Starting phenix.real_space_refine
on Tue Feb 11 15:53:49 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ug6_42215/02_2025/8ug6_42215.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ug6_42215/02_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_42215/02_2025/8ug6_42215.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ug6_42215/02_2025/8ug6_42215.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ug6_42215/02_2025/8ug6_42215.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ug6_42215/02_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-5592/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: 5.12, per 1000 atoms: 0.82
  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: 1.40
  Conformation dependent library (CDL) restraints added in 935.8 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: 0.48
  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: 1.98

  Time building geometry restraints manager: 1.65 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:             1.280
  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:          0.240
  Check model and map are aligned:         0.050
  Set scattering table:                    0.050
  Process input model:                     18.590
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.740
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.090
-------------------------------------------------------------------------------
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  : 0.619 
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: 0.1711
  time to fit residues: 46.9167
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  : 0.748 
-------------------------------------------------------------------------------
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 = 0.208972 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4185 r_free = 0.4185 target = 0.174894 restraints weight = 9637.101|
|-----------------------------------------------------------------------------|
r_work (start): 0.4169 rms_B_bonded: 2.44
r_work: 0.4013 rms_B_bonded: 4.19 restraints_weight: 0.5000
r_work (final): 0.4013
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7264
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  : 0.710 
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: 0.7015 (OUTLIER) cc_final: 0.6787 (tp)
REVERT: B  174 MET cc_start: 0.7789 (mmt) cc_final: 0.7518 (mmt)
REVERT: B  245 TYR cc_start: 0.5284 (t80) cc_final: 0.2675 (t80)
  outliers start: 21
  outliers final: 10
  residues processed: 176
  average time/residue: 0.1316
  time to fit residues: 33.1031
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  : 0.696 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 67 optimal weight:    2.9990
   chunk 54 optimal weight:    0.0670
   chunk 32 optimal weight:   10.0000
   chunk 48 optimal weight:    0.7980
   chunk 10 optimal weight:    1.9990
   chunk 76 optimal weight:    1.9990
   chunk 58 optimal weight:    6.9990
   chunk 64 optimal weight:    0.9980
   chunk 16 optimal weight:    0.9990
   chunk 65 optimal weight:    0.9980
   overall best weight:    0.7718

-------------------------------------------------------------------------------
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 = 0.4451 r_free = 0.4451 target = 0.198337 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.160864 restraints weight = 9500.784|
|-----------------------------------------------------------------------------|
r_work (start): 0.4014 rms_B_bonded: 2.38
r_work: 0.3846 rms_B_bonded: 4.14 restraints_weight: 0.5000
r_work (final): 0.3846
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7547
moved from start:          0.4949

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061   6396  Z= 0.216
  Angle     :  0.565  11.837   8698  Z= 0.286
  Chirality :  0.038   0.177   1032
  Planarity :  0.004   0.056   1042
  Dihedral  :  3.670  27.116    846
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 10.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.80 %
    Favored  : 99.20 %
  Rotamer:
    Outliers :  4.18 %
    Allowed  : 22.99 %
    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:  2.87 (0.29), residues: 754
  helix:  2.33 (0.19), residues: 652
  sheet:  None (None), residues: 0
  loop : -1.07 (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   0.020   0.001   PHE B 332 
 TYR   0.022   0.002   TYR A 311 
 ARG   0.002   0.000   ARG B 490 

*********************** 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
  163 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 135
  time to evaluate  : 0.654 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  245 TYR cc_start: 0.5298 (t80) cc_final: 0.3138 (t80)
REVERT: A  264 LYS cc_start: 0.8104 (ttmt) cc_final: 0.7677 (ttmt)
REVERT: A  509 TRP cc_start: 0.7467 (t60) cc_final: 0.6813 (t60)
REVERT: B  174 MET cc_start: 0.8150 (mmt) cc_final: 0.7933 (mmt)
REVERT: B  185 MET cc_start: 0.8271 (tpp) cc_final: 0.7976 (tpp)
REVERT: B  245 TYR cc_start: 0.5218 (t80) cc_final: 0.3039 (t80)
REVERT: B  264 LYS cc_start: 0.8146 (ttmt) cc_final: 0.7751 (ttmt)
REVERT: B  366 ARG cc_start: 0.2235 (OUTLIER) cc_final: 0.1775 (tpt170)
REVERT: B  368 LEU cc_start: 0.5253 (tm) cc_final: 0.4708 (tp)
REVERT: B  509 TRP cc_start: 0.7516 (t60) cc_final: 0.6921 (t60)
  outliers start: 28
  outliers final: 18
  residues processed: 155
  average time/residue: 0.1494
  time to fit residues: 32.0773
Evaluate side-chains
  138 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 119
  time to evaluate  : 0.659 
-------------------------------------------------------------------------------
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  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  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:    0.2980
   chunk 59 optimal weight:    4.9990
   chunk 62 optimal weight:    0.8980
   chunk 1 optimal weight:    0.6980
   chunk 58 optimal weight:    7.9990
   chunk 45 optimal weight:    2.9990
   chunk 6 optimal weight:    3.9990
   chunk 44 optimal weight:    0.9990
   chunk 61 optimal weight:    1.9990
   overall best weight:    0.7382

