Starting phenix.real_space_refine
on Tue Mar 11 15:26:24 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ug6_42215/03_2025/8ug6_42215.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ug6_42215/03_2025/8ug6_42215.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ug6_42215/03_2025/8ug6_42215.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ug6_42215/03_2025/8ug6_42215.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ug6_42215/03_2025/8ug6_42215.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ug6_42215/03_2025/8ug6_42215.cif"
  }
  resolution = 3.06
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.000
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      42      5.16       5
     C    4156      2.51       5
     N    1006      2.21       5
     O    1038      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 6242
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3121
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 393, 3121
          Classifications: {'peptide': 393}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 9, 'TRANS': 383}
          Chain breaks: 7
  Restraints were copied for chains:
    B
  Time building chain proxies: 5.57, per 1000 atoms: 0.89
  Number of scatterers: 6242
  At special positions: 0
  Unit cell: (87.15, 98.77, 70.55, 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      42     16.00
     O    1038      8.00
     N    1006      7.00
     C    4156      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.62
  Conformation dependent library (CDL) restraints added in 977.8 milliseconds
  

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1468

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 0 sheets defined
      85.8% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.57
  Creating SS restraints...
    Processing helix  chain 'A' and resid 28 through 53
      removed outlier: 3.540A  pdb=" N   ASN A  53 " --> pdb=" O   GLY A  49 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 59 through 85
    Processing helix  chain 'A' and resid 101 through 128
      removed outlier: 4.304A  pdb=" N   GLY A 105 " --> pdb=" O   ILE A 101 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   SER A 127 " --> pdb=" O   GLY A 123 " (cutoff:3.500A)
      removed outlier: 4.120A  pdb=" N   PHE A 128 " --> pdb=" O   TYR A 124 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 134 through 156
      Proline residue:  A 140  - end of helix
    Processing helix  chain 'A' and resid 165 through 194
    Processing helix  chain 'A' and resid 247 through 265
    Processing helix  chain 'A' and resid 292 through 312
    Processing helix  chain 'A' and resid 322 through 353
      removed outlier: 3.562A  pdb=" N   PHE A 353 " --> pdb=" O   VAL A 349 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 366 through 393
      removed outlier: 4.506A  pdb=" N   GLY A 379 " --> pdb=" O   GLY A 375 " (cutoff:3.500A)
      removed outlier: 4.531A  pdb=" N   GLN A 380 " --> pdb=" O   ALA A 376 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 398 through 429
      removed outlier: 3.564A  pdb=" N   GLY A 429 " --> pdb=" O   SER A 425 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 488 through 508
      removed outlier: 3.572A  pdb=" N   ASP A 496 " --> pdb=" O   ARG A 492 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 509 through 515
    Processing helix  chain 'A' and resid 522 through 530
    Processing helix  chain 'A' and resid 530 through 563
      Proline residue:  A 543  - end of helix
      removed outlier: 3.500A  pdb=" N   ILE A 546 " --> pdb=" O   LEU A 542 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   PHE A 547 " --> pdb=" O   PRO A 543 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 28 through 53
      removed outlier: 3.539A  pdb=" N   ASN B  53 " --> pdb=" O   GLY B  49 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 59 through 85
    Processing helix  chain 'B' and resid 101 through 128
      removed outlier: 4.304A  pdb=" N   GLY B 105 " --> pdb=" O   ILE B 101 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   SER B 127 " --> pdb=" O   GLY B 123 " (cutoff:3.500A)
      removed outlier: 4.120A  pdb=" N   PHE B 128 " --> pdb=" O   TYR B 124 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 134 through 156
      Proline residue:  B 140  - end of helix
    Processing helix  chain 'B' and resid 165 through 194
    Processing helix  chain 'B' and resid 247 through 265
    Processing helix  chain 'B' and resid 292 through 312
    Processing helix  chain 'B' and resid 322 through 353
      removed outlier: 3.562A  pdb=" N   PHE B 353 " --> pdb=" O   VAL B 349 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 366 through 393
      removed outlier: 4.505A  pdb=" N   GLY B 379 " --> pdb=" O   GLY B 375 " (cutoff:3.500A)
      removed outlier: 4.531A  pdb=" N   GLN B 380 " --> pdb=" O   ALA B 376 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 398 through 429
      removed outlier: 3.564A  pdb=" N   GLY B 429 " --> pdb=" O   SER B 425 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 488 through 508
      removed outlier: 3.573A  pdb=" N   ASP B 496 " --> pdb=" O   ARG B 492 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 509 through 515
    Processing helix  chain 'B' and resid 522 through 530
    Processing helix  chain 'B' and resid 530 through 563
      Proline residue:  B 543  - end of helix
      removed outlier: 3.500A  pdb=" N   ILE B 546 " --> pdb=" O   LEU B 542 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   PHE B 547 " --> pdb=" O   PRO B 543 " (cutoff:3.500A)

    528 hydrogen bonds defined for protein.
    1584 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.82

