0.070 -    0.105: 48
       0.105 -    0.139: 20
       0.139 -    0.174: 5
  Chirality restraints: 578
  Sorted by residual:
  chirality pdb=" CA  ASP C 571 "
            pdb=" N   ASP C 571 "
            pdb=" C   ASP C 571 "
            pdb=" CB  ASP C 571 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.59e-01
  chirality pdb=" CA  GLU L  42 "
            pdb=" N   GLU L  42 "
            pdb=" C   GLU L  42 "
            pdb=" CB  GLU L  42 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.79e-01
  chirality pdb=" CB  ILE C 587 "
            pdb=" CA  ILE C 587 "
            pdb=" CG1 ILE C 587 "
            pdb=" CG2 ILE C 587 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.80   -0.15 2.00e-01 2.50e+01 5.89e-01
  ... (remaining 575 not shown)

  Planarity restraints: 696
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP H  52 "   -0.052 5.00e-02 4.00e+02   7.77e-02 9.66e+00
        pdb=" N   PRO H  53 "    0.134 5.00e-02 4.00e+02
        pdb=" CA  PRO H  53 "   -0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO H  53 "   -0.043 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG C 498 "   -0.035 5.00e-02 4.00e+02   5.36e-02 4.60e+00
        pdb=" N   PRO C 499 "    0.093 5.00e-02 4.00e+02
        pdb=" CA  PRO C 499 "   -0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO C 499 "   -0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP H 103 "   -0.014 2.00e-02 2.50e+03   1.11e-02 3.08e+00
        pdb=" CG  TRP H 103 "    0.030 2.00e-02 2.50e+03
        pdb=" CD1 TRP H 103 "   -0.011 2.00e-02 2.50e+03
        pdb=" CD2 TRP H 103 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP H 103 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP H 103 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP H 103 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP H 103 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ3 TRP H 103 "    0.000 2.00e-02 2.50e+03
        pdb=" CH2 TRP H 103 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 693 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 173
        2.71 -     3.25: 4022
        3.25 -     3.80: 6254
        3.80 -     4.35: 7703
        4.35 -     4.90: 12347
  Nonbonded interactions: 30499
  Sorted by model distance:
  nonbonded pdb=" O   GLY L  24 "
            pdb=" OG1 THR L  70 "
     model   vdw
     2.157 3.040
  nonbonded pdb=" OD1 ASP C 364 "
            pdb=" OG  SER C 366 "
     model   vdw
     2.173 3.040
  nonbonded pdb=" OE1 GLU H  10 "
            pdb=" OG1 THR H 114 "
     model   vdw
     2.175 3.040
  nonbonded pdb=" O   PHE H 107 "
            pdb=" OH  TYR L  37 "
     model   vdw
     2.176 3.040
  nonbonded pdb=" OH  TYR C 351 "
            pdb=" O   ILE C 468 "
     model   vdw
     2.201 3.040
  ... (remaining 30494 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:             4.420
  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:          0.040
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     4.480
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.000
  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:0.960
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.930
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6743
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   0.045   3937  Z= 0.168
  Angle     :  0.815  10.489   5354  Z= 0.416
  Chirality :  0.046   0.174    578
  Planarity :  0.006   0.078    696
  Dihedral  : 18.162  85.928   1434
  Min Nonbonded Distance : 2.157

Molprobity Statistics.
  All-atom Clashscore : 21.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.95 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  : 42.03 %
    Favored  : 57.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.72 (0.37), residues: 485
  helix: -3.03 (0.83), residues: 20
  sheet: -0.36 (0.40), residues: 160
  loop : -0.28 (0.35), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C 457 
 TYR   0.011   0.001   TYR L  50 
 PHE   0.008   0.001   PHE C 497 
 TRP   0.030   0.003   TRP H 103 
 HIS   0.004   0.001   HIS C 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 ( 3933)
  covalent geometry    : angle       0.81517 ( 5346)
  SS BOND              : bond        0.00118 (    4)
  SS BOND              : angle       0.44020 (    8)
  hydrogen bonds       : bond        0.29193 (   72)
  hydrogen bonds       : angle      11.34694 (  183)

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

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

  970 Ramachandran restraints generated.
    485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  970 Ramachandran restraints generated.
    485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 137
  time to evaluate  : 0.096 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  400 PHE cc_start: 0.7668 (p90) cc_final: 0.6958 (p90)
  outliers start: 3
  outliers final: 2
  residues processed: 137
  average time/residue: 0.0618
  time to fit residues: 10.3773
Evaluate side-chains
  132 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 130
  time to evaluate  : 0.084 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  394 ASN
Chi-restraints excluded: chain C residue  428 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 24 optimal weight:    0.7980
   chunk 26 optimal weight:    4.9990
   chunk 2 optimal weight:    0.9990
   chunk 16 optimal weight:    0.0050
   chunk 32 optimal weight:    0.0870
   chunk 31 optimal weight:    0.7980
   chunk 25 optimal weight:    0.9980
   chunk 19 optimal weight:    0.6980
   chunk 30 optimal weight:    0.9990
   chunk 22 optimal weight:    0.7980
   chunk 37 optimal weight:    0.0770
   overall best weight:    0.3330

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

Flipped N/Q/H residues before XYZ refinement:
** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 580 GLN
H  77 ASN
L  28 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4021 r_free = 0.4021 target = 0.146658 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.127385 restraints weight = 8013.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.131549 restraints weight = 4409.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.134368 restraints weight = 2769.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.136325 restraints weight = 1913.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.137698 restraints weight = 1411.573|
|-----------------------------------------------------------------------------|
r_work (final): 0.3908
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6691
moved from start:          0.1184

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.067   3937  Z= 0.135
  Angle     :  0.651   5.815   5354  Z= 0.340
  Chirality :  0.045   0.171    578
  Planarity :  0.005   0.051    696
  Dihedral  :  4.712  25.544    580
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 13.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.74 %
    Favored  : 95.26 %
  Rotamer:
    Outliers :  9.42 %
    Allowed  : 31.40 %
    Favored  : 59.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.76 (0.38), residues: 485
  helix: -2.72 (0.74), residues: 32
  sheet: -0.51 (0.42), residues: 143
  loop : -0.16 (0.36), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C 457 
 TYR   0.011   0.001   TYR C 351 
 PHE   0.015   0.001   PHE H  64 
 TRP   0.017   0.002   TRP H 103 
 HIS   0.005   0.002   HIS C 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 3933)
  covalent geometry    : angle       0.65160 ( 5346)
  SS BOND              : bond        0.00092 (    4)
  SS BOND              : angle       0.48452 (    8)
  hydrogen bonds       : bond        0.04842 (   72)
  hydrogen bonds       : angle       7.81874 (  183)