-------------------------------------------------------------------------------
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 = 0.4381 r_free = 0.4381 target = 0.191487 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.153018 restraints weight = 9213.013|
|-----------------------------------------------------------------------------|
r_work (start): 0.3926 rms_B_bonded: 2.44
r_work: 0.3730 rms_B_bonded: 4.14 restraints_weight: 0.5000
r_work (final): 0.3730
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7743
moved from start:          0.6331

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= 0.195
  Angle     :  0.577  12.997   8698  Z= 0.283
  Chirality :  0.039   0.180   1032
  Planarity :  0.005   0.055   1042
  Dihedral  :  3.676  27.093    846
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 9.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  4.93 %
    Allowed  : 23.73 %
    Favored  : 71.34 %
  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:  3.02 (0.29), residues: 754
  helix:  2.48 (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   0.011   0.001   TRP B 102 
 HIS   0.003   0.001   HIS B 551 
 PHE   0.013   0.001   PHE B 514 
 TYR   0.011   0.001   TYR B 311 
 ARG   0.005   0.000   ARG A 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
  161 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 128
  time to evaluate  : 0.619 
Fit side-chains
REVERT: A  143 GLN cc_start: 0.8044 (OUTLIER) cc_final: 0.5787 (tp-100)
REVERT: A  156 ILE cc_start: 0.8423 (mm) cc_final: 0.8185 (tt)
REVERT: A  245 TYR cc_start: 0.5356 (t80) cc_final: 0.3355 (t80)
REVERT: A  264 LYS cc_start: 0.8121 (ttmt) cc_final: 0.7686 (tptt)
REVERT: A  511 MET cc_start: 0.6002 (mpp) cc_final: 0.5723 (mmm)
REVERT: B   65 LEU cc_start: 0.7402 (OUTLIER) cc_final: 0.7108 (tp)
REVERT: B  143 GLN cc_start: 0.8128 (OUTLIER) cc_final: 0.5806 (tp-100)
REVERT: B  156 ILE cc_start: 0.8455 (mm) cc_final: 0.8214 (tt)
REVERT: B  245 TYR cc_start: 0.5336 (t80) cc_final: 0.3341 (t80)
REVERT: B  264 LYS cc_start: 0.8111 (ttmt) cc_final: 0.7694 (tptt)
REVERT: B  366 ARG cc_start: 0.2637 (OUTLIER) cc_final: 0.2126 (tpt90)
REVERT: B  368 LEU cc_start: 0.6123 (tm) cc_final: 0.5907 (tp)
  outliers start: 33
  outliers final: 13
  residues processed: 152
  average time/residue: 0.1562
  time to fit residues: 31.9330
Evaluate side-chains
  126 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 109
  time to evaluate  : 0.632 
-------------------------------------------------------------------------------
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  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:    0.5980
   chunk 11 optimal weight:    0.9980
   chunk 29 optimal weight:    0.6980
   chunk 23 optimal weight:    0.7980
   chunk 71 optimal weight:    7.9990
   chunk 43 optimal weight:    0.9990
   chunk 20 optimal weight:    4.9990
   chunk 61 optimal weight:    5.9990
   chunk 51 optimal weight:    7.9990
   chunk 22 optimal weight:    0.9980
   chunk 46 optimal weight:    0.8980
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4321 r_free = 0.4321 target = 0.185596 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.145897 restraints weight = 9175.697|
|-----------------------------------------------------------------------------|
r_work (start): 0.3827 rms_B_bonded: 2.69
r_work: 0.3645 rms_B_bonded: 4.23 restraints_weight: 0.5000
r_work (final): 0.3645
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7856
moved from start:          0.6933