  Time building geometry restraints manager: 1.91 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1267
        1.33 -     1.45: 1564
        1.45 -     1.57: 3499
        1.57 -     1.69: 0
        1.69 -     1.81: 66
  Bond restraints: 6396
  Sorted by residual:
  bond pdb=" CA  SER B 256 "
       pdb=" CB  SER B 256 "
    ideal  model  delta    sigma   weight residual
    1.528  1.467  0.061 1.56e-02 4.11e+03 1.54e+01
  bond pdb=" CA  SER A 256 "
       pdb=" CB  SER A 256 "
    ideal  model  delta    sigma   weight residual
    1.528  1.468  0.060 1.56e-02 4.11e+03 1.50e+01
  bond pdb=" CA  SER B 346 "
       pdb=" CB  SER B 346 "
    ideal  model  delta    sigma   weight residual
    1.528  1.479  0.049 1.56e-02 4.11e+03 9.99e+00
  bond pdb=" CA  SER A 346 "
       pdb=" CB  SER A 346 "
    ideal  model  delta    sigma   weight residual
    1.528  1.480  0.049 1.56e-02 4.11e+03 9.85e+00
  bond pdb=" N   VAL A 307 "
       pdb=" CA  VAL A 307 "
    ideal  model  delta    sigma   weight residual
    1.459  1.498 -0.039 1.30e-02 5.92e+03 8.78e+00
  ... (remaining 6391 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.53: 8335
        1.53 -     3.06: 290
        3.06 -     4.60: 57
        4.60 -     6.13: 12
        6.13 -     7.66: 4
  Bond angle restraints: 8698
  Sorted by residual:
  angle pdb=" N   TYR B 124 "
        pdb=" CA  TYR B 124 "
        pdb=" C   TYR B 124 "
      ideal   model   delta    sigma   weight residual
     111.40  106.84    4.56 1.22e+00 6.72e-01 1.40e+01
  angle pdb=" N   TYR A 124 "
        pdb=" CA  TYR A 124 "
        pdb=" C   TYR A 124 "
      ideal   model   delta    sigma   weight residual
     111.40  106.86    4.54 1.22e+00 6.72e-01 1.39e+01
  angle pdb=" C   GLN A 238 "
        pdb=" N   GLN A 239 "
        pdb=" CA  GLN A 239 "
      ideal   model   delta    sigma   weight residual
     120.71  114.71    6.00 1.67e+00 3.59e-01 1.29e+01
  angle pdb=" C   GLN B 238 "
        pdb=" N   GLN B 239 "
        pdb=" CA  GLN B 239 "
      ideal   model   delta    sigma   weight residual
     120.71  114.73    5.98 1.67e+00 3.59e-01 1.28e+01
  angle pdb=" CA  ARG B 366 "
        pdb=" C   ARG B 366 "
        pdb=" O   ARG B 366 "
      ideal   model   delta    sigma   weight residual
     122.41  118.12    4.29 1.21e+00 6.83e-01 1.26e+01
  ... (remaining 8693 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    12.55: 2886
       12.55 -    25.10: 454
       25.10 -    37.66: 198
       37.66 -    50.21: 78
       50.21 -    62.76: 22
  Dihedral angle restraints: 3638
    sinusoidal: 1358
      harmonic: 2280
  Sorted by residual:
  dihedral pdb=" CD  ARG B 366 "
           pdb=" NE  ARG B 366 "
           pdb=" CZ  ARG B 366 "
           pdb=" NH1 ARG B 366 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -30.55   30.55     1      1.00e+01 1.00e-02 1.33e+01
  dihedral pdb=" CD  ARG A 366 "
           pdb=" NE  ARG A 366 "
           pdb=" CZ  ARG A 366 "
           pdb=" NH1 ARG A 366 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -30.49   30.49     1      1.00e+01 1.00e-02 1.33e+01
  dihedral pdb=" CG  ARG B 104 "
           pdb=" CD  ARG B 104 "
           pdb=" NE  ARG B 104 "
           pdb=" CZ  ARG B 104 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00  134.89  -44.89     2      1.50e+01 4.44e-03 1.06e+01
  ... (remaining 3635 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.090: 995
       0.090 -    0.179: 28
       0.179 -    0.269: 7
       0.269 -    0.359: 0
       0.359 -    0.448: 2
  Chirality restraints: 1032
  Sorted by residual:
  chirality pdb=" CB  VAL B 389 "
            pdb=" CA  VAL B 389 "
            pdb=" CG1 VAL B 389 "
            pdb=" CG2 VAL B 389 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.18   -0.45 2.00e-01 2.50e+01 5.02e+00
  chirality pdb=" CB  VAL A 389 "
            pdb=" CA  VAL A 389 "
            pdb=" CG1 VAL A 389 "
            pdb=" CG2 VAL A 389 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.18   -0.45 2.00e-01 2.50e+01 5.02e+00
  chirality pdb=" CA  ILE A 546 "
            pdb=" N   ILE A 546 "
            pdb=" C   ILE A 546 "
            pdb=" CB  ILE A 546 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.67   -0.23 2.00e-01 2.50e+01 1.35e+00
  ... (remaining 1029 not shown)

  Planarity restraints: 1042
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 366 "    0.544 9.50e-02 1.11e+02   2.44e-01 3.64e+01
        pdb=" NE  ARG B 366 "   -0.033 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 366 "   -0.004 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 366 "   -0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 366 "    0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 366 "   -0.544 9.50e-02 1.11e+02   2.44e-01 3.63e+01
        pdb=" NE  ARG A 366 "    0.033 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 366 "    0.004 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 366 "    0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 366 "   -0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 293 "   -0.038 5.00e-02 4.00e+02   5.79e-02 5.36e+00
        pdb=" N   PRO A 294 "    0.100 5.00e-02 4.00e+02
        pdb=" CA  PRO A 294 "   -0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO A 294 "   -0.032 5.00e-02 4.00e+02
  ... (remaining 1039 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 964
        2.75 -     3.29: 6261
        3.29 -     3.83: 11054
        3.83 -     4.36: 12647
        4.36 -     4.90: 22100
  Nonbonded interactions: 53026
  Sorted by model distance:
  nonbonded pdb=" O   PHE B 421 "
            pdb=" OG  SER B 425 "
     model   vdw
     2.215 3.040
  nonbonded pdb=" O   PHE A 421 "
            pdb=" OG  SER A 425 "
     model   vdw
     2.215 3.040
  nonbonded pdb=" O   ASN A 248 "
            pdb=" OG  SER A 252 "
     model   vdw
     2.243 3.040
  nonbonded pdb=" O   ASN B 248 "
            pdb=" OG  SER B 252 "
     model   vdw
     2.244 3.040
  nonbonded pdb=" O   VAL A 147 "
            pdb=" OG1 THR A 151 "
     model   vdw
     2.272 3.040
  ... (remaining 53021 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.010
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.290
  Check model and map are aligned:         0.050
  Set scattering table:                    0.050
  Process input model:                     20.150
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.110
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.820
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6497
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      :  0.005   0.073   6396  Z= 0.320
  Angle     :  0.664   7.660   8698  Z= 0.436
  Chirality :  0.046   0.448   1032
  Planarity :  0.012   0.244   1042
  Dihedral  : 16.571  62.762   2170
  Min Nonbonded Distance : 2.215

Molprobity Statistics.
  All-atom Clashscore : 7.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 29.55 %
    Favored  : 70.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.97 (0.30), residues: 754
  helix:  1.80 (0.19), residues: 652
  sheet:  None (None), residues: 0
  loop : -1.92 (0.63), residues: 102

