Starting phenix.real_space_refine
on Fri Aug 22 16:58:19 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ug6_42215/08_2025/8ug6_42215.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ug6_42215/08_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_42215/08_2025/8ug6_42215.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ug6_42215/08_2025/8ug6_42215.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ug6_42215/08_2025/8ug6_42215.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ug6_42215/08_2025/8ug6_42215.cif"
  }
  resolution = 3.06
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.000
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 2.43, per 1000 atoms: 0.39
  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: 0.62
  Conformation dependent library (CDL) restraints added in 456.7 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 0.17
  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: 1.00

  Time building geometry restraints manager: 0.83 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: 0.01
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:             2.150
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.010
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     8.870
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.600
-------------------------------------------------------------------------------
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= 0.304
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.004   0.000   ARG B 490 
 TYR   0.024   0.002   TYR B 560 
 PHE   0.009   0.001   PHE A 110 
 TRP   0.013   0.001   TRP A 509 
 HIS   0.003   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00489 ( 6396)
  covalent geometry    : angle       0.66365 ( 8698)
  hydrogen bonds       : bond        0.19409 (  528)
  hydrogen bonds       : angle       6.18270 ( 1584)

*********************** 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  : 0.280 
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: 0.0747
  time to fit residues: 20.7010
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  : 0.186 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 49 optimal weight:    0.5980
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    7.9990
   chunk 38 optimal weight:    0.8980
   chunk 61 optimal weight:    0.6980
   chunk 45 optimal weight:    4.9990
   chunk 74 optimal weight:    1.9990
   overall best weight:    0.7982

-------------------------------------------------------------------------------
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 = 0.4530 r_free = 0.4530 target = 0.207230 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4158 r_free = 0.4158 target = 0.172376 restraints weight = 9813.859|
|-----------------------------------------------------------------------------|
r_work (start): 0.4141 rms_B_bonded: 2.47
r_work: 0.3983 rms_B_bonded: 4.24 restraints_weight: 0.5000
r_work (final): 0.3983
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7311
moved from start:          0.3747

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= 0.164
  Angle     :  0.586   6.976   8698  Z= 0.306
  Chirality :  0.040   0.163   1032
  Planarity :  0.005   0.054   1042
  Dihedral  :  3.745  30.775    846
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 8.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 21.94 %
    Favored  : 74.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.62 (0.29), residues: 754
  helix:  2.19 (0.19), residues: 658
  sheet:  None (None), residues: 0
  loop : -1.60 (0.62), residues: 96

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 428 
 TYR   0.012   0.002   TYR A 351 
 PHE   0.010   0.002   PHE A 544 
 TRP   0.010   0.001   TRP A 102 
 HIS   0.004   0.001   HIS A 139 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 6396)
  covalent geometry    : angle       0.58624 ( 8698)
  hydrogen bonds       : bond        0.04714 (  528)
  hydrogen bonds       : angle       4.20310 ( 1584)

*********************** 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
  187 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 166
  time to evaluate  : 0.169 
Fit side-chains
REVERT: A  174 MET cc_start: 0.7791 (mmt) cc_final: 0.7528 (mmt)
REVERT: A  245 TYR cc_start: 0.5455 (t80) cc_final: 0.2870 (t80)
REVERT: B   65 LEU cc_start: 0.7055 (OUTLIER) cc_final: 0.6829 (tp)
REVERT: B  174 MET cc_start: 0.7826 (mmt) cc_final: 0.7597 (mmt)
REVERT: B  245 TYR cc_start: 0.5302 (t80) cc_final: 0.2694 (t80)
  outliers start: 21
  outliers final: 6
  residues processed: 178
  average time/residue: 0.0472
  time to fit residues: 12.2205
Evaluate side-chains
  142 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 135
  time to evaluate  : 0.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 LEU
Chi-restraints excluded: chain A residue  194 HIS
Chi-restraints excluded: chain A residue  389 VAL
Chi-restraints excluded: chain B residue   65 LEU
Chi-restraints excluded: chain B residue   75 LEU
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 76 optimal weight:    1.9990
   chunk 69 optimal weight:    0.6980
   chunk 62 optimal weight:    0.8980
   chunk 14 optimal weight:    1.9990
   chunk 30 optimal weight:    0.8980
   chunk 77 optimal weight:    0.9990
   chunk 44 optimal weight:    4.9990
   chunk 72 optimal weight:    2.9990
   chunk 35 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 39 optimal weight:    0.9980
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
A 180 ASN
A 321 HIS
A 407 HIS
** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 519 HIS
B 180 ASN
B 400 GLN
B 407 HIS
** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 519 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4385 r_free = 0.4385 target = 0.191367 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.152697 restraints weight = 9244.409|
|-----------------------------------------------------------------------------|
r_work (start): 0.3917 rms_B_bonded: 2.53
r_work: 0.3721 rms_B_bonded: 4.28 restraints_weight: 0.5000
r_work (final): 0.3721
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7729
moved from start:          0.5734