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6396  Z= 0.191
  Angle     :  0.535   9.364   8698  Z= 0.267
  Chirality :  0.038   0.178   1032
  Planarity :  0.004   0.052   1042
  Dihedral  :  3.699  27.921    846
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 8.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.80 %
    Favored  : 99.20 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 25.07 %
    Favored  : 71.34 %
  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:  2.95 (0.29), residues: 754
  helix:  2.54 (0.19), residues: 642
  sheet:  None (None), residues: 0
  loop : -1.83 (0.55), residues: 112

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   0.014   0.001   PHE A 332 
 TYR   0.014   0.001   TYR A 329 
 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
  141 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 117
  time to evaluate  : 0.689 
Fit side-chains
REVERT: A  143 GLN cc_start: 0.8086 (OUTLIER) cc_final: 0.5898 (tp-100)
REVERT: A  156 ILE cc_start: 0.8520 (mm) cc_final: 0.8272 (tt)
REVERT: A  264 LYS cc_start: 0.8160 (ttmt) cc_final: 0.7752 (tptt)
REVERT: A  509 TRP cc_start: 0.7633 (t60) cc_final: 0.7234 (t60)
REVERT: B   65 LEU cc_start: 0.7607 (OUTLIER) cc_final: 0.7334 (tp)
REVERT: B  143 GLN cc_start: 0.8102 (OUTLIER) cc_final: 0.5964 (tp-100)
REVERT: B  156 ILE cc_start: 0.8516 (mm) cc_final: 0.8299 (tt)
REVERT: B  264 LYS cc_start: 0.8203 (ttmt) cc_final: 0.7736 (tptt)
REVERT: B  366 ARG cc_start: 0.3035 (OUTLIER) cc_final: 0.2572 (tpt90)
REVERT: B  490 ARG cc_start: 0.6649 (ttm-80) cc_final: 0.6369 (ptp-170)
  outliers start: 24
  outliers final: 11
  residues processed: 138
  average time/residue: 0.1562
  time to fit residues: 29.7020
Evaluate side-chains
  116 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 101
  time to evaluate  : 0.700 
-------------------------------------------------------------------------------
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  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  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:    0.9980
   chunk 31 optimal weight:    1.9990
   chunk 72 optimal weight:    2.9990
   chunk 45 optimal weight:    0.9990
   chunk 16 optimal weight:    2.9990
   chunk 34 optimal weight:    0.0470
   chunk 32 optimal weight:    3.9990
   chunk 54 optimal weight:    9.9990
   chunk 76 optimal weight:    0.9980
   chunk 21 optimal weight:    2.9990
   chunk 68 optimal weight:    0.6980
   overall best weight:    0.7480

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

Flipped N/Q/H residues before XYZ refinement:
A 180 ASN
A 551 HIS
B 180 ASN
B 551 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4285 r_free = 0.4285 target = 0.182091 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.140815 restraints weight = 8984.787|
|-----------------------------------------------------------------------------|
r_work (start): 0.3776 rms_B_bonded: 2.41
r_work: 0.3604 rms_B_bonded: 3.96 restraints_weight: 0.5000
r_work (final): 0.3604
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7927
moved from start:          0.7824