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 509 
 HIS   0.003   0.001   HIS A 519 
 PHE   0.009   0.001   PHE A 110 
 TYR   0.024   0.002   TYR B 560 
 ARG   0.004   0.000   ARG B 490 

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

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

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 206
  time to evaluate  : 0.688 
Fit side-chains
REVERT: A  245 TYR cc_start: 0.4530 (t80) cc_final: 0.2606 (t80)
REVERT: B  245 TYR cc_start: 0.4502 (t80) cc_final: 0.2548 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 206
  average time/residue: 0.1680
  time to fit residues: 45.8591
Evaluate side-chains
  120 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 0.658 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 65 optimal weight:    4.9990
   chunk 59 optimal weight:    0.2980
   chunk 32 optimal weight:    0.8980
   chunk 20 optimal weight:    0.9980
   chunk 39 optimal weight:    0.6980
   chunk 31 optimal weight:    5.9990
   chunk 61 optimal weight:    1.9990
   chunk 23 optimal weight:    0.5980
   chunk 37 optimal weight:    1.9990
   chunk 45 optimal weight:    4.9990
   chunk 70 optimal weight:   10.0000
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A  53 ASN
A 139 HIS
A 143 GLN
A 150 GLN
A 180 ASN
A 333 ASN
** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 139 HIS
B 143 GLN
B 150 GLN
B 180 ASN
B 333 ASN
** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4546 r_free = 0.4546 target = 0.208970 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4183 r_free = 0.4183 target = 0.174749 restraints weight = 9637.624|
|-----------------------------------------------------------------------------|
r_work (start): 0.4168 rms_B_bonded: 2.46
r_work: 0.4011 rms_B_bonded: 4.22 restraints_weight: 0.5000
r_work (final): 0.4011
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7266
moved from start:          0.3683

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6396  Z= 0.206
  Angle     :  0.571   7.065   8698  Z= 0.298
  Chirality :  0.039   0.169   1032
  Planarity :  0.005   0.055   1042
  Dihedral  :  3.724  30.562    846
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 8.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 22.24 %
    Favored  : 74.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.62 (0.29), residues: 754
  helix:  2.19 (0.19), residues: 658
  sheet:  None (None), residues: 0
  loop : -1.61 (0.62), residues: 96

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 102 
 HIS   0.004   0.001   HIS A 165 
 PHE   0.009   0.002   PHE B 544 
 TYR   0.010   0.001   TYR B 351 
 ARG   0.002   0.000   ARG A 428 

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

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

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 164
  time to evaluate  : 0.633 
Fit side-chains
   revert: symmetry clash
REVERT: A  245 TYR cc_start: 0.5463 (t80) cc_final: 0.2917 (t80)
REVERT: B   65 LEU cc_start: 0.7017 (OUTLIER) cc_final: 0.6788 (tp)
REVERT: B  174 MET cc_start: 0.7790 (mmt) cc_final: 0.7519 (mmt)
REVERT: B  245 TYR cc_start: 0.5286 (t80) cc_final: 0.2675 (t80)
  outliers start: 21
  outliers final: 10
  residues processed: 176
  average time/residue: 0.1290
  time to fit residues: 32.5224
Evaluate side-chains
  142 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 131
  time to evaluate  : 0.652 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 LEU
Chi-restraints excluded: chain A residue  180 ASN
Chi-restraints excluded: chain A residue  194 HIS
Chi-restraints excluded: chain A residue  389 VAL
Chi-restraints excluded: chain A residue  557 LEU
Chi-restraints excluded: chain B residue   35 LEU
Chi-restraints excluded: chain B residue   65 LEU
Chi-restraints excluded: chain B residue   75 LEU
Chi-restraints excluded: chain B residue  180 ASN
Chi-restraints excluded: chain B residue  194 HIS
Chi-restraints excluded: chain B residue  389 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 18 optimal weight:    8.9990
   chunk 67 optimal weight:    0.9980
   chunk 54 optimal weight:    0.3980
   chunk 32 optimal weight:    8.9990
   chunk 48 optimal weight:    0.7980
   chunk 10 optimal weight:    3.9990
   chunk 76 optimal weight:    1.9990
   chunk 58 optimal weight:    6.9990
   chunk 64 optimal weight:    0.9980
   chunk 16 optimal weight:    0.7980
   chunk 65 optimal weight:    0.7980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 418 GLN
A 519 HIS
** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 400 GLN
B 418 GLN
B 519 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4452 r_free = 0.4452 target = 0.198519 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.164035 restraints weight = 9510.118|
|-----------------------------------------------------------------------------|
r_work (start): 0.4053 rms_B_bonded: 2.29
r_work: 0.3857 rms_B_bonded: 4.02 restraints_weight: 0.5000
r_work (final): 0.3857
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7533
moved from start:          0.4939

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   6396  Z= 0.206
  Angle     :  0.565  12.200   8698  Z= 0.286
  Chirality :  0.039   0.188   1032
  Planarity :  0.004   0.056   1042
  Dihedral  :  3.675  27.026    846
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 10.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.80 %
    Favored  : 99.20 %
  Rotamer:
    Outliers :  4.33 %
    Allowed  : 22.84 %
    Favored  : 72.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.88 (0.29), residues: 754
  helix:  2.34 (0.19), residues: 652
  sheet:  None (None), residues: 0
  loop : -1.06 (0.60), residues: 102

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A 184 
 HIS   0.003   0.001   HIS B 551 
 PHE   0.021   0.001   PHE B 332 
 TYR   0.021   0.002   TYR A 311 
 ARG   0.002   0.000   ARG B 428 