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6396  Z= 0.156
  Angle     :  0.611  12.330   8698  Z= 0.305
  Chirality :  0.040   0.207   1032
  Planarity :  0.005   0.058   1042
  Dihedral  :  3.755  26.262    846
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 9.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.06 %
    Favored  : 98.94 %
  Rotamer:
    Outliers :  6.12 %
    Allowed  : 21.34 %
    Favored  : 72.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.80 (0.29), residues: 754
  helix:  2.32 (0.19), residues: 652
  sheet:  None (None), residues: 0
  loop : -1.35 (0.60), residues: 102

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 366 
 TYR   0.023   0.002   TYR B 311 
 PHE   0.017   0.002   PHE B 332 
 TRP   0.011   0.002   TRP A 102 
 HIS   0.006   0.001   HIS A 551 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 6396)
  covalent geometry    : angle       0.61057 ( 8698)
  hydrogen bonds       : bond        0.04490 (  528)
  hydrogen bonds       : angle       4.13469 ( 1584)

*********************** 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
  172 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 131
  time to evaluate  : 0.168 
Fit side-chains
REVERT: A  143 GLN cc_start: 0.8161 (OUTLIER) cc_final: 0.5934 (tp-100)
REVERT: A  245 TYR cc_start: 0.5569 (t80) cc_final: 0.3543 (t80)
REVERT: A  264 LYS cc_start: 0.8134 (ttmt) cc_final: 0.7722 (tptt)
REVERT: A  332 PHE cc_start: 0.7709 (t80) cc_final: 0.7503 (t80)
REVERT: A  366 ARG cc_start: 0.2713 (OUTLIER) cc_final: 0.2185 (tpt170)
REVERT: A  368 LEU cc_start: 0.5917 (tm) cc_final: 0.5651 (tp)
REVERT: A  509 TRP cc_start: 0.7674 (t60) cc_final: 0.7387 (t60)
REVERT: A  511 MET cc_start: 0.5916 (mpp) cc_final: 0.5391 (mmm)
REVERT: B   66 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7907 (mm)
REVERT: B  143 GLN cc_start: 0.8163 (OUTLIER) cc_final: 0.5916 (tp-100)
REVERT: B  185 MET cc_start: 0.8425 (tpp) cc_final: 0.8177 (tpp)
REVERT: B  245 TYR cc_start: 0.5515 (t80) cc_final: 0.3453 (t80)
REVERT: B  264 LYS cc_start: 0.8161 (ttmt) cc_final: 0.7728 (tptt)
REVERT: B  366 ARG cc_start: 0.2586 (OUTLIER) cc_final: 0.2001 (tpt90)
REVERT: B  368 LEU cc_start: 0.5788 (tm) cc_final: 0.5460 (tp)
REVERT: B  509 TRP cc_start: 0.7688 (t60) cc_final: 0.7430 (t60)
REVERT: B  511 MET cc_start: 0.5971 (mpp) cc_final: 0.5391 (mmm)
  outliers start: 41
  outliers final: 10
  residues processed: 160
  average time/residue: 0.0562
  time to fit residues: 12.5016
Evaluate side-chains
  135 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 120
  time to evaluate  : 0.221 
-------------------------------------------------------------------------------
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  366 ARG
Chi-restraints excluded: chain A residue  389 VAL
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  194 HIS
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 20 optimal weight:    2.9990
   chunk 16 optimal weight:    2.9990
   chunk 49 optimal weight:    0.0970
   chunk 19 optimal weight:    0.9980
   chunk 29 optimal weight:    2.9990
   chunk 14 optimal weight:    0.8980
   chunk 24 optimal weight:    0.7980
   chunk 62 optimal weight:    0.9980
   chunk 47 optimal weight:    0.7980
   chunk 72 optimal weight:    0.9980
   chunk 13 optimal weight:    0.6980
   overall best weight:    0.6578