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= 0.182
  Angle     :  0.535   8.388   8698  Z= 0.267
  Chirality :  0.038   0.181   1032
  Planarity :  0.004   0.051   1042
  Dihedral  :  3.807  28.217    846
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 8.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.06 %
    Favored  : 98.94 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 25.82 %
    Favored  : 70.60 %
  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:  3.00 (0.29), residues: 754
  helix:  2.55 (0.19), residues: 646
  sheet:  None (None), residues: 0
  loop : -1.77 (0.56), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP B 102 
 HIS   0.003   0.001   HIS B 551 
 PHE   0.021   0.001   PHE A 353 
 TYR   0.009   0.001   TYR A  58 
 ARG   0.016   0.001   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
  129 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 105
  time to evaluate  : 0.637 
Fit side-chains
REVERT: A   34 LEU cc_start: 0.8965 (tp) cc_final: 0.8648 (tp)
REVERT: A  143 GLN cc_start: 0.8224 (OUTLIER) cc_final: 0.6065 (tp-100)
REVERT: A  156 ILE cc_start: 0.8525 (mm) cc_final: 0.8223 (tt)
REVERT: A  264 LYS cc_start: 0.8075 (ttmt) cc_final: 0.7689 (tptt)
REVERT: A  366 ARG cc_start: 0.3491 (OUTLIER) cc_final: 0.3021 (tpt90)
REVERT: A  509 TRP cc_start: 0.7687 (t60) cc_final: 0.7167 (t60)
REVERT: B   34 LEU cc_start: 0.8883 (tp) cc_final: 0.8582 (tp)
REVERT: B   65 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7589 (tp)
REVERT: B  143 GLN cc_start: 0.8179 (OUTLIER) cc_final: 0.5992 (tp-100)
REVERT: B  156 ILE cc_start: 0.8534 (mm) cc_final: 0.8238 (tt)
REVERT: B  264 LYS cc_start: 0.8183 (ttmt) cc_final: 0.7710 (tptt)
REVERT: B  288 GLU cc_start: 0.3637 (OUTLIER) cc_final: 0.3184 (tp30)
REVERT: B  366 ARG cc_start: 0.3630 (OUTLIER) cc_final: 0.3057 (tpt90)
REVERT: B  509 TRP cc_start: 0.7714 (t60) cc_final: 0.7417 (t60)
REVERT: B  511 MET cc_start: 0.6966 (mmt) cc_final: 0.6646 (mtt)
  outliers start: 24
  outliers final: 11
  residues processed: 125
  average time/residue: 0.1648
  time to fit residues: 27.9902
Evaluate side-chains
  113 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 96
  time to evaluate  : 0.676 
-------------------------------------------------------------------------------
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  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  165 HIS
Chi-restraints excluded: chain B residue  194 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
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 46 optimal weight:    0.9990
   chunk 75 optimal weight:    2.9990
   chunk 17 optimal weight:    0.1980
   chunk 33 optimal weight:    2.9990
   chunk 49 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9980
   chunk 61 optimal weight:    3.9990
   chunk 35 optimal weight:    0.7980
   chunk 72 optimal weight:    4.9990
   chunk 41 optimal weight:    3.9990
   chunk 69 optimal weight:    0.7980
   overall best weight:    0.7582

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4259 r_free = 0.4259 target = 0.179187 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.137852 restraints weight = 9135.766|
|-----------------------------------------------------------------------------|
r_work (start): 0.3738 rms_B_bonded: 2.42
r_work: 0.3574 rms_B_bonded: 3.89 restraints_weight: 0.5000
r_work (final): 0.3574
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7961
moved from start:          0.8174

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6396  Z= 0.186
  Angle     :  0.565  12.321   8698  Z= 0.273
  Chirality :  0.042   0.515   1032
  Planarity :  0.004   0.050   1042
  Dihedral  :  3.807  26.505    846
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 7.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.93 %
    Favored  : 99.07 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 24.63 %
    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:  3.09 (0.29), residues: 754
  helix:  2.62 (0.19), residues: 646
  sheet:  None (None), residues: 0
  loop : -1.82 (0.55), 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   0.014   0.001   PHE A 332 
 TYR   0.018   0.001   TYR A 351 
 ARG   0.002   0.000   ARG A 428 