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

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

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 135
  time to evaluate  : 0.701 
Fit side-chains
   revert: symmetry clash
REVERT: A  245 TYR cc_start: 0.5276 (t80) cc_final: 0.3133 (t80)
REVERT: A  264 LYS cc_start: 0.8072 (ttmt) cc_final: 0.7661 (ttmt)
REVERT: A  509 TRP cc_start: 0.7492 (t60) cc_final: 0.6805 (t60)
REVERT: A  511 MET cc_start: 0.5599 (mpp) cc_final: 0.5038 (mmm)
REVERT: B  174 MET cc_start: 0.8143 (mmt) cc_final: 0.7930 (mmt)
REVERT: B  245 TYR cc_start: 0.5199 (t80) cc_final: 0.3033 (t80)
REVERT: B  264 LYS cc_start: 0.8113 (ttmt) cc_final: 0.7724 (ttmt)
REVERT: B  366 ARG cc_start: 0.2254 (OUTLIER) cc_final: 0.1788 (tpt170)
REVERT: B  368 LEU cc_start: 0.5265 (tm) cc_final: 0.4738 (tp)
REVERT: B  509 TRP cc_start: 0.7549 (t60) cc_final: 0.6921 (t60)
  outliers start: 29
  outliers final: 17
  residues processed: 155
  average time/residue: 0.1497
  time to fit residues: 32.0513
Evaluate side-chains
  137 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 119
  time to evaluate  : 0.684 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 VAL
Chi-restraints excluded: chain A residue   66 LEU
Chi-restraints excluded: chain A residue   71 LEU
Chi-restraints excluded: chain A residue   75 LEU
Chi-restraints excluded: chain A residue  194 HIS
Chi-restraints excluded: chain A residue  298 LEU
Chi-restraints excluded: chain A residue  342 LEU
Chi-restraints excluded: chain A residue  389 VAL
Chi-restraints excluded: chain A residue  503 LEU
Chi-restraints excluded: chain B residue   55 VAL
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain B residue   71 LEU
Chi-restraints excluded: chain B residue   75 LEU
Chi-restraints excluded: chain B residue  165 HIS
Chi-restraints excluded: chain B residue  194 HIS
Chi-restraints excluded: chain B residue  342 LEU
Chi-restraints excluded: chain B residue  366 ARG
Chi-restraints excluded: chain B residue  389 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 21 optimal weight:    5.9990
   chunk 77 optimal weight:    0.7980
   chunk 9 optimal weight:    0.6980
   chunk 59 optimal weight:    3.9990
   chunk 62 optimal weight:    0.7980
   chunk 1 optimal weight:    0.5980
   chunk 58 optimal weight:    6.9990
   chunk 45 optimal weight:    4.9990
   chunk 6 optimal weight:    4.9990
   chunk 44 optimal weight:    0.8980
   chunk 61 optimal weight:    0.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 150 GLN
A 180 ASN
A 321 HIS
B 150 GLN
B 180 ASN
B 321 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4378 r_free = 0.4378 target = 0.191156 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.152990 restraints weight = 9231.451|
|-----------------------------------------------------------------------------|
r_work (start): 0.3925 rms_B_bonded: 2.40
r_work: 0.3727 rms_B_bonded: 4.11 restraints_weight: 0.5000
r_work (final): 0.3727
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7744
moved from start:          0.6291

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   6396  Z= 0.205
  Angle     :  0.569  10.377   8698  Z= 0.281
  Chirality :  0.038   0.178   1032
  Planarity :  0.005   0.053   1042
  Dihedral  :  3.669  27.336    846
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 9.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  4.78 %
    Allowed  : 24.33 %
    Favored  : 70.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.03 (0.29), residues: 754
  helix:  2.49 (0.19), residues: 652
  sheet:  None (None), residues: 0
  loop : -1.41 (0.59), residues: 102

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP B 102 
 HIS   0.004   0.001   HIS B 551 
 PHE   0.013   0.001   PHE B 514 
 TYR   0.010   0.001   TYR B 311 
 ARG   0.004   0.000   ARG B 323 

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

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

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 126
  time to evaluate  : 0.689 
Fit side-chains
REVERT: A  143 GLN cc_start: 0.8067 (OUTLIER) cc_final: 0.5806 (tp-100)
REVERT: A  156 ILE cc_start: 0.8476 (mm) cc_final: 0.8222 (tt)
REVERT: A  245 TYR cc_start: 0.5345 (t80) cc_final: 0.3345 (t80)
REVERT: A  264 LYS cc_start: 0.8126 (ttmt) cc_final: 0.7706 (tptt)
REVERT: A  509 TRP cc_start: 0.7721 (t60) cc_final: 0.7397 (t60)
REVERT: A  511 MET cc_start: 0.5936 (mpp) cc_final: 0.5619 (mmm)
REVERT: B   65 LEU cc_start: 0.7390 (OUTLIER) cc_final: 0.7099 (tp)
REVERT: B  143 GLN cc_start: 0.8069 (OUTLIER) cc_final: 0.5711 (tp-100)
REVERT: B  156 ILE cc_start: 0.8456 (mm) cc_final: 0.8191 (tt)
REVERT: B  185 MET cc_start: 0.8402 (tpp) cc_final: 0.8153 (tpp)
REVERT: B  245 TYR cc_start: 0.5361 (t80) cc_final: 0.3347 (t80)
REVERT: B  264 LYS cc_start: 0.8118 (ttmt) cc_final: 0.7691 (tptt)
REVERT: B  366 ARG cc_start: 0.2620 (OUTLIER) cc_final: 0.2141 (tpt90)
REVERT: B  368 LEU cc_start: 0.6092 (tm) cc_final: 0.5876 (tp)
REVERT: B  511 MET cc_start: 0.6004 (mpp) cc_final: 0.5715 (mmm)
  outliers start: 32
  outliers final: 14
  residues processed: 150
  average time/residue: 0.1552
  time to fit residues: 31.6548
Evaluate side-chains
  126 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 108
  time to evaluate  : 0.631 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 VAL
Chi-restraints excluded: chain A residue   66 LEU
Chi-restraints excluded: chain A residue  143 GLN
Chi-restraints excluded: chain A residue  165 HIS
Chi-restraints excluded: chain A residue  180 ASN
Chi-restraints excluded: chain A residue  298 LEU
Chi-restraints excluded: chain A residue  342 LEU
Chi-restraints excluded: chain A residue  389 VAL
Chi-restraints excluded: chain B residue   55 VAL
Chi-restraints excluded: chain B residue   65 LEU
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain B residue  143 GLN
Chi-restraints excluded: chain B residue  165 HIS
Chi-restraints excluded: chain B residue  180 ASN
Chi-restraints excluded: chain B residue  298 LEU
Chi-restraints excluded: chain B residue  342 LEU
Chi-restraints excluded: chain B residue  366 ARG
Chi-restraints excluded: chain B residue  389 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 45 optimal weight:    0.8980
   chunk 11 optimal weight:    4.9990
   chunk 29 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9990
   chunk 71 optimal weight:    6.9990
   chunk 43 optimal weight:    0.9990
   chunk 20 optimal weight:    3.9990
   chunk 61 optimal weight:    5.9990
   chunk 51 optimal weight:    5.9990
   chunk 22 optimal weight:    2.9990
   chunk 46 optimal weight:    0.9980
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
A 180 ASN
** A 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 551 HIS
B 180 ASN
** B 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4294 r_free = 0.4294 target = 0.183063 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.145817 restraints weight = 9173.935|
|-----------------------------------------------------------------------------|
r_work (start): 0.3830 rms_B_bonded: 2.51
r_work: 0.3611 rms_B_bonded: 4.10 restraints_weight: 0.5000
r_work (final): 0.3611
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7893
moved from start:          0.7147