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

Flipped N/Q/H residues before XYZ refinement:
A 180 ASN
A 418 GLN
B 150 GLN
B 180 ASN
B 321 HIS
B 418 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4357 r_free = 0.4357 target = 0.188812 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.148649 restraints weight = 9232.578|
|-----------------------------------------------------------------------------|
r_work (start): 0.3875 rms_B_bonded: 2.47
r_work: 0.3706 rms_B_bonded: 4.09 restraints_weight: 0.5000
r_work (final): 0.3706
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7785
moved from start:          0.6520

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6396  Z= 0.131
  Angle     :  0.535   9.658   8698  Z= 0.266
  Chirality :  0.038   0.158   1032
  Planarity :  0.004   0.053   1042
  Dihedral  :  3.664  27.357    846
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 8.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.46 %
    Favored  : 98.54 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 24.18 %
    Favored  : 72.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.07 (0.29), residues: 754
  helix:  2.51 (0.19), residues: 652
  sheet:  None (None), residues: 0
  loop : -1.32 (0.59), residues: 102

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 366 
 TYR   0.011   0.001   TYR B 351 
 PHE   0.022   0.001   PHE B 514 
 TRP   0.008   0.001   TRP A 155 
 HIS   0.002   0.000   HIS B 415 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 6396)
  covalent geometry    : angle       0.53501 ( 8698)
  hydrogen bonds       : bond        0.04057 (  528)
  hydrogen bonds       : angle       3.87542 ( 1584)

*********************** 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
  143 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 120
  time to evaluate  : 0.229 
Fit side-chains
REVERT: A  156 ILE cc_start: 0.8553 (mm) cc_final: 0.8239 (tt)
REVERT: A  366 ARG cc_start: 0.2551 (OUTLIER) cc_final: 0.2289 (tpt90)
REVERT: A  368 LEU cc_start: 0.6350 (tm) cc_final: 0.6066 (tp)
REVERT: A  509 TRP cc_start: 0.7732 (t60) cc_final: 0.7511 (t60)
REVERT: B   65 LEU cc_start: 0.7505 (OUTLIER) cc_final: 0.7209 (tp)
REVERT: B  156 ILE cc_start: 0.8484 (mm) cc_final: 0.8213 (tt)
REVERT: B  185 MET cc_start: 0.8302 (tpp) cc_final: 0.8068 (tpp)
REVERT: B  264 LYS cc_start: 0.8087 (ttmt) cc_final: 0.7691 (tptt)
REVERT: B  366 ARG cc_start: 0.2732 (OUTLIER) cc_final: 0.2210 (tpt90)
REVERT: B  368 LEU cc_start: 0.6224 (tm) cc_final: 0.5924 (tp)
REVERT: B  509 TRP cc_start: 0.7669 (t60) cc_final: 0.7441 (t60)
  outliers start: 23
  outliers final: 9
  residues processed: 137
  average time/residue: 0.0528
  time to fit residues: 10.0211
Evaluate side-chains
  119 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 107
  time to evaluate  : 0.133 
-------------------------------------------------------------------------------
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  366 ARG
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  165 HIS
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 49 optimal weight:    0.6980
   chunk 18 optimal weight:    0.3980
   chunk 68 optimal weight:    1.9990
   chunk 6 optimal weight:    0.3980
   chunk 23 optimal weight:    0.7980
   chunk 35 optimal weight:    0.9980
   chunk 16 optimal weight:    1.9990
   chunk 51 optimal weight:    7.9990
   chunk 1 optimal weight:    0.5980
   chunk 30 optimal weight:    0.6980
   chunk 56 optimal weight:    0.7980
   overall best weight:    0.5580