*********************** 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
  131 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 113
  time to evaluate  : 0.626 
Fit side-chains
REVERT: A  125 TYR cc_start: 0.4897 (m-10) cc_final: 0.4687 (m-10)
REVERT: A  264 LYS cc_start: 0.8174 (ttmt) cc_final: 0.7751 (tptt)
REVERT: A  288 GLU cc_start: 0.3650 (OUTLIER) cc_final: 0.3209 (tp30)
REVERT: A  509 TRP cc_start: 0.7744 (t60) cc_final: 0.7166 (t60)
REVERT: B  125 TYR cc_start: 0.5199 (m-10) cc_final: 0.4964 (m-10)
REVERT: B  264 LYS cc_start: 0.8180 (ttmt) cc_final: 0.7708 (tptt)
REVERT: B  366 ARG cc_start: 0.3952 (OUTLIER) cc_final: 0.3252 (tpt90)
REVERT: B  509 TRP cc_start: 0.7665 (t60) cc_final: 0.7062 (t60)
REVERT: B  511 MET cc_start: 0.7310 (mmt) cc_final: 0.7058 (mtt)
  outliers start: 18
  outliers final: 11
  residues processed: 129
  average time/residue: 0.1526
  time to fit residues: 27.1996
Evaluate side-chains
  118 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 105
  time to evaluate  : 0.711 
-------------------------------------------------------------------------------
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  165 HIS
Chi-restraints excluded: chain A residue  194 HIS
Chi-restraints excluded: chain A residue  288 GLU
Chi-restraints excluded: chain A residue  342 LEU
Chi-restraints excluded: chain B residue   55 VAL
Chi-restraints excluded: chain B residue  165 HIS
Chi-restraints excluded: chain B residue  180 ASN
Chi-restraints excluded: chain B residue  342 LEU
Chi-restraints excluded: chain B residue  351 TYR
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:    0.9990
   chunk 32 optimal weight:    3.9990
   chunk 64 optimal weight:    0.6980
   chunk 38 optimal weight:    0.8980
   chunk 62 optimal weight:    0.6980
   chunk 23 optimal weight:    0.9980
   chunk 10 optimal weight:    0.9990
   chunk 65 optimal weight:    0.7980
   chunk 52 optimal weight:    0.5980
   chunk 39 optimal weight:    7.9990
   chunk 36 optimal weight:    4.9990
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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  38 ASN
B 180 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4214 r_free = 0.4214 target = 0.176156 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.135859 restraints weight = 8900.025|
|-----------------------------------------------------------------------------|
r_work (start): 0.3717 rms_B_bonded: 2.72
r_work: 0.3524 rms_B_bonded: 4.15 restraints_weight: 0.5000
r_work (final): 0.3524
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8019
moved from start:          0.8564

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= 0.178
  Angle     :  0.554   9.276   8698  Z= 0.269
  Chirality :  0.039   0.209   1032
  Planarity :  0.004   0.049   1042
  Dihedral  :  3.837  25.660    846
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 8.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.06 %
    Favored  : 98.94 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 25.67 %
    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:  2.64 (0.19), residues: 646
  sheet:  None (None), residues: 0
  loop : -1.96 (0.53), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP B 102 
 HIS   0.003   0.000   HIS B 415 
 PHE   0.014   0.001   PHE A 332 
 TYR   0.023   0.001   TYR A 548 
 ARG   0.002   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
  132 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 111
  time to evaluate  : 0.702 
Fit side-chains
REVERT: A  264 LYS cc_start: 0.8165 (ttmt) cc_final: 0.7788 (tptt)
REVERT: A  288 GLU cc_start: 0.3607 (OUTLIER) cc_final: 0.3131 (tp30)
REVERT: A  366 ARG cc_start: 0.4690 (OUTLIER) cc_final: 0.4157 (mmm160)
REVERT: A  519 HIS cc_start: 0.5697 (t70) cc_final: 0.5204 (m90)
REVERT: B  143 GLN cc_start: 0.7789 (OUTLIER) cc_final: 0.7512 (tt0)
REVERT: B  264 LYS cc_start: 0.8142 (ttmt) cc_final: 0.7701 (tptt)
REVERT: B  288 GLU cc_start: 0.3568 (OUTLIER) cc_final: 0.3105 (tp30)
REVERT: B  296 LEU cc_start: 0.8271 (mt) cc_final: 0.8011 (mp)
REVERT: B  366 ARG cc_start: 0.4464 (OUTLIER) cc_final: 0.4048 (mmm160)
REVERT: B  519 HIS cc_start: 0.5528 (t70) cc_final: 0.5280 (m90)
  outliers start: 21
  outliers final: 11
  residues processed: 129
  average time/residue: 0.1528
  time to fit residues: 27.1413
Evaluate side-chains
  124 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 108
  time to evaluate  : 0.628 
-------------------------------------------------------------------------------
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  165 HIS
Chi-restraints excluded: chain A residue  180 ASN
Chi-restraints excluded: chain A residue  288 GLU
Chi-restraints excluded: chain A residue  342 LEU
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  143 GLN
Chi-restraints excluded: chain B residue  165 HIS
Chi-restraints excluded: chain B residue  180 ASN
Chi-restraints excluded: chain B residue  288 GLU
Chi-restraints excluded: chain B residue  342 LEU
Chi-restraints excluded: chain B residue  351 TYR
Chi-restraints excluded: chain B residue  366 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 54 optimal weight:    0.0270
   chunk 74 optimal weight:    0.0770
   chunk 17 optimal weight:    0.7980
   chunk 0 optimal weight:   10.0000
   chunk 1 optimal weight:    0.7980
   chunk 50 optimal weight:    1.9990
   chunk 9 optimal weight:    0.8980
   chunk 31 optimal weight:    3.9990
   chunk 51 optimal weight:    0.9980
   chunk 77 optimal weight:    0.6980
   chunk 56 optimal weight:    0.7980
   overall best weight:    0.4796