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6396  Z= 0.210
  Angle     :  0.551   9.468   8698  Z= 0.278
  Chirality :  0.040   0.170   1032
  Planarity :  0.004   0.055   1042
  Dihedral  :  3.799  29.127    846
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 9.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.80 %
    Favored  : 99.20 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  : 25.07 %
    Favored  : 71.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.88 (0.29), residues: 754
  helix:  2.45 (0.19), residues: 646
  sheet:  None (None), residues: 0
  loop : -1.71 (0.56), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP B 102 
 HIS   0.007   0.001   HIS B 551 
 PHE   0.015   0.001   PHE B 332 
 TYR   0.014   0.002   TYR A  58 
 ARG   0.002   0.000   ARG B 323 

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

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

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 118
  time to evaluate  : 0.647 
Fit side-chains
REVERT: A  143 GLN cc_start: 0.8127 (OUTLIER) cc_final: 0.5998 (tp-100)
REVERT: A  156 ILE cc_start: 0.8593 (mm) cc_final: 0.8299 (tt)
REVERT: A  264 LYS cc_start: 0.8187 (ttmt) cc_final: 0.7726 (tptt)
REVERT: A  509 TRP cc_start: 0.7890 (t60) cc_final: 0.7456 (t60)
REVERT: B   65 LEU cc_start: 0.7763 (OUTLIER) cc_final: 0.7498 (tp)
REVERT: B  143 GLN cc_start: 0.8159 (OUTLIER) cc_final: 0.5886 (tp-100)
REVERT: B  156 ILE cc_start: 0.8513 (mm) cc_final: 0.8269 (tt)
REVERT: B  264 LYS cc_start: 0.8256 (ttmt) cc_final: 0.7736 (tptt)
REVERT: B  366 ARG cc_start: 0.3258 (OUTLIER) cc_final: 0.2777 (tpt90)
REVERT: B  490 ARG cc_start: 0.6670 (ttm-80) cc_final: 0.6388 (ptp-170)
REVERT: B  509 TRP cc_start: 0.7629 (t60) cc_final: 0.7165 (t60)
  outliers start: 25
  outliers final: 10
  residues processed: 139
  average time/residue: 0.1658
  time to fit residues: 31.0438
Evaluate side-chains
  113 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 99
  time to evaluate  : 0.677 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 VAL
Chi-restraints excluded: chain A residue   66 LEU
Chi-restraints excluded: chain A residue  143 GLN
Chi-restraints excluded: chain A residue  165 HIS
Chi-restraints excluded: chain A residue  194 HIS
Chi-restraints excluded: chain A residue  389 VAL
Chi-restraints excluded: chain B residue   55 VAL
Chi-restraints excluded: chain B residue   65 LEU
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain B residue  143 GLN
Chi-restraints excluded: chain B residue  165 HIS
Chi-restraints excluded: chain B residue  194 HIS
Chi-restraints excluded: chain B residue  366 ARG
Chi-restraints excluded: chain B residue  389 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 25 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   chunk 72 optimal weight:    0.9980
   chunk 45 optimal weight:    0.0980
   chunk 16 optimal weight:    0.6980
   chunk 34 optimal weight:    0.9990
   chunk 32 optimal weight:    0.7980
   chunk 54 optimal weight:   10.0000
   chunk 76 optimal weight:    0.8980
   chunk 21 optimal weight:    0.8980
   chunk 68 optimal weight:    0.7980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 180 ASN
** A 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 180 ASN
** B 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 551 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4290 r_free = 0.4290 target = 0.182361 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.140894 restraints weight = 8977.783|
|-----------------------------------------------------------------------------|
r_work (start): 0.3777 rms_B_bonded: 2.43
r_work: 0.3607 rms_B_bonded: 3.95 restraints_weight: 0.5000
r_work (final): 0.3607
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7915
moved from start:          0.7724

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6396  Z= 0.175
  Angle     :  0.530   9.224   8698  Z= 0.260
  Chirality :  0.038   0.188   1032
  Planarity :  0.004   0.051   1042
  Dihedral  :  3.729  27.278    846
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 8.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.06 %
    Favored  : 98.94 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 26.12 %
    Favored  : 71.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.09 (0.29), residues: 754
  helix:  2.61 (0.19), residues: 646
  sheet:  None (None), residues: 0
  loop : -1.72 (0.56), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP B 102 
 HIS   0.003   0.001   HIS A 427 
 PHE   0.017   0.001   PHE B 353 
 TYR   0.009   0.001   TYR B 548 
 ARG   0.002   0.000   ARG A 428 