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

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

  970 Ramachandran restraints generated.
    485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  970 Ramachandran restraints generated.
    485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 151
  time to evaluate  : 0.087 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  417 ASN cc_start: 0.8373 (t0) cc_final: 0.8091 (t0)
REVERT: C  425 LEU cc_start: 0.8676 (tp) cc_final: 0.8405 (tp)
REVERT: C  441 LEU cc_start: 0.7447 (OUTLIER) cc_final: 0.7245 (pp)
REVERT: C  442 ASP cc_start: 0.7905 (OUTLIER) cc_final: 0.7662 (m-30)
REVERT: C  495 TYR cc_start: 0.7567 (OUTLIER) cc_final: 0.6582 (p90)
REVERT: C  558 LYS cc_start: 0.7526 (mmtm) cc_final: 0.6497 (mmtm)
REVERT: H   48 MET cc_start: 0.6267 (mmm) cc_final: 0.6023 (mmm)
REVERT: H   81 MET cc_start: 0.7711 (ppp) cc_final: 0.7408 (ppp)
REVERT: H   83 MET cc_start: 0.3641 (tpt) cc_final: 0.3407 (tpt)
REVERT: L   39 GLN cc_start: 0.6773 (OUTLIER) cc_final: 0.6455 (tp40)
REVERT: L   55 ARG cc_start: 0.7261 (ptp90) cc_final: 0.6881 (ptp90)
  outliers start: 39
  outliers final: 18
  residues processed: 166
  average time/residue: 0.0628
  time to fit residues: 12.6208
Evaluate side-chains
  171 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 149
  time to evaluate  : 0.099 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  350 VAL
Chi-restraints excluded: chain C residue  383 SER
Chi-restraints excluded: chain C residue  399 SER
Chi-restraints excluded: chain C residue  405 ASN
Chi-restraints excluded: chain C residue  424 LYS
Chi-restraints excluded: chain C residue  441 LEU
Chi-restraints excluded: chain C residue  442 ASP
Chi-restraints excluded: chain C residue  495 TYR
Chi-restraints excluded: chain C residue  534 VAL
Chi-restraints excluded: chain C residue  555 SER
Chi-restraints excluded: chain C residue  560 LEU
Chi-restraints excluded: chain C residue  569 ILE
Chi-restraints excluded: chain H residue   28 THR
Chi-restraints excluded: chain H residue  102 LYS
Chi-restraints excluded: chain H residue  107 PHE
Chi-restraints excluded: chain L residue   25 SER
Chi-restraints excluded: chain L residue   34 VAL
Chi-restraints excluded: chain L residue   37 TYR
Chi-restraints excluded: chain L residue   39 GLN
Chi-restraints excluded: chain L residue   50 TYR
Chi-restraints excluded: chain L residue   52 ASN
Chi-restraints excluded: chain L residue   68 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 45 optimal weight:    0.9980
   chunk 6 optimal weight:    0.8980
   chunk 42 optimal weight:    0.0010
   chunk 1 optimal weight:    0.6980
   chunk 27 optimal weight:    0.8980
   chunk 19 optimal weight:    0.4980
   chunk 20 optimal weight:    0.0770
   chunk 39 optimal weight:    0.8980
   chunk 46 optimal weight:    0.9980
   chunk 12 optimal weight:    1.9990
   chunk 21 optimal weight:    0.1980
   overall best weight:    0.2944

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

Flipped N/Q/H residues before XYZ refinement:
C 409 GLN
C 414 GLN
** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4043 r_free = 0.4043 target = 0.150102 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.129549 restraints weight = 7776.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.134155 restraints weight = 4139.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.137277 restraints weight = 2539.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.139393 restraints weight = 1712.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.140734 restraints weight = 1240.754|
|-----------------------------------------------------------------------------|
r_work (final): 0.3894
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6683
moved from start:          0.1568

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062   3937  Z= 0.127
  Angle     :  0.661   7.382   5354  Z= 0.337
  Chirality :  0.046   0.202    578
  Planarity :  0.005   0.047    696
  Dihedral  :  4.432  15.021    576
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 12.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.54 %
    Favored  : 95.46 %
  Rotamer:
    Outliers :  8.94 %
    Allowed  : 34.06 %
    Favored  : 57.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.77 (0.38), residues: 485
  helix: -2.78 (0.69), residues: 32
  sheet: -0.38 (0.43), residues: 135
  loop : -0.25 (0.36), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG H  45 
 TYR   0.014   0.001   TYR C 495 
 PHE   0.024   0.002   PHE H  64 
 TRP   0.018   0.002   TRP H 103 
 HIS   0.004   0.002   HIS C 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 3933)
  covalent geometry    : angle       0.66108 ( 5346)
  SS BOND              : bond        0.00090 (    4)
  SS BOND              : angle       0.50861 (    8)
  hydrogen bonds       : bond        0.04356 (   72)
  hydrogen bonds       : angle       7.24935 (  183)