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4335 r_free = 0.4335 target = 0.186253 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.145363 restraints weight = 9232.210|
|-----------------------------------------------------------------------------|
r_work (start): 0.3839 rms_B_bonded: 2.56
r_work: 0.3654 rms_B_bonded: 4.09 restraints_weight: 0.5000
r_work (final): 0.3654
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7845
moved from start:          0.7094

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= 0.119
  Angle     :  0.529   9.589   8698  Z= 0.259
  Chirality :  0.038   0.182   1032
  Planarity :  0.004   0.054   1042
  Dihedral  :  3.671  26.430    846
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 8.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.80 %
    Favored  : 99.20 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 24.78 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.11 (0.29), residues: 754
  helix:  2.61 (0.19), residues: 646
  sheet:  None (None), residues: 0
  loop : -1.65 (0.57), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 428 
 TYR   0.016   0.001   TYR B 329 
 PHE   0.016   0.001   PHE B 514 
 TRP   0.012   0.001   TRP B 155 
 HIS   0.003   0.000   HIS B 415 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 ( 6396)
  covalent geometry    : angle       0.52906 ( 8698)
  hydrogen bonds       : bond        0.03894 (  528)
  hydrogen bonds       : angle       3.83185 ( 1584)

*********************** 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
  136 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 116
  time to evaluate  : 0.157 
Fit side-chains
   revert: symmetry clash
REVERT: A  143 GLN cc_start: 0.8056 (OUTLIER) cc_final: 0.5937 (tp-100)
REVERT: A  156 ILE cc_start: 0.8542 (mm) cc_final: 0.8281 (tt)
REVERT: A  264 LYS cc_start: 0.8037 (mtmt) cc_final: 0.7443 (mmtt)
REVERT: A  288 GLU cc_start: 0.3575 (OUTLIER) cc_final: 0.3166 (tp30)
REVERT: A  366 ARG cc_start: 0.3015 (OUTLIER) cc_final: 0.2630 (tpt90)
REVERT: A  550 MET cc_start: 0.7725 (mtt) cc_final: 0.7441 (mtt)
REVERT: B  143 GLN cc_start: 0.8083 (OUTLIER) cc_final: 0.5765 (tp-100)
REVERT: B  156 ILE cc_start: 0.8533 (mm) cc_final: 0.8276 (tt)
REVERT: B  185 MET cc_start: 0.8351 (tpp) cc_final: 0.8070 (tpp)
REVERT: B  264 LYS cc_start: 0.8155 (ttmt) cc_final: 0.7679 (tptt)
REVERT: B  366 ARG cc_start: 0.2991 (OUTLIER) cc_final: 0.2530 (tpt90)
REVERT: B  368 LEU cc_start: 0.6976 (tm) cc_final: 0.6774 (tp)
REVERT: B  490 ARG cc_start: 0.6635 (ttm-80) cc_final: 0.6376 (ptp-170)
REVERT: B  511 MET cc_start: 0.6262 (mmt) cc_final: 0.5946 (mmm)
REVERT: B  550 MET cc_start: 0.7750 (mtt) cc_final: 0.7479 (mtt)
  outliers start: 20
  outliers final: 8
  residues processed: 134
  average time/residue: 0.0657
  time to fit residues: 11.9478
Evaluate side-chains
  115 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 102
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
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  288 GLU
Chi-restraints excluded: chain A residue  366 ARG
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  194 HIS
Chi-restraints excluded: chain B residue  366 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 73 optimal weight:    0.7980
   chunk 35 optimal weight:    0.8980
   chunk 39 optimal weight:    4.9990
   chunk 75 optimal weight:    3.9990
   chunk 71 optimal weight:    8.9990
   chunk 70 optimal weight:    1.9990
   chunk 19 optimal weight:    0.8980
   chunk 13 optimal weight:    0.5980
   chunk 38 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9980
   overall best weight:    0.8380

-------------------------------------------------------------------------------
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
** B 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4262 r_free = 0.4262 target = 0.180035 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.138592 restraints weight = 9067.773|
|-----------------------------------------------------------------------------|
r_work (start): 0.3746 rms_B_bonded: 2.42
r_work: 0.3568 rms_B_bonded: 3.97 restraints_weight: 0.5000
r_work (final): 0.3568
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7975
moved from start:          0.7917