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

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

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 106
  time to evaluate  : 0.717 
Fit side-chains
REVERT: A  143 GLN cc_start: 0.8170 (OUTLIER) cc_final: 0.6001 (tp-100)
REVERT: A  156 ILE cc_start: 0.8523 (mm) cc_final: 0.8232 (tt)
REVERT: A  264 LYS cc_start: 0.8111 (ttmt) cc_final: 0.7703 (tptt)
REVERT: A  366 ARG cc_start: 0.3396 (OUTLIER) cc_final: 0.2892 (tpt90)
REVERT: A  509 TRP cc_start: 0.7916 (t60) cc_final: 0.7497 (t60)
REVERT: A  511 MET cc_start: 0.6801 (mmt) cc_final: 0.6523 (mmt)
REVERT: B   34 LEU cc_start: 0.8887 (tp) cc_final: 0.8668 (tp)
REVERT: B   65 LEU cc_start: 0.7809 (OUTLIER) cc_final: 0.7556 (tp)
REVERT: B  143 GLN cc_start: 0.8146 (OUTLIER) cc_final: 0.5946 (tp-100)
REVERT: B  156 ILE cc_start: 0.8555 (mm) cc_final: 0.8255 (tt)
REVERT: B  264 LYS cc_start: 0.8156 (ttmt) cc_final: 0.7677 (tptt)
REVERT: B  366 ARG cc_start: 0.3503 (OUTLIER) cc_final: 0.2979 (tpt90)
REVERT: B  509 TRP cc_start: 0.7743 (t60) cc_final: 0.7047 (t60)
  outliers start: 18
  outliers final: 11
  residues processed: 121
  average time/residue: 0.1583
  time to fit residues: 26.3390
Evaluate side-chains
  113 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 97
  time to evaluate  : 0.717 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 VAL
Chi-restraints excluded: chain A residue   66 LEU
Chi-restraints excluded: chain A residue  143 GLN
Chi-restraints excluded: chain A residue  165 HIS
Chi-restraints excluded: chain A residue  180 ASN
Chi-restraints excluded: chain A residue  194 HIS
Chi-restraints excluded: chain A residue  342 LEU
Chi-restraints excluded: chain A residue  351 TYR
Chi-restraints excluded: chain A residue  366 ARG
Chi-restraints excluded: chain B residue   55 VAL
Chi-restraints excluded: chain B residue   65 LEU
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain B residue  143 GLN
Chi-restraints excluded: chain B residue  180 ASN
Chi-restraints excluded: chain B residue  342 LEU
Chi-restraints excluded: chain B residue  366 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 46 optimal weight:    2.9990
   chunk 75 optimal weight:    0.9990
   chunk 17 optimal weight:    3.9990
   chunk 33 optimal weight:    1.9990
   chunk 49 optimal weight:    2.9990
   chunk 43 optimal weight:    1.9990
   chunk 61 optimal weight:    2.9990
   chunk 35 optimal weight:    0.8980
   chunk 72 optimal weight:    5.9990
   chunk 41 optimal weight:    2.9990
   chunk 69 optimal weight:    0.7980
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
A  38 ASN
A 180 ASN
B 180 ASN
B 505 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4187 r_free = 0.4187 target = 0.172568 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.134845 restraints weight = 9163.334|
|-----------------------------------------------------------------------------|
r_work (start): 0.3709 rms_B_bonded: 2.32
r_work: 0.3489 rms_B_bonded: 3.84 restraints_weight: 0.5000
r_work (final): 0.3489
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8067
moved from start:          0.8678

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   6396  Z= 0.240
  Angle     :  0.629  12.303   8698  Z= 0.309
  Chirality :  0.044   0.446   1032
  Planarity :  0.005   0.052   1042
  Dihedral  :  4.132  31.820    846
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 8.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.66 %
    Favored  : 99.34 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 23.73 %
    Favored  : 72.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.65 (0.29), residues: 754
  helix:  2.29 (0.19), residues: 650
  sheet:  None (None), residues: 0
  loop : -1.92 (0.57), residues: 104

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP B 102 
 HIS   0.004   0.001   HIS B 415 
 PHE   0.018   0.002   PHE A 332 
 TYR   0.011   0.002   TYR A 245 
 ARG   0.002   0.000   ARG A 323 

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

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

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 126
  time to evaluate  : 0.714 
Fit side-chains
REVERT: A   58 TYR cc_start: 0.6013 (m-80) cc_final: 0.5259 (m-80)
REVERT: A   63 PHE cc_start: 0.8182 (m-10) cc_final: 0.7757 (m-80)
REVERT: A  120 PHE cc_start: 0.6506 (m-80) cc_final: 0.6173 (m-80)
REVERT: A  124 TYR cc_start: 0.3292 (t80) cc_final: 0.1904 (t80)
REVERT: A  125 TYR cc_start: 0.5402 (m-10) cc_final: 0.5028 (m-10)
REVERT: A  143 GLN cc_start: 0.7832 (OUTLIER) cc_final: 0.7521 (tt0)
REVERT: A  264 LYS cc_start: 0.8213 (ttmt) cc_final: 0.7797 (tptt)
REVERT: A  296 LEU cc_start: 0.8234 (mt) cc_final: 0.8003 (mp)
REVERT: A  351 TYR cc_start: 0.6690 (OUTLIER) cc_final: 0.6206 (m-80)
REVERT: A  366 ARG cc_start: 0.4515 (OUTLIER) cc_final: 0.3854 (mmm160)
REVERT: A  509 TRP cc_start: 0.8048 (t60) cc_final: 0.7749 (t60)
REVERT: A  511 MET cc_start: 0.7677 (mmt) cc_final: 0.7454 (mtt)
REVERT: A  519 HIS cc_start: 0.5709 (t70) cc_final: 0.5252 (m90)
REVERT: B  124 TYR cc_start: 0.3081 (t80) cc_final: 0.1828 (t80)
REVERT: B  125 TYR cc_start: 0.5334 (m-10) cc_final: 0.4933 (m-10)
REVERT: B  143 GLN cc_start: 0.7834 (OUTLIER) cc_final: 0.7546 (tt0)
REVERT: B  264 LYS cc_start: 0.8168 (ttmt) cc_final: 0.7734 (tptt)
REVERT: B  296 LEU cc_start: 0.8294 (mt) cc_final: 0.8032 (mp)
REVERT: B  366 ARG cc_start: 0.4567 (OUTLIER) cc_final: 0.3806 (tpt90)
REVERT: B  511 MET cc_start: 0.7842 (mmm) cc_final: 0.7639 (mmm)
  outliers start: 22
  outliers final: 11
  residues processed: 145
  average time/residue: 0.1456
  time to fit residues: 29.2548
Evaluate side-chains
  136 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 120
  time to evaluate  : 0.631 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 VAL
Chi-restraints excluded: chain A residue  143 GLN
Chi-restraints excluded: chain A residue  165 HIS
Chi-restraints excluded: chain A residue  194 HIS
Chi-restraints excluded: chain A residue  298 LEU
Chi-restraints excluded: chain A residue  342 LEU
Chi-restraints excluded: chain A residue  351 TYR
Chi-restraints excluded: chain A residue  366 ARG
Chi-restraints excluded: chain A residue  389 VAL
Chi-restraints excluded: chain A residue  409 LEU
Chi-restraints excluded: chain B residue   55 VAL
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain B residue  143 GLN
Chi-restraints excluded: chain B residue  165 HIS
Chi-restraints excluded: chain B residue  366 ARG
Chi-restraints excluded: chain B residue  389 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 29 optimal weight:    0.8980
   chunk 32 optimal weight:    1.9990
   chunk 64 optimal weight:    0.0980
   chunk 38 optimal weight:    0.6980
   chunk 62 optimal weight:    0.6980
   chunk 23 optimal weight:    0.6980
   chunk 10 optimal weight:    0.9990
   chunk 65 optimal weight:    0.9990
   chunk 52 optimal weight:    0.6980
   chunk 39 optimal weight:    1.9990
   chunk 36 optimal weight:    0.7980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A 150 GLN
A 180 ASN
A 505 ASN
B 150 GLN
B 180 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4184 r_free = 0.4184 target = 0.172722 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.134051 restraints weight = 8913.548|
|-----------------------------------------------------------------------------|
r_work (start): 0.3696 rms_B_bonded: 2.32
r_work: 0.3529 rms_B_bonded: 3.77 restraints_weight: 0.5000
r_work (final): 0.3529
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8014
moved from start:          0.8948