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

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

  970 Ramachandran restraints generated.
    485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  970 Ramachandran restraints generated.
    485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 144
  time to evaluate  : 0.102 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  417 ASN cc_start: 0.8536 (t0) cc_final: 0.8314 (t0)
REVERT: C  425 LEU cc_start: 0.8577 (tp) cc_final: 0.8303 (tp)
REVERT: C  441 LEU cc_start: 0.7437 (OUTLIER) cc_final: 0.7223 (pp)
REVERT: C  442 ASP cc_start: 0.7897 (OUTLIER) cc_final: 0.7619 (m-30)
REVERT: C  453 TYR cc_start: 0.7134 (p90) cc_final: 0.6676 (p90)
REVERT: C  495 TYR cc_start: 0.7487 (OUTLIER) cc_final: 0.6376 (p90)
REVERT: C  497 PHE cc_start: 0.8055 (m-80) cc_final: 0.7497 (m-80)
REVERT: C  558 LYS cc_start: 0.7415 (mmtm) cc_final: 0.6942 (mmtm)
REVERT: H   13 LYS cc_start: 0.5824 (OUTLIER) cc_final: 0.4446 (tppt)
REVERT: H   48 MET cc_start: 0.6393 (mmm) cc_final: 0.5981 (mmm)
REVERT: H   81 MET cc_start: 0.7785 (ppp) cc_final: 0.7419 (ppp)
REVERT: H   83 MET cc_start: 0.3727 (tpt) cc_final: 0.3474 (tpt)
REVERT: L   51 ASN cc_start: 0.7581 (m-40) cc_final: 0.7106 (m-40)
REVERT: L   55 ARG cc_start: 0.7161 (ptp90) cc_final: 0.6769 (ptp90)
REVERT: L   66 SER cc_start: 0.7946 (t) cc_final: 0.7743 (p)
  outliers start: 37
  outliers final: 19
  residues processed: 160
  average time/residue: 0.0582
  time to fit residues: 11.2378
Evaluate side-chains
  163 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 140
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  350 VAL
Chi-restraints excluded: chain C residue  356 LYS
Chi-restraints excluded: chain C residue  383 SER
Chi-restraints excluded: chain C residue  399 SER
Chi-restraints excluded: chain C residue  407 VAL
Chi-restraints excluded: chain C residue  424 LYS
Chi-restraints excluded: chain C residue  441 LEU
Chi-restraints excluded: chain C residue  442 ASP
Chi-restraints excluded: chain C residue  495 TYR
Chi-restraints excluded: chain C residue  514 SER
Chi-restraints excluded: chain C residue  555 SER
Chi-restraints excluded: chain C residue  560 LEU
Chi-restraints excluded: chain C residue  569 ILE
Chi-restraints excluded: chain C residue  581 THR
Chi-restraints excluded: chain H residue   13 LYS
Chi-restraints excluded: chain H residue   28 THR
Chi-restraints excluded: chain H residue   37 LEU
Chi-restraints excluded: chain H residue  102 LYS
Chi-restraints excluded: chain H residue  107 PHE
Chi-restraints excluded: chain L residue    4 LEU
Chi-restraints excluded: chain L residue   34 VAL
Chi-restraints excluded: chain L residue   50 TYR
Chi-restraints excluded: chain L residue   52 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 7 optimal weight:    0.7980
   chunk 43 optimal weight:    2.9990
   chunk 27 optimal weight:    0.0970
   chunk 12 optimal weight:    0.7980
   chunk 33 optimal weight:    1.9990
   chunk 1 optimal weight:    0.5980
   chunk 10 optimal weight:    2.9990
   chunk 24 optimal weight:    0.0970
   chunk 26 optimal weight:    0.2980
   chunk 21 optimal weight:    0.8980
   chunk 32 optimal weight:    2.9990
   overall best weight:    0.3776

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

Flipped N/Q/H residues before XYZ refinement:
** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 519 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.148124 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.127946 restraints weight = 7612.304|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.132492 restraints weight = 4091.300|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.135462 restraints weight = 2533.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.137562 restraints weight = 1721.167|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.138918 restraints weight = 1254.656|
|-----------------------------------------------------------------------------|
r_work (final): 0.3879
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6699
moved from start:          0.2098

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.069   3937  Z= 0.147
  Angle     :  0.650   7.683   5354  Z= 0.340
  Chirality :  0.045   0.205    578
  Planarity :  0.005   0.045    696
  Dihedral  :  4.492  14.865    576
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 13.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.77 %
    Favored  : 94.23 %
  Rotamer:
    Outliers :  9.66 %
    Allowed  : 31.88 %
    Favored  : 58.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.66 (0.38), residues: 485
  helix: -2.62 (0.77), residues: 26
  sheet: -0.37 (0.42), residues: 144
  loop : -0.20 (0.37), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG H  45 
 TYR   0.014   0.001   TYR C 495 
 PHE   0.017   0.001   PHE H 107 
 TRP   0.021   0.002   TRP L 101 
 HIS   0.006   0.002   HIS C 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 ( 3933)
  covalent geometry    : angle       0.65065 ( 5346)
  SS BOND              : bond        0.00119 (    4)
  SS BOND              : angle       0.44965 (    8)
  hydrogen bonds       : bond        0.04099 (   72)
  hydrogen bonds       : angle       7.09350 (  183)

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

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

  970 Ramachandran restraints generated.
    485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  970 Ramachandran restraints generated.
    485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 147
  time to evaluate  : 0.085 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  423 TYR cc_start: 0.4784 (OUTLIER) cc_final: 0.3686 (t80)
REVERT: C  425 LEU cc_start: 0.8551 (tp) cc_final: 0.8311 (tp)
REVERT: C  441 LEU cc_start: 0.7478 (OUTLIER) cc_final: 0.7254 (pp)
REVERT: C  442 ASP cc_start: 0.7911 (m-30) cc_final: 0.7656 (m-30)
REVERT: C  453 TYR cc_start: 0.7341 (p90) cc_final: 0.6931 (p90)
REVERT: C  495 TYR cc_start: 0.7651 (OUTLIER) cc_final: 0.6392 (p90)
REVERT: C  497 PHE cc_start: 0.8017 (m-80) cc_final: 0.7418 (m-80)
REVERT: C  557 LYS cc_start: 0.7156 (tptt) cc_final: 0.6921 (tptt)
REVERT: C  558 LYS cc_start: 0.7450 (mmtm) cc_final: 0.7029 (mmtm)
REVERT: C  559 PHE cc_start: 0.7445 (OUTLIER) cc_final: 0.6600 (m-10)
REVERT: C  585 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.8085 (mt)
REVERT: H   13 LYS cc_start: 0.5816 (OUTLIER) cc_final: 0.4473 (tppt)
REVERT: H   48 MET cc_start: 0.6263 (mmm) cc_final: 0.5913 (mmm)
REVERT: H   95 TYR cc_start: 0.7169 (m-80) cc_final: 0.6961 (m-80)
REVERT: L   55 ARG cc_start: 0.7237 (ptp90) cc_final: 0.6825 (ptp90)
REVERT: L   66 SER cc_start: 0.7919 (t) cc_final: 0.7714 (p)
REVERT: L   92 TRP cc_start: 0.8492 (t-100) cc_final: 0.7933 (t-100)
  outliers start: 40
  outliers final: 26
  residues processed: 160
  average time/residue: 0.0509
  time to fit residues: 10.0030
Evaluate side-chains
  175 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 143
  time to evaluate  : 0.088 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  349 SER
Chi-restraints excluded: chain C residue  350 VAL
Chi-restraints excluded: chain C residue  356 LYS
Chi-restraints excluded: chain C residue  377 PHE
Chi-restraints excluded: chain C residue  383 SER
Chi-restraints excluded: chain C residue  399 SER
Chi-restraints excluded: chain C residue  423 TYR
Chi-restraints excluded: chain C residue  438 SER
Chi-restraints excluded: chain C residue  441 LEU
Chi-restraints excluded: chain C residue  459 SER
Chi-restraints excluded: chain C residue  461 LEU
Chi-restraints excluded: chain C residue  495 TYR
Chi-restraints excluded: chain C residue  514 SER
Chi-restraints excluded: chain C residue  555 SER
Chi-restraints excluded: chain C residue  559 PHE
Chi-restraints excluded: chain C residue  560 LEU
Chi-restraints excluded: chain C residue  569 ILE
Chi-restraints excluded: chain C residue  581 THR
Chi-restraints excluded: chain C residue  585 LEU
Chi-restraints excluded: chain H residue   13 LYS
Chi-restraints excluded: chain H residue   28 THR
Chi-restraints excluded: chain H residue   37 LEU
Chi-restraints excluded: chain H residue   98 ARG
Chi-restraints excluded: chain H residue  102 LYS
Chi-restraints excluded: chain H residue  107 PHE
Chi-restraints excluded: chain L residue    4 LEU
Chi-restraints excluded: chain L residue   25 SER
Chi-restraints excluded: chain L residue   34 VAL
Chi-restraints excluded: chain L residue   37 TYR
Chi-restraints excluded: chain L residue   50 TYR
Chi-restraints excluded: chain L residue   52 ASN
Chi-restraints excluded: chain L residue  102 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 26 optimal weight:    3.9990
   chunk 40 optimal weight:    0.9990
   chunk 11 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9980
   chunk 9 optimal weight:    0.5980
   chunk 2 optimal weight:    0.6980
   chunk 21 optimal weight:    0.0770
   chunk 19 optimal weight:    0.6980
   chunk 12 optimal weight:    0.0050
   chunk 15 optimal weight:    4.9990
   chunk 18 optimal weight:    0.5980
   overall best weight:    0.3952