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6396  Z= 0.134
  Angle     :  0.536   8.665   8698  Z= 0.268
  Chirality :  0.039   0.193   1032
  Planarity :  0.004   0.052   1042
  Dihedral  :  3.793  28.276    846
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 8.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.80 %
    Favored  : 99.20 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 23.88 %
    Favored  : 72.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.09 (0.29), residues: 754
  helix:  2.58 (0.19), residues: 648
  sheet:  None (None), residues: 0
  loop : -1.65 (0.58), residues: 106

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  83 
 TYR   0.017   0.001   TYR A 251 
 PHE   0.020   0.001   PHE B 353 
 TRP   0.008   0.001   TRP A  76 
 HIS   0.003   0.001   HIS B 415 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 6396)
  covalent geometry    : angle       0.53582 ( 8698)
  hydrogen bonds       : bond        0.03999 (  528)
  hydrogen bonds       : angle       3.81680 ( 1584)

*********************** 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
  134 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 110
  time to evaluate  : 0.138 
Fit side-chains
REVERT: A  125 TYR cc_start: 0.5165 (m-10) cc_final: 0.4885 (m-10)
REVERT: A  143 GLN cc_start: 0.8169 (OUTLIER) cc_final: 0.6017 (tp-100)
REVERT: A  156 ILE cc_start: 0.8530 (mm) cc_final: 0.8230 (tt)
REVERT: A  288 GLU cc_start: 0.3586 (OUTLIER) cc_final: 0.3098 (tp30)
REVERT: A  366 ARG cc_start: 0.3641 (OUTLIER) cc_final: 0.2945 (tpt90)
REVERT: A  509 TRP cc_start: 0.7947 (t60) cc_final: 0.7725 (t60)
REVERT: A  511 MET cc_start: 0.7033 (mmt) cc_final: 0.6730 (mtt)
REVERT: A  550 MET cc_start: 0.8143 (mtt) cc_final: 0.7884 (mtt)
REVERT: B   65 LEU cc_start: 0.7952 (OUTLIER) cc_final: 0.7746 (tp)
REVERT: B  125 TYR cc_start: 0.5126 (m-10) cc_final: 0.4858 (m-10)
REVERT: B  143 GLN cc_start: 0.8171 (OUTLIER) cc_final: 0.6044 (tp-100)
REVERT: B  156 ILE cc_start: 0.8584 (mm) cc_final: 0.8276 (tt)
REVERT: B  185 MET cc_start: 0.8377 (tpp) cc_final: 0.8090 (tpp)
REVERT: B  264 LYS cc_start: 0.8213 (ttmt) cc_final: 0.7732 (tptt)
REVERT: B  288 GLU cc_start: 0.3694 (OUTLIER) cc_final: 0.3208 (tp30)
REVERT: B  366 ARG cc_start: 0.3606 (OUTLIER) cc_final: 0.2838 (tpt90)
REVERT: B  509 TRP cc_start: 0.7960 (t60) cc_final: 0.7709 (t60)
REVERT: B  511 MET cc_start: 0.7129 (mmt) cc_final: 0.6754 (mtt)
REVERT: B  550 MET cc_start: 0.8107 (mtt) cc_final: 0.7853 (mtt)
  outliers start: 24
  outliers final: 11
  residues processed: 132
  average time/residue: 0.0543
  time to fit residues: 9.8151
Evaluate side-chains
  121 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 103
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
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  288 GLU
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  342 LEU
Chi-restraints excluded: chain B residue  366 ARG
Chi-restraints excluded: chain B residue  409 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 7 optimal weight:    0.9990
   chunk 34 optimal weight:    0.9980
   chunk 63 optimal weight:    0.2980
   chunk 22 optimal weight:    3.9990
   chunk 76 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9980
   chunk 26 optimal weight:    1.9990
   chunk 19 optimal weight:    2.9990
   chunk 72 optimal weight:    0.9990
   chunk 48 optimal weight:    4.9990
   chunk 15 optimal weight:    1.9990
   overall best weight:    0.8584

-------------------------------------------------------------------------------
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
B 143 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4228 r_free = 0.4228 target = 0.176592 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.135221 restraints weight = 9050.581|
|-----------------------------------------------------------------------------|
r_work (start): 0.3708 rms_B_bonded: 2.39
r_work: 0.3536 rms_B_bonded: 3.94 restraints_weight: 0.5000
r_work (final): 0.3536
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8011
moved from start:          0.8484