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4199 r_free = 0.4199 target = 0.174533 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.135055 restraints weight = 9201.366|
|-----------------------------------------------------------------------------|
r_work (start): 0.3707 rms_B_bonded: 2.42
r_work: 0.3539 rms_B_bonded: 3.93 restraints_weight: 0.5000
r_work (final): 0.3539
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7989
moved from start:          0.8717

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= 0.170
  Angle     :  0.553   9.591   8698  Z= 0.267
  Chirality :  0.038   0.198   1032
  Planarity :  0.004   0.049   1042
  Dihedral  :  3.757  24.916    846
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 8.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.80 %
    Favored  : 99.20 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 26.42 %
    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:  3.20 (0.29), residues: 754
  helix:  2.72 (0.19), residues: 646
  sheet:  None (None), residues: 0
  loop : -1.98 (0.52), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP B 102 
 HIS   0.002   0.000   HIS B 415 
 PHE   0.013   0.001   PHE A  79 
 TYR   0.024   0.001   TYR A 548 
 ARG   0.001   0.000   ARG A 490 

*********************** 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
  125 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 107
  time to evaluate  : 0.732 
Fit side-chains
REVERT: A   58 TYR cc_start: 0.5963 (m-80) cc_final: 0.5154 (m-80)
REVERT: A  264 LYS cc_start: 0.8108 (ttmt) cc_final: 0.7731 (tptt)
REVERT: A  288 GLU cc_start: 0.3711 (OUTLIER) cc_final: 0.3241 (tp30)
REVERT: A  296 LEU cc_start: 0.8225 (mt) cc_final: 0.7997 (mp)
REVERT: A  366 ARG cc_start: 0.4611 (OUTLIER) cc_final: 0.4205 (mmm160)
REVERT: A  509 TRP cc_start: 0.7693 (t60) cc_final: 0.7227 (t60)
REVERT: A  519 HIS cc_start: 0.5592 (t70) cc_final: 0.5056 (m90)
REVERT: B  264 LYS cc_start: 0.8098 (ttmt) cc_final: 0.7694 (tptt)
REVERT: B  288 GLU cc_start: 0.3769 (OUTLIER) cc_final: 0.3310 (tp30)
REVERT: B  296 LEU cc_start: 0.8245 (mt) cc_final: 0.7993 (mp)
REVERT: B  509 TRP cc_start: 0.7673 (t60) cc_final: 0.7197 (t60)
REVERT: B  519 HIS cc_start: 0.5620 (t70) cc_final: 0.5169 (m90)
  outliers start: 18
  outliers final: 11
  residues processed: 123
  average time/residue: 0.1477
  time to fit residues: 25.4244
Evaluate side-chains
  120 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 106
  time to evaluate  : 0.709 
-------------------------------------------------------------------------------
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  180 ASN
Chi-restraints excluded: chain A residue  288 GLU
Chi-restraints excluded: chain A residue  342 LEU
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   71 LEU
Chi-restraints excluded: chain B residue  180 ASN
Chi-restraints excluded: chain B residue  288 GLU
Chi-restraints excluded: chain B residue  342 LEU
Chi-restraints excluded: chain B residue  351 TYR
Chi-restraints excluded: chain B residue  426 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 12 optimal weight:    7.9990
   chunk 58 optimal weight:    0.9990
   chunk 38 optimal weight:    2.9990
   chunk 34 optimal weight:    6.9990
   chunk 3 optimal weight:    6.9990
   chunk 24 optimal weight:    2.9990
   chunk 67 optimal weight:    3.9990
   chunk 69 optimal weight:    0.9990
   chunk 13 optimal weight:    1.9990
   chunk 77 optimal weight:    0.8980
   chunk 20 optimal weight:    0.7980
   overall best weight:    1.1386