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

Flipped N/Q/H residues before XYZ refinement:
C 409 GLN
** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 448 ASN
** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4009 r_free = 0.4009 target = 0.147330 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 23)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.127154 restraints weight = 7836.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.131659 restraints weight = 4162.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.134677 restraints weight = 2559.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.136716 restraints weight = 1729.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.138033 restraints weight = 1260.721|
|-----------------------------------------------------------------------------|
r_work (final): 0.3872
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6715
moved from start:          0.2370

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.071   3937  Z= 0.146
  Angle     :  0.647   8.120   5354  Z= 0.337
  Chirality :  0.045   0.205    578
  Planarity :  0.004   0.043    696
  Dihedral  :  4.532  14.776    576
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 14.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.36 %
    Favored  : 94.64 %
  Rotamer:
    Outliers : 11.11 %
    Allowed  : 32.61 %
    Favored  : 56.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.77 (0.38), residues: 485
  helix: -2.57 (0.82), residues: 26
  sheet: -0.50 (0.42), residues: 144
  loop : -0.25 (0.37), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG H  45 
 TYR   0.015   0.001   TYR C 495 
 PHE   0.016   0.001   PHE H  64 
 TRP   0.020   0.002   TRP H 103 
 HIS   0.002   0.001   HIS C 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 3933)
  covalent geometry    : angle       0.64666 ( 5346)
  SS BOND              : bond        0.00206 (    4)
  SS BOND              : angle       0.55471 (    8)
  hydrogen bonds       : bond        0.03889 (   72)
  hydrogen bonds       : angle       6.93118 (  183)

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

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

  970 Ramachandran restraints generated.
    485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  970 Ramachandran restraints generated.
    485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 145
  time to evaluate  : 0.141 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  423 TYR cc_start: 0.4895 (OUTLIER) cc_final: 0.3544 (t80)
REVERT: C  425 LEU cc_start: 0.8565 (tp) cc_final: 0.8322 (tp)
REVERT: C  453 TYR cc_start: 0.7290 (p90) cc_final: 0.6923 (p90)
REVERT: C  495 TYR cc_start: 0.7532 (OUTLIER) cc_final: 0.6333 (p90)
REVERT: C  497 PHE cc_start: 0.8010 (m-80) cc_final: 0.7410 (m-80)
REVERT: C  516 GLU cc_start: 0.7440 (tp30) cc_final: 0.7140 (tp30)
REVERT: C  557 LYS cc_start: 0.7141 (tptt) cc_final: 0.6862 (tptt)
REVERT: C  558 LYS cc_start: 0.7550 (mmtm) cc_final: 0.7035 (mmtm)
REVERT: C  559 PHE cc_start: 0.7433 (OUTLIER) cc_final: 0.6644 (m-10)
REVERT: H   48 MET cc_start: 0.6275 (mmm) cc_final: 0.5899 (mmm)
REVERT: H   95 TYR cc_start: 0.7189 (m-80) cc_final: 0.6971 (m-80)
REVERT: L   55 ARG cc_start: 0.7254 (ptp90) cc_final: 0.6943 (ptp90)
REVERT: L   66 SER cc_start: 0.7873 (t) cc_final: 0.7664 (p)
REVERT: L   92 TRP cc_start: 0.8492 (t-100) cc_final: 0.7693 (t-100)
REVERT: L   96 LEU cc_start: 0.7757 (mt) cc_final: 0.7537 (mt)
  outliers start: 46
  outliers final: 27
  residues processed: 165
  average time/residue: 0.0620
  time to fit residues: 12.5779
Evaluate side-chains
  173 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 143
  time to evaluate  : 0.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  349 SER
Chi-restraints excluded: chain C residue  350 VAL
Chi-restraints excluded: chain C residue  356 LYS
Chi-restraints excluded: chain C residue  383 SER
Chi-restraints excluded: chain C residue  399 SER
Chi-restraints excluded: chain C residue  409 GLN
Chi-restraints excluded: chain C residue  423 TYR
Chi-restraints excluded: chain C residue  461 LEU
Chi-restraints excluded: chain C residue  495 TYR
Chi-restraints excluded: chain C residue  531 THR
Chi-restraints excluded: chain C residue  555 SER
Chi-restraints excluded: chain C residue  559 PHE
Chi-restraints excluded: chain C residue  560 LEU
Chi-restraints excluded: chain C residue  565 PHE
Chi-restraints excluded: chain C residue  569 ILE
Chi-restraints excluded: chain C residue  581 THR
Chi-restraints excluded: chain H residue   18 VAL
Chi-restraints excluded: chain H residue   28 THR
Chi-restraints excluded: chain H residue   37 LEU
Chi-restraints excluded: chain H residue   87 LYS
Chi-restraints excluded: chain H residue  102 LYS
Chi-restraints excluded: chain H residue  107 PHE
Chi-restraints excluded: chain H residue  114 THR
Chi-restraints excluded: chain L residue    4 LEU
Chi-restraints excluded: chain L residue   25 SER
Chi-restraints excluded: chain L residue   34 VAL
Chi-restraints excluded: chain L residue   37 TYR
Chi-restraints excluded: chain L residue   50 TYR
Chi-restraints excluded: chain L residue   52 ASN
Chi-restraints excluded: chain L residue  102 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 28 optimal weight:    3.9990
   chunk 14 optimal weight:    0.9990
   chunk 6 optimal weight:    0.5980
   chunk 21 optimal weight:    0.2980
   chunk 10 optimal weight:    0.6980
   chunk 9 optimal weight:    0.9980
   chunk 31 optimal weight:    0.9990
   chunk 16 optimal weight:    2.9990
   chunk 44 optimal weight:    1.9990
   chunk 35 optimal weight:    3.9990
   chunk 23 optimal weight:    0.8980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 506 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 = 0.3966 r_free = 0.3966 target = 0.144079 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.123956 restraints weight = 7801.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.128486 restraints weight = 4174.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.131532 restraints weight = 2565.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.133602 restraints weight = 1734.424|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.134938 restraints weight = 1261.262|
|-----------------------------------------------------------------------------|
r_work (final): 0.3831
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6783
moved from start:          0.2682