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= 0.126
  Angle     :  0.524   8.062   8698  Z= 0.258
  Chirality :  0.038   0.216   1032
  Planarity :  0.004   0.052   1042
  Dihedral  :  3.796  26.379    846
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 8.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.80 %
    Favored  : 99.20 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 22.99 %
    Favored  : 73.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.18 (0.29), residues: 754
  helix:  2.68 (0.19), residues: 646
  sheet:  None (None), residues: 0
  loop : -1.73 (0.56), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 549 
 TYR   0.026   0.001   TYR B 548 
 PHE   0.017   0.001   PHE B 301 
 TRP   0.007   0.001   TRP A  76 
 HIS   0.003   0.000   HIS A 415 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 6396)
  covalent geometry    : angle       0.52369 ( 8698)
  hydrogen bonds       : bond        0.03870 (  528)
  hydrogen bonds       : angle       3.82425 ( 1584)

*********************** 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
  139 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 115
  time to evaluate  : 0.234 
Fit side-chains
REVERT: A  124 TYR cc_start: 0.3009 (t80) cc_final: 0.1819 (t80)
REVERT: A  125 TYR cc_start: 0.5305 (m-10) cc_final: 0.4977 (m-10)
REVERT: A  143 GLN cc_start: 0.8205 (OUTLIER) cc_final: 0.6079 (tp-100)
REVERT: A  264 LYS cc_start: 0.8160 (mtpt) cc_final: 0.7633 (mmtt)
REVERT: A  288 GLU cc_start: 0.3488 (OUTLIER) cc_final: 0.3013 (tp30)
REVERT: A  366 ARG cc_start: 0.3925 (OUTLIER) cc_final: 0.3614 (mmm160)
REVERT: A  509 TRP cc_start: 0.7957 (t60) cc_final: 0.7733 (t60)
REVERT: A  511 MET cc_start: 0.7386 (mmt) cc_final: 0.7151 (mtt)
REVERT: A  519 HIS cc_start: 0.5580 (t70) cc_final: 0.5188 (m90)
REVERT: A  550 MET cc_start: 0.8280 (mtt) cc_final: 0.8033 (mtt)
REVERT: B  125 TYR cc_start: 0.5344 (m-10) cc_final: 0.5041 (m-10)
REVERT: B  185 MET cc_start: 0.8396 (tpp) cc_final: 0.8173 (tpp)
REVERT: B  264 LYS cc_start: 0.8189 (ttmt) cc_final: 0.7738 (tptt)
REVERT: B  288 GLU cc_start: 0.3547 (OUTLIER) cc_final: 0.3062 (tp30)
REVERT: B  366 ARG cc_start: 0.3866 (OUTLIER) cc_final: 0.3536 (mmm160)
REVERT: B  509 TRP cc_start: 0.7933 (t60) cc_final: 0.7714 (t60)
REVERT: B  519 HIS cc_start: 0.5550 (t70) cc_final: 0.5232 (m90)
REVERT: B  550 MET cc_start: 0.8300 (mtt) cc_final: 0.8070 (mtt)
  outliers start: 24
  outliers final: 9
  residues processed: 137
  average time/residue: 0.0601
  time to fit residues: 11.5497
Evaluate side-chains
  121 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 107
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
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  288 GLU
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   66 LEU
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 14 optimal weight:    3.9990
   chunk 74 optimal weight:    0.9990
   chunk 33 optimal weight:    2.9990
   chunk 18 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   chunk 17 optimal weight:    0.5980
   chunk 58 optimal weight:    0.9980
   chunk 38 optimal weight:    0.7980
   chunk 28 optimal weight:    0.6980
   chunk 76 optimal weight:    0.8980
   chunk 61 optimal weight:    3.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 180 ASN
B 143 GLN
B 505 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4179 r_free = 0.4179 target = 0.172951 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.133677 restraints weight = 9081.653|
|-----------------------------------------------------------------------------|
r_work (start): 0.3689 rms_B_bonded: 2.32
r_work: 0.3514 rms_B_bonded: 3.86 restraints_weight: 0.5000
r_work (final): 0.3514
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8039
moved from start:          0.8848