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6396  Z= 0.173
  Angle     :  0.565  14.203   8698  Z= 0.271
  Chirality :  0.040   0.351   1032
  Planarity :  0.004   0.050   1042
  Dihedral  :  3.822  24.408    846
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 8.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.33 %
    Favored  : 98.67 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 24.93 %
    Favored  : 71.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.18 (0.30), residues: 754
  helix:  2.68 (0.19), residues: 646
  sheet:  None (None), residues: 0
  loop : -1.81 (0.55), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B 102 
 HIS   0.003   0.000   HIS A 415 
 PHE   0.019   0.001   PHE A 353 
 TYR   0.018   0.001   TYR B 548 
 ARG   0.001   0.000   ARG A 366 

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

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

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 119
  time to evaluate  : 0.794 
Fit side-chains
REVERT: A   63 PHE cc_start: 0.8189 (m-10) cc_final: 0.7838 (m-80)
REVERT: A  124 TYR cc_start: 0.3469 (t80) cc_final: 0.2130 (t80)
REVERT: A  264 LYS cc_start: 0.8238 (ttmt) cc_final: 0.7779 (tptt)
REVERT: A  288 GLU cc_start: 0.3518 (OUTLIER) cc_final: 0.2983 (tp30)
REVERT: A  296 LEU cc_start: 0.8246 (mt) cc_final: 0.8035 (mp)
REVERT: A  351 TYR cc_start: 0.6587 (OUTLIER) cc_final: 0.6070 (m-80)
REVERT: A  366 ARG cc_start: 0.4970 (OUTLIER) cc_final: 0.4384 (mmm160)
REVERT: A  519 HIS cc_start: 0.5667 (t70) cc_final: 0.5151 (m90)
REVERT: B  124 TYR cc_start: 0.3098 (t80) cc_final: 0.2055 (t80)
REVERT: B  125 TYR cc_start: 0.5433 (m-10) cc_final: 0.5114 (m-10)
REVERT: B  264 LYS cc_start: 0.8112 (ttmt) cc_final: 0.7673 (tptt)
REVERT: B  288 GLU cc_start: 0.3576 (OUTLIER) cc_final: 0.3034 (tp30)
REVERT: B  296 LEU cc_start: 0.8290 (mt) cc_final: 0.8046 (mp)
REVERT: B  366 ARG cc_start: 0.4704 (OUTLIER) cc_final: 0.4242 (mmm160)
REVERT: B  509 TRP cc_start: 0.7730 (t60) cc_final: 0.7485 (t60)
  outliers start: 21
  outliers final: 8
  residues processed: 136
  average time/residue: 0.1572
  time to fit residues: 29.3840
Evaluate side-chains
  126 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 113
  time to evaluate  : 0.645 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 VAL
Chi-restraints excluded: chain A residue  165 HIS
Chi-restraints excluded: chain A residue  288 GLU
Chi-restraints excluded: chain A residue  351 TYR
Chi-restraints excluded: chain A residue  366 ARG
Chi-restraints excluded: chain A residue  426 LEU
Chi-restraints excluded: chain B residue   55 VAL
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain B residue  165 HIS
Chi-restraints excluded: chain B residue  288 GLU
Chi-restraints excluded: chain B residue  366 ARG
Chi-restraints excluded: chain B residue  389 VAL
Chi-restraints excluded: chain B residue  426 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 54 optimal weight:    0.0670
   chunk 74 optimal weight:    4.9990
   chunk 17 optimal weight:    0.5980
   chunk 0 optimal weight:    9.9990
   chunk 1 optimal weight:    3.9990
   chunk 50 optimal weight:    2.9990
   chunk 9 optimal weight:    4.9990
   chunk 31 optimal weight:    4.9990
   chunk 51 optimal weight:    2.9990
   chunk 77 optimal weight:    0.9990
   chunk 56 optimal weight:    0.5980
   overall best weight:    1.0522

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4126 r_free = 0.4126 target = 0.167349 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.127984 restraints weight = 9059.267|
|-----------------------------------------------------------------------------|
r_work (start): 0.3622 rms_B_bonded: 2.35
r_work: 0.3442 rms_B_bonded: 3.88 restraints_weight: 0.5000
r_work (final): 0.3442
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8124
moved from start:          0.9488

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6396  Z= 0.211
  Angle     :  0.589  11.787   8698  Z= 0.286
  Chirality :  0.041   0.297   1032
  Planarity :  0.005   0.051   1042
  Dihedral  :  3.996  26.286    846
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 7.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.80 %
    Favored  : 99.20 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 25.82 %
    Favored  : 72.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.15 (0.30), residues: 754
  helix:  2.65 (0.19), residues: 650
  sheet:  None (None), residues: 0
  loop : -1.91 (0.54), residues: 104

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B 102 
 HIS   0.004   0.001   HIS B 415 
 PHE   0.019   0.001   PHE B  79 
 TYR   0.030   0.002   TYR B 548 
 ARG   0.002   0.000   ARG B  86 