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.103   3937  Z= 0.210
  Angle     :  0.719   9.806   5354  Z= 0.374
  Chirality :  0.048   0.210    578
  Planarity :  0.005   0.044    696
  Dihedral  :  4.916  15.630    576
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 16.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.60 %
    Favored  : 93.40 %
  Rotamer:
    Outliers :  7.25 %
    Allowed  : 36.96 %
    Favored  : 55.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.18 (0.37), residues: 485
  helix: -3.28 (0.64), residues: 32
  sheet: -0.77 (0.42), residues: 144
  loop : -0.43 (0.36), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG H  45 
 TYR   0.016   0.002   TYR C 495 
 PHE   0.018   0.002   PHE H  64 
 TRP   0.018   0.003   TRP H 103 
 HIS   0.003   0.001   HIS C 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00478 ( 3933)
  covalent geometry    : angle       0.71887 ( 5346)
  SS BOND              : bond        0.00242 (    4)
  SS BOND              : angle       0.46331 (    8)
  hydrogen bonds       : bond        0.04581 (   72)
  hydrogen bonds       : angle       7.14878 (  183)

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

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

  970 Ramachandran restraints generated.
    485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  970 Ramachandran restraints generated.
    485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 150
  time to evaluate  : 0.089 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  400 PHE cc_start: 0.7056 (p90) cc_final: 0.6607 (p90)
REVERT: C  403 ARG cc_start: 0.8453 (ttm110) cc_final: 0.7829 (ttm110)
REVERT: C  453 TYR cc_start: 0.7345 (p90) cc_final: 0.7101 (p90)
REVERT: C  495 TYR cc_start: 0.7563 (OUTLIER) cc_final: 0.6406 (p90)
REVERT: C  497 PHE cc_start: 0.8043 (m-80) cc_final: 0.7542 (m-80)
REVERT: C  516 GLU cc_start: 0.7511 (tp30) cc_final: 0.7203 (tp30)
REVERT: C  556 ASN cc_start: 0.8157 (p0) cc_final: 0.7776 (p0)
REVERT: C  557 LYS cc_start: 0.7235 (tptt) cc_final: 0.6812 (tptt)
REVERT: C  559 PHE cc_start: 0.7451 (OUTLIER) cc_final: 0.6384 (m-10)
REVERT: H   48 MET cc_start: 0.6366 (mmm) cc_final: 0.5927 (mmm)
REVERT: L   51 ASN cc_start: 0.7671 (m-40) cc_final: 0.7170 (m-40)
REVERT: L   92 TRP cc_start: 0.8540 (t-100) cc_final: 0.7722 (t-100)
  outliers start: 30
  outliers final: 22
  residues processed: 160
  average time/residue: 0.0627
  time to fit residues: 12.2724
Evaluate side-chains
  173 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 149
  time to evaluate  : 0.133 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  350 VAL
Chi-restraints excluded: chain C residue  383 SER
Chi-restraints excluded: chain C residue  399 SER
Chi-restraints excluded: chain C residue  466 ARG
Chi-restraints excluded: chain C residue  495 TYR
Chi-restraints excluded: chain C residue  531 THR
Chi-restraints excluded: chain C residue  555 SER
Chi-restraints excluded: chain C residue  559 PHE
Chi-restraints excluded: chain C residue  560 LEU
Chi-restraints excluded: chain C residue  565 PHE
Chi-restraints excluded: chain C residue  581 THR
Chi-restraints excluded: chain H residue   18 VAL
Chi-restraints excluded: chain H residue   28 THR
Chi-restraints excluded: chain H residue   37 LEU
Chi-restraints excluded: chain H residue   87 LYS
Chi-restraints excluded: chain H residue  102 LYS
Chi-restraints excluded: chain H residue  107 PHE
Chi-restraints excluded: chain H residue  114 THR
Chi-restraints excluded: chain L residue    4 LEU
Chi-restraints excluded: chain L residue   34 VAL
Chi-restraints excluded: chain L residue   37 TYR
Chi-restraints excluded: chain L residue   50 TYR
Chi-restraints excluded: chain L residue   52 ASN
Chi-restraints excluded: chain L residue  102 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 15 optimal weight:    0.9980
   chunk 32 optimal weight:    0.7980
   chunk 39 optimal weight:    2.9990
   chunk 2 optimal weight:    0.1980
   chunk 46 optimal weight:    0.6980
   chunk 25 optimal weight:    0.5980
   chunk 34 optimal weight:    0.9990
   chunk 7 optimal weight:    0.4980
   chunk 45 optimal weight:    0.6980
   chunk 23 optimal weight:    0.0670
   chunk 40 optimal weight:    0.1980
   overall best weight:    0.3118

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.143899 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.124773 restraints weight = 7928.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.129025 restraints weight = 4302.263|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.131800 restraints weight = 2662.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.133782 restraints weight = 1818.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.135022 restraints weight = 1338.366|
|-----------------------------------------------------------------------------|
r_work (final): 0.3881
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6721
moved from start:          0.2849

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   3937  Z= 0.137
  Angle     :  0.688   8.434   5354  Z= 0.355
  Chirality :  0.046   0.184    578
  Planarity :  0.004   0.045    696
  Dihedral  :  4.620  15.118    576
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 15.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.95 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  7.49 %
    Allowed  : 38.16 %
    Favored  : 54.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.14 (0.38), residues: 485
  helix: -2.99 (0.78), residues: 26
  sheet: -0.74 (0.42), residues: 144
  loop : -0.50 (0.36), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG C 567 
 TYR   0.018   0.001   TYR C 495 
 PHE   0.014   0.001   PHE C 377 
 TRP   0.023   0.002   TRP H 103 
 HIS   0.002   0.001   HIS H  33 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 3933)
  covalent geometry    : angle       0.68836 ( 5346)
  SS BOND              : bond        0.00124 (    4)
  SS BOND              : angle       0.45395 (    8)
  hydrogen bonds       : bond        0.03697 (   72)
  hydrogen bonds       : angle       6.76891 (  183)