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4135 r_free = 0.4135 target = 0.168489 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.129012 restraints weight = 9177.934|
|-----------------------------------------------------------------------------|
r_work (start): 0.3631 rms_B_bonded: 2.39
r_work: 0.3456 rms_B_bonded: 3.89 restraints_weight: 0.5000
r_work (final): 0.3456
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8100
moved from start:          0.9211

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   6396  Z= 0.217
  Angle     :  0.593   9.213   8698  Z= 0.290
  Chirality :  0.040   0.183   1032
  Planarity :  0.004   0.049   1042
  Dihedral  :  4.012  28.741    846
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 8.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.06 %
    Favored  : 98.94 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 25.97 %
    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:  3.10 (0.29), residues: 754
  helix:  2.65 (0.19), residues: 646
  sheet:  None (None), residues: 0
  loop : -2.01 (0.52), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 102 
 HIS   0.004   0.001   HIS A 415 
 PHE   0.017   0.002   PHE A 332 
 TYR   0.030   0.002   TYR A 548 
 ARG   0.002   0.000   ARG B 366 

********************** 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
  139 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 125
  time to evaluate  : 0.710 
Fit side-chains
REVERT: A  120 PHE cc_start: 0.6611 (m-80) cc_final: 0.6262 (m-80)
REVERT: A  121 LYS cc_start: 0.6410 (mptt) cc_final: 0.6158 (mptt)
REVERT: A  264 LYS cc_start: 0.8156 (ttmt) cc_final: 0.7755 (tptt)
REVERT: A  366 ARG cc_start: 0.4915 (OUTLIER) cc_final: 0.4525 (mmm160)
REVERT: A  519 HIS cc_start: 0.5624 (t70) cc_final: 0.5015 (m90)
REVERT: B   63 PHE cc_start: 0.8238 (m-10) cc_final: 0.7883 (m-80)
REVERT: B  120 PHE cc_start: 0.6700 (m-80) cc_final: 0.6332 (m-80)
REVERT: B  121 LYS cc_start: 0.6516 (mptt) cc_final: 0.6273 (mptt)
REVERT: B  264 LYS cc_start: 0.8197 (ttmt) cc_final: 0.7681 (tptt)
REVERT: B  351 TYR cc_start: 0.6700 (OUTLIER) cc_final: 0.6100 (m-80)
REVERT: B  519 HIS cc_start: 0.5609 (t70) cc_final: 0.5096 (m90)
  outliers start: 14
  outliers final: 8
  residues processed: 137
  average time/residue: 0.1549
  time to fit residues: 29.4568
Evaluate side-chains
  126 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 116
  time to evaluate  : 0.674 
-------------------------------------------------------------------------------
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  180 ASN
Chi-restraints excluded: chain A residue  342 LEU
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  342 LEU
Chi-restraints excluded: chain B residue  351 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 19 optimal weight:    0.9980
   chunk 28 optimal weight:    0.9990
   chunk 72 optimal weight:    0.9980
   chunk 61 optimal weight:    6.9990
   chunk 43 optimal weight:    0.8980
   chunk 73 optimal weight:    0.0670
   chunk 47 optimal weight:    0.9990
   chunk 63 optimal weight:    9.9990
   chunk 42 optimal weight:    3.9990
   chunk 35 optimal weight:    0.8980
   chunk 33 optimal weight:    4.9990
   overall best weight:    0.7718

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4137 r_free = 0.4137 target = 0.168578 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.129696 restraints weight = 9291.849|
|-----------------------------------------------------------------------------|
r_work (start): 0.3645 rms_B_bonded: 2.40
r_work: 0.3477 rms_B_bonded: 3.84 restraints_weight: 0.5000
r_work (final): 0.3477
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8075
moved from start:          0.9483

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6396  Z= 0.189
  Angle     :  0.563   8.229   8698  Z= 0.277
  Chirality :  0.038   0.170   1032
  Planarity :  0.004   0.049   1042
  Dihedral  :  3.937  26.676    846
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 8.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.66 %
    Favored  : 99.34 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 26.87 %
    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:  3.33 (0.30), residues: 754
  helix:  2.81 (0.19), residues: 646
  sheet:  None (None), residues: 0
  loop : -1.98 (0.53), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 102 
 HIS   0.003   0.000   HIS B 415 
 PHE   0.021   0.001   PHE A 301 
 TYR   0.034   0.002   TYR A 351 
 ARG   0.002   0.000   ARG A 428 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2967.04 seconds
wall clock time: 53 minutes 23.39 seconds (3203.39 seconds total)