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

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

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 127
  time to evaluate  : 0.657 
Fit side-chains
REVERT: A  120 PHE cc_start: 0.6912 (m-80) cc_final: 0.6514 (m-80)
REVERT: A  135 ILE cc_start: 0.7578 (OUTLIER) cc_final: 0.7063 (mt)
REVERT: A  264 LYS cc_start: 0.8201 (ttmt) cc_final: 0.7710 (tptt)
REVERT: A  351 TYR cc_start: 0.6638 (OUTLIER) cc_final: 0.6043 (m-80)
REVERT: A  366 ARG cc_start: 0.5329 (OUTLIER) cc_final: 0.4704 (mmm160)
REVERT: A  519 HIS cc_start: 0.5631 (t70) cc_final: 0.4999 (m90)
REVERT: B  120 PHE cc_start: 0.6825 (m-80) cc_final: 0.6451 (m-80)
REVERT: B  264 LYS cc_start: 0.8172 (ttmt) cc_final: 0.7672 (tptt)
  outliers start: 13
  outliers final: 5
  residues processed: 136
  average time/residue: 0.1403
  time to fit residues: 26.7432
Evaluate side-chains
  132 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 124
  time to evaluate  : 0.630 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 VAL
Chi-restraints excluded: chain A residue  135 ILE
Chi-restraints excluded: chain A residue  165 HIS
Chi-restraints excluded: chain A residue  351 TYR
Chi-restraints excluded: chain A residue  366 ARG
Chi-restraints excluded: chain A residue  389 VAL
Chi-restraints excluded: chain B residue   55 VAL
Chi-restraints excluded: chain B residue  389 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 12 optimal weight:    2.9990
   chunk 58 optimal weight:    1.9990
   chunk 38 optimal weight:    0.8980
   chunk 34 optimal weight:    0.6980
   chunk 3 optimal weight:    4.9990
   chunk 24 optimal weight:   10.0000
   chunk 67 optimal weight:    6.9990
   chunk 69 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9990
   chunk 77 optimal weight:    3.9990
   chunk 20 optimal weight:    4.9990
   overall best weight:    1.0984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4114 r_free = 0.4114 target = 0.165657 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.126710 restraints weight = 9118.199|
|-----------------------------------------------------------------------------|
r_work (start): 0.3610 rms_B_bonded: 2.39
r_work: 0.3437 rms_B_bonded: 3.84 restraints_weight: 0.5000
r_work (final): 0.3437
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8125
moved from start:          0.9792

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6396  Z= 0.210
  Angle     :  0.574   9.743   8698  Z= 0.286
  Chirality :  0.041   0.267   1032
  Planarity :  0.005   0.051   1042
  Dihedral  :  4.023  26.533    846
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 8.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.80 %
    Favored  : 99.20 %
  Rotamer:
    Outliers :  1.19 %
    Allowed  : 26.12 %
    Favored  : 72.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.19 (0.30), residues: 754
  helix:  2.70 (0.19), residues: 646
  sheet:  None (None), residues: 0
  loop : -1.89 (0.53), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B 509 
 HIS   0.004   0.001   HIS B 415 
 PHE   0.021   0.001   PHE B  79 
 TYR   0.027   0.002   TYR B 548 
 ARG   0.002   0.000   ARG B 352 

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

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

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 126
  time to evaluate  : 0.693 
Fit side-chains
REVERT: A  264 LYS cc_start: 0.8215 (ttmt) cc_final: 0.7714 (tptt)
REVERT: A  351 TYR cc_start: 0.6705 (OUTLIER) cc_final: 0.6109 (m-80)
REVERT: A  519 HIS cc_start: 0.5649 (t70) cc_final: 0.4953 (m90)
REVERT: B  264 LYS cc_start: 0.8169 (ttmt) cc_final: 0.7678 (tptt)
REVERT: B  351 TYR cc_start: 0.6650 (m-80) cc_final: 0.6380 (m-80)
REVERT: B  353 PHE cc_start: 0.6440 (m-10) cc_final: 0.6197 (m-10)
  outliers start: 8
  outliers final: 5
  residues processed: 132
  average time/residue: 0.1582
  time to fit residues: 28.5714
Evaluate side-chains
  126 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 120
  time to evaluate  : 0.703 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 VAL
Chi-restraints excluded: chain A residue   66 LEU
Chi-restraints excluded: chain A residue  135 ILE
Chi-restraints excluded: chain A residue  351 TYR
Chi-restraints excluded: chain B residue   55 VAL
Chi-restraints excluded: chain B residue  389 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 19 optimal weight:    0.9990
   chunk 28 optimal weight:    8.9990
   chunk 72 optimal weight:    0.9990
   chunk 61 optimal weight:    5.9990
   chunk 43 optimal weight:    0.7980
   chunk 73 optimal weight:    0.9990
   chunk 47 optimal weight:    2.9990
   chunk 63 optimal weight:    0.9990
   chunk 42 optimal weight:    7.9990
   chunk 35 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9980
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
A 400 GLN
B 400 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4108 r_free = 0.4108 target = 0.165132 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.126535 restraints weight = 9161.577|
|-----------------------------------------------------------------------------|
r_work (start): 0.3604 rms_B_bonded: 2.38
r_work: 0.3437 rms_B_bonded: 3.77 restraints_weight: 0.5000
r_work (final): 0.3437
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8127
moved from start:          1.0096

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6396  Z= 0.204
  Angle     :  0.575   9.776   8698  Z= 0.285
  Chirality :  0.041   0.265   1032
  Planarity :  0.004   0.051   1042
  Dihedral  :  4.097  26.569    846
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 8.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.80 %
    Favored  : 99.20 %
  Rotamer:
    Outliers :  1.19 %
    Allowed  : 25.97 %
    Favored  : 72.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.34 (0.30), residues: 754
  helix:  2.77 (0.19), residues: 648
  sheet:  None (None), residues: 0
  loop : -1.70 (0.54), residues: 106

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B 509 
 HIS   0.003   0.001   HIS B 415 
 PHE   0.021   0.001   PHE B  79 
 TYR   0.026   0.002   TYR B 548 
 ARG   0.003   0.000   ARG B 490 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3054.80 seconds
wall clock time: 53 minutes 8.88 seconds (3188.88 seconds total)