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

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

  970 Ramachandran restraints generated.
    485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  970 Ramachandran restraints generated.
    485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 149
  time to evaluate  : 0.085 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  403 ARG cc_start: 0.8442 (ttm110) cc_final: 0.7944 (ttm110)
REVERT: C  423 TYR cc_start: 0.5032 (OUTLIER) cc_final: 0.3629 (t80)
REVERT: C  453 TYR cc_start: 0.7318 (p90) cc_final: 0.7036 (p90)
REVERT: C  495 TYR cc_start: 0.7474 (OUTLIER) cc_final: 0.6415 (p90)
REVERT: C  516 GLU cc_start: 0.7579 (tp30) cc_final: 0.7285 (tp30)
REVERT: C  557 LYS cc_start: 0.7161 (tptt) cc_final: 0.6937 (tptt)
REVERT: C  559 PHE cc_start: 0.7154 (OUTLIER) cc_final: 0.6387 (m-10)
REVERT: H   48 MET cc_start: 0.6225 (mmm) cc_final: 0.5833 (mmm)
REVERT: H   98 ARG cc_start: 0.7142 (tmt90) cc_final: 0.6911 (tmt90)
REVERT: L   51 ASN cc_start: 0.7565 (m-40) cc_final: 0.7060 (m-40)
REVERT: L   92 TRP cc_start: 0.8498 (t-100) cc_final: 0.7628 (t-100)
  outliers start: 31
  outliers final: 23
  residues processed: 160
  average time/residue: 0.0612
  time to fit residues: 12.0047
Evaluate side-chains
  174 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 148
  time to evaluate  : 0.134 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  350 VAL
Chi-restraints excluded: chain C residue  383 SER
Chi-restraints excluded: chain C residue  399 SER
Chi-restraints excluded: chain C residue  423 TYR
Chi-restraints excluded: chain C residue  442 ASP
Chi-restraints excluded: chain C residue  495 TYR
Chi-restraints excluded: chain C residue  529 LYS
Chi-restraints excluded: chain C residue  531 THR
Chi-restraints excluded: chain C residue  555 SER
Chi-restraints excluded: chain C residue  559 PHE
Chi-restraints excluded: chain C residue  560 LEU
Chi-restraints excluded: chain C residue  565 PHE
Chi-restraints excluded: chain C residue  581 THR
Chi-restraints excluded: chain H residue   28 THR
Chi-restraints excluded: chain H residue   37 LEU
Chi-restraints excluded: chain H residue   87 LYS
Chi-restraints excluded: chain H residue   95 TYR
Chi-restraints excluded: chain H residue  102 LYS
Chi-restraints excluded: chain H residue  107 PHE
Chi-restraints excluded: chain H residue  114 THR
Chi-restraints excluded: chain L residue    4 LEU
Chi-restraints excluded: chain L residue   34 VAL
Chi-restraints excluded: chain L residue   37 TYR
Chi-restraints excluded: chain L residue   50 TYR
Chi-restraints excluded: chain L residue   52 ASN
Chi-restraints excluded: chain L residue  102 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 18 optimal weight:    0.9990
   chunk 45 optimal weight:    0.0170
   chunk 19 optimal weight:    0.8980
   chunk 7 optimal weight:    0.0870
   chunk 14 optimal weight:    0.9990
   chunk 5 optimal weight:    0.4980
   chunk 39 optimal weight:    0.6980
   chunk 32 optimal weight:    0.9980
   chunk 44 optimal weight:    0.9990
   chunk 1 optimal weight:    0.0770
   chunk 40 optimal weight:    0.6980
   overall best weight:    0.2754

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4020 r_free = 0.4020 target = 0.147523 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.127295 restraints weight = 7822.589|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.131925 restraints weight = 4154.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.134919 restraints weight = 2542.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.137001 restraints weight = 1723.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.138425 restraints weight = 1249.003|
|-----------------------------------------------------------------------------|
r_work (final): 0.3888
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6697
moved from start:          0.3038

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   3937  Z= 0.133
  Angle     :  0.708   9.085   5354  Z= 0.357
  Chirality :  0.046   0.195    578
  Planarity :  0.004   0.044    696
  Dihedral  :  4.508  15.353    576
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 13.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.36 %
    Favored  : 94.64 %
  Rotamer:
    Outliers :  7.73 %
    Allowed  : 38.41 %
    Favored  : 53.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.13 (0.38), residues: 485
  helix: -2.84 (0.80), residues: 26
  sheet: -0.77 (0.42), residues: 144
  loop : -0.49 (0.36), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG C 567 
 TYR   0.018   0.001   TYR C 495 
 PHE   0.017   0.001   PHE C 497 
 TRP   0.024   0.002   TRP H 103 
 HIS   0.001   0.001   HIS C 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 3933)
  covalent geometry    : angle       0.70810 ( 5346)
  SS BOND              : bond        0.00077 (    4)
  SS BOND              : angle       0.47218 (    8)
  hydrogen bonds       : bond        0.03421 (   72)
  hydrogen bonds       : angle       6.59897 (  183)

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

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

  970 Ramachandran restraints generated.
    485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  970 Ramachandran restraints generated.
    485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 146
  time to evaluate  : 0.179 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  403 ARG cc_start: 0.8390 (ttm110) cc_final: 0.7908 (ttm110)
REVERT: C  423 TYR cc_start: 0.5005 (OUTLIER) cc_final: 0.3541 (t80)
REVERT: C  453 TYR cc_start: 0.7295 (p90) cc_final: 0.6961 (p90)
REVERT: C  466 ARG cc_start: 0.2275 (OUTLIER) cc_final: 0.1403 (mmt-90)
REVERT: C  495 TYR cc_start: 0.7357 (OUTLIER) cc_final: 0.6057 (p90)
REVERT: C  516 GLU cc_start: 0.7629 (tp30) cc_final: 0.7306 (tp30)
REVERT: C  529 LYS cc_start: 0.7139 (OUTLIER) cc_final: 0.6748 (tptp)
REVERT: H   48 MET cc_start: 0.6230 (mmm) cc_final: 0.5834 (mmm)
REVERT: L   29 ILE cc_start: 0.8480 (tt) cc_final: 0.8214 (pt)
REVERT: L   51 ASN cc_start: 0.7547 (m-40) cc_final: 0.7031 (m-40)
REVERT: L   88 PHE cc_start: 0.6047 (p90) cc_final: 0.5602 (p90)
REVERT: L   92 TRP cc_start: 0.8472 (t-100) cc_final: 0.7597 (t-100)
  outliers start: 32
  outliers final: 25
  residues processed: 156
  average time/residue: 0.0654
  time to fit residues: 12.4897
Evaluate side-chains
  171 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 142
  time to evaluate  : 0.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  333 THR
Chi-restraints excluded: chain C residue  350 VAL
Chi-restraints excluded: chain C residue  356 LYS
Chi-restraints excluded: chain C residue  378 LYS
Chi-restraints excluded: chain C residue  383 SER
Chi-restraints excluded: chain C residue  399 SER
Chi-restraints excluded: chain C residue  423 TYR
Chi-restraints excluded: chain C residue  442 ASP
Chi-restraints excluded: chain C residue  466 ARG
Chi-restraints excluded: chain C residue  495 TYR
Chi-restraints excluded: chain C residue  529 LYS
Chi-restraints excluded: chain C residue  531 THR
Chi-restraints excluded: chain C residue  560 LEU
Chi-restraints excluded: chain C residue  565 PHE
Chi-restraints excluded: chain C residue  569 ILE
Chi-restraints excluded: chain C residue  581 THR
Chi-restraints excluded: chain H residue   28 THR
Chi-restraints excluded: chain H residue   37 LEU
Chi-restraints excluded: chain H residue   87 LYS
Chi-restraints excluded: chain H residue   95 TYR
Chi-restraints excluded: chain H residue  102 LYS
Chi-restraints excluded: chain H residue  107 PHE
Chi-restraints excluded: chain H residue  114 THR
Chi-restraints excluded: chain L residue    4 LEU
Chi-restraints excluded: chain L residue   34 VAL
Chi-restraints excluded: chain L residue   37 TYR
Chi-restraints excluded: chain L residue   50 TYR
Chi-restraints excluded: chain L residue   52 ASN
Chi-restraints excluded: chain L residue  102 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 28 optimal weight:    4.9990
   chunk 39 optimal weight:    2.9990
   chunk 32 optimal weight:    0.3980
   chunk 18 optimal weight:    0.6980
   chunk 21 optimal weight:    0.2980
   chunk 6 optimal weight:    0.0050
   chunk 45 optimal weight:    0.6980
   chunk 5 optimal weight:    0.6980
   chunk 36 optimal weight:    0.4980
   chunk 34 optimal weight:    0.0970
   chunk 23 optimal weight:    0.0870
   overall best weight:    0.1770

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4038 r_free = 0.4038 target = 0.148491 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.128714 restraints weight = 7896.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.133277 restraints weight = 4229.029|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.136229 restraints weight = 2591.221|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.138090 restraints weight = 1740.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.139558 restraints weight = 1278.431|
|-----------------------------------------------------------------------------|
r_work (final): 0.3920
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6656
moved from start:          0.3291

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   3937  Z= 0.128
  Angle     :  0.716   9.290   5354  Z= 0.360
  Chirality :  0.045   0.170    578
  Planarity :  0.004   0.044    696
  Dihedral  :  4.264  15.604    576
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 12.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.95 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  6.76 %
    Allowed  : 40.82 %
    Favored  : 52.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.03 (0.38), residues: 485
  helix: -2.75 (0.84), residues: 26
  sheet: -0.74 (0.43), residues: 137
  loop : -0.41 (0.36), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 567 
 TYR   0.017   0.001   TYR C 495 
 PHE   0.014   0.001   PHE C 497 
 TRP   0.024   0.002   TRP H 103 
 HIS   0.001   0.001   HIS H  33 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 3933)
  covalent geometry    : angle       0.71590 ( 5346)
  SS BOND              : bond        0.00072 (    4)
  SS BOND              : angle       0.45496 (    8)
  hydrogen bonds       : bond        0.03167 (   72)
  hydrogen bonds       : angle       6.38465 (  183)

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

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

  970 Ramachandran restraints generated.
    485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  970 Ramachandran restraints generated.
    485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 141
  time to evaluate  : 0.144 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  423 TYR cc_start: 0.5078 (OUTLIER) cc_final: 0.3715 (t80)
REVERT: C  453 TYR cc_start: 0.7288 (p90) cc_final: 0.6949 (p90)
REVERT: C  466 ARG cc_start: 0.2177 (OUTLIER) cc_final: 0.1311 (mmt-90)
REVERT: C  495 TYR cc_start: 0.7347 (OUTLIER) cc_final: 0.6127 (p90)
REVERT: C  516 GLU cc_start: 0.7598 (tp30) cc_final: 0.7265 (tp30)
REVERT: C  529 LYS cc_start: 0.7112 (OUTLIER) cc_final: 0.6711 (tptp)
REVERT: H   48 MET cc_start: 0.6182 (mmm) cc_final: 0.5841 (mmm)
REVERT: L   29 ILE cc_start: 0.8500 (tt) cc_final: 0.8263 (pt)
REVERT: L   55 ARG cc_start: 0.7142 (ptp90) cc_final: 0.6903 (ptp90)
REVERT: L   88 PHE cc_start: 0.6019 (p90) cc_final: 0.5731 (p90)
REVERT: L   92 TRP cc_start: 0.8424 (t-100) cc_final: 0.7748 (t-100)
  outliers start: 28
  outliers final: 20
  residues processed: 151
  average time/residue: 0.0694
  time to fit residues: 12.7888
Evaluate side-chains
  159 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 135
  time to evaluate  : 0.137 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  356 LYS
Chi-restraints excluded: chain C residue  383 SER
Chi-restraints excluded: chain C residue  399 SER
Chi-restraints excluded: chain C residue  423 TYR
Chi-restraints excluded: chain C residue  442 ASP
Chi-restraints excluded: chain C residue  466 ARG
Chi-restraints excluded: chain C residue  495 TYR
Chi-restraints excluded: chain C residue  529 LYS
Chi-restraints excluded: chain C residue  531 THR
Chi-restraints excluded: chain C residue  560 LEU
Chi-restraints excluded: chain C residue  565 PHE
Chi-restraints excluded: chain C residue  569 ILE
Chi-restraints excluded: chain C residue  581 THR
Chi-restraints excluded: chain H residue   37 LEU
Chi-restraints excluded: chain H residue   87 LYS
Chi-restraints excluded: chain H residue   95 TYR
Chi-restraints excluded: chain H residue  102 LYS
Chi-restraints excluded: chain H residue  107 PHE
Chi-restraints excluded: chain H residue  114 THR
Chi-restraints excluded: chain L residue    4 LEU
Chi-restraints excluded: chain L residue   34 VAL
Chi-restraints excluded: chain L residue   37 TYR
Chi-restraints excluded: chain L residue   50 TYR
Chi-restraints excluded: chain L residue   52 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 22 optimal weight:    0.9980
   chunk 29 optimal weight:    0.8980
   chunk 12 optimal weight:    0.0070
   chunk 33 optimal weight:    0.3980
   chunk 41 optimal weight:    1.9990
   chunk 17 optimal weight:    0.0970
   chunk 38 optimal weight:    0.7980
   chunk 2 optimal weight:    0.5980
   chunk 10 optimal weight:    0.9980
   chunk 23 optimal weight:    0.9990
   chunk 28 optimal weight:    2.9990
   overall best weight:    0.3796

-------------------------------------------------------------------------------
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 580 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4016 r_free = 0.4016 target = 0.147440 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.127564 restraints weight = 7961.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.132144 restraints weight = 4221.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.135092 restraints weight = 2575.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.137122 restraints weight = 1737.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.138539 restraints weight = 1261.927|
|-----------------------------------------------------------------------------|
r_work (final): 0.3884
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6703
moved from start:          0.3393

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.070   3937  Z= 0.150
  Angle     :  0.734   8.955   5354  Z= 0.373
  Chirality :  0.047   0.202    578
  Planarity :  0.004   0.044    696
  Dihedral  :  4.545  16.088    576
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 14.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.98 %
    Favored  : 94.02 %
  Rotamer:
    Outliers :  6.76 %
    Allowed  : 39.86 %
    Favored  : 53.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.12 (0.38), residues: 485
  helix: -2.82 (0.75), residues: 32
  sheet: -0.68 (0.45), residues: 127
  loop : -0.51 (0.35), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C 403 
 TYR   0.016   0.001   TYR C 495 
 PHE   0.017   0.002   PHE C 377 
 TRP   0.026   0.003   TRP L  36 
 HIS   0.002   0.001   HIS C 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 ( 3933)
  covalent geometry    : angle       0.73252 ( 5346)
  SS BOND              : bond        0.00159 (    4)
  SS BOND              : angle       1.24019 (    8)
  hydrogen bonds       : bond        0.03446 (   72)
  hydrogen bonds       : angle       6.48545 (  183)

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

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

  970 Ramachandran restraints generated.
    485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  970 Ramachandran restraints generated.
    485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 148
  time to evaluate  : 0.117 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  400 PHE cc_start: 0.6755 (p90) cc_final: 0.6427 (p90)
REVERT: C  423 TYR cc_start: 0.4989 (OUTLIER) cc_final: 0.3459 (t80)
REVERT: C  466 ARG cc_start: 0.2398 (OUTLIER) cc_final: 0.1485 (mmt-90)
REVERT: C  495 TYR cc_start: 0.7338 (OUTLIER) cc_final: 0.6150 (p90)
REVERT: C  516 GLU cc_start: 0.7593 (tp30) cc_final: 0.7270 (tp30)
REVERT: C  529 LYS cc_start: 0.7172 (OUTLIER) cc_final: 0.6770 (tptp)
REVERT: H   48 MET cc_start: 0.6247 (mmm) cc_final: 0.5843 (mmm)
REVERT: H   98 ARG cc_start: 0.7037 (tmt90) cc_final: 0.5914 (tmm-80)
REVERT: L   29 ILE cc_start: 0.8494 (tt) cc_final: 0.8255 (pt)
REVERT: L   88 PHE cc_start: 0.6113 (p90) cc_final: 0.5702 (p90)
REVERT: L   92 TRP cc_start: 0.8480 (t-100) cc_final: 0.7762 (t-100)
  outliers start: 28
  outliers final: 18
  residues processed: 158
  average time/residue: 0.0471
  time to fit residues: 9.1537
Evaluate side-chains
  168 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 146
  time to evaluate  : 0.126 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  333 THR
Chi-restraints excluded: chain C residue  356 LYS
Chi-restraints excluded: chain C residue  383 SER
Chi-restraints excluded: chain C residue  423 TYR
Chi-restraints excluded: chain C residue  442 ASP
Chi-restraints excluded: chain C residue  466 ARG
Chi-restraints excluded: chain C residue  495 TYR
Chi-restraints excluded: chain C residue  497 PHE
Chi-restraints excluded: chain C residue  529 LYS
Chi-restraints excluded: chain C residue  531 THR
Chi-restraints excluded: chain C residue  560 LEU
Chi-restraints excluded: chain C residue  565 PHE
Chi-restraints excluded: chain C residue  569 ILE
Chi-restraints excluded: chain C residue  581 THR
Chi-restraints excluded: chain H residue   37 LEU
Chi-restraints excluded: chain H residue   95 TYR
Chi-restraints excluded: chain H residue  102 LYS
Chi-restraints excluded: chain H residue  107 PHE
Chi-restraints excluded: chain H residue  114 THR
Chi-restraints excluded: chain L residue   34 VAL
Chi-restraints excluded: chain L residue   37 TYR
Chi-restraints excluded: chain L residue   50 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 41 optimal weight:    0.6980
   chunk 1 optimal weight:    0.0980
   chunk 0 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9980
   chunk 20 optimal weight:    1.9990
   chunk 17 optimal weight:    2.9990
   chunk 23 optimal weight:    0.0970
   chunk 8 optimal weight:    0.6980
   chunk 38 optimal weight:    0.5980
   chunk 9 optimal weight:    0.5980
   chunk 10 optimal weight:    0.8980
   overall best weight:    0.4178

-------------------------------------------------------------------------------
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**
** H 109 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 = 0.4011 r_free = 0.4011 target = 0.147015 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.127327 restraints weight = 7789.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.131760 restraints weight = 4148.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.134724 restraints weight = 2536.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.136728 restraints weight = 1714.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.138049 restraints weight = 1249.599|
|-----------------------------------------------------------------------------|
r_work (final): 0.3879
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6712
moved from start:          0.3488

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.079   3937  Z= 0.158
  Angle     :  0.750   9.377   5354  Z= 0.380
  Chirality :  0.046   0.206    578
  Planarity :  0.005   0.044    696
  Dihedral  :  4.609  16.676    576
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 15.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.15 %
    Favored  : 94.85 %
  Rotamer:
    Outliers :  5.31 %
    Allowed  : 41.79 %
    Favored  : 52.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.18 (0.37), residues: 485
  helix: -2.83 (0.73), residues: 32
  sheet: -0.68 (0.45), residues: 127
  loop : -0.57 (0.34), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C 567 
 TYR   0.020   0.001   TYR C 495 
 PHE   0.017   0.002   PHE C 377 
 TRP   0.022   0.003   TRP H 103 
 HIS   0.002   0.001   HIS C 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 ( 3933)
  covalent geometry    : angle       0.74942 ( 5346)
  SS BOND              : bond        0.00148 (    4)
  SS BOND              : angle       1.16918 (    8)
  hydrogen bonds       : bond        0.03452 (   72)
  hydrogen bonds       : angle       6.51608 (  183)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 875.47 seconds
wall clock time: 15 minutes 42.66 seconds (942.66 seconds total)