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= 0.125
  Angle     :  0.529   8.010   8698  Z= 0.261
  Chirality :  0.039   0.239   1032
  Planarity :  0.004   0.051   1042
  Dihedral  :  3.751  25.436    846
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 8.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.93 %
    Favored  : 99.07 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 24.63 %
    Favored  : 72.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.29 (0.30), residues: 754
  helix:  2.76 (0.19), residues: 646
  sheet:  None (None), residues: 0
  loop : -1.77 (0.55), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 366 
 TYR   0.027   0.002   TYR A 548 
 PHE   0.014   0.001   PHE A 332 
 TRP   0.013   0.002   TRP A 155 
 HIS   0.003   0.000   HIS B 415 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 6396)
  covalent geometry    : angle       0.52860 ( 8698)
  hydrogen bonds       : bond        0.03835 (  528)
  hydrogen bonds       : angle       3.76099 ( 1584)

*********************** 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
  135 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 115
  time to evaluate  : 0.237 
Fit side-chains
REVERT: A   63 PHE cc_start: 0.8213 (m-10) cc_final: 0.7866 (m-80)
REVERT: A  124 TYR cc_start: 0.3423 (t80) cc_final: 0.2220 (t80)
REVERT: A  125 TYR cc_start: 0.5552 (m-10) cc_final: 0.5220 (m-10)
REVERT: A  264 LYS cc_start: 0.8171 (mtpt) cc_final: 0.7653 (mmtt)
REVERT: A  288 GLU cc_start: 0.3509 (OUTLIER) cc_final: 0.2984 (tp30)
REVERT: A  519 HIS cc_start: 0.5659 (t70) cc_final: 0.5101 (m90)
REVERT: A  550 MET cc_start: 0.8363 (mtt) cc_final: 0.8136 (mtt)
REVERT: B  124 TYR cc_start: 0.3142 (t80) cc_final: 0.2058 (t80)
REVERT: B  125 TYR cc_start: 0.5437 (m-10) cc_final: 0.5104 (m-10)
REVERT: B  143 GLN cc_start: 0.7721 (OUTLIER) cc_final: 0.7478 (tt0)
REVERT: B  185 MET cc_start: 0.8368 (tpp) cc_final: 0.8085 (tpp)
REVERT: B  264 LYS cc_start: 0.8210 (ttmt) cc_final: 0.7784 (tptt)
REVERT: B  288 GLU cc_start: 0.3548 (OUTLIER) cc_final: 0.3021 (tp30)
REVERT: B  374 MET cc_start: 0.8046 (OUTLIER) cc_final: 0.7579 (mpp)
REVERT: B  519 HIS cc_start: 0.5619 (t70) cc_final: 0.5103 (m90)
REVERT: B  550 MET cc_start: 0.8387 (mtt) cc_final: 0.8174 (mtt)
  outliers start: 20
  outliers final: 9
  residues processed: 132
  average time/residue: 0.0592
  time to fit residues: 11.3219
Evaluate side-chains
  125 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 112
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
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  180 ASN
Chi-restraints excluded: chain A residue  194 HIS
Chi-restraints excluded: chain A residue  288 GLU
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  194 HIS
Chi-restraints excluded: chain B residue  288 GLU
Chi-restraints excluded: chain B residue  374 MET
Chi-restraints excluded: chain B residue  389 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 70 optimal weight:    0.7980
   chunk 76 optimal weight:    0.2980
   chunk 61 optimal weight:    3.9990
   chunk 25 optimal weight:    1.9990
   chunk 29 optimal weight:    4.9990
   chunk 40 optimal weight:    0.6980
   chunk 72 optimal weight:    0.5980
   chunk 9 optimal weight:    0.6980
   chunk 21 optimal weight:    3.9990
   chunk 31 optimal weight:   10.0000
   chunk 20 optimal weight:    0.8980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 180 ASN
B 143 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4176 r_free = 0.4176 target = 0.172308 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.133348 restraints weight = 9016.134|
|-----------------------------------------------------------------------------|
r_work (start): 0.3688 rms_B_bonded: 2.33
r_work: 0.3515 rms_B_bonded: 3.87 restraints_weight: 0.5000
r_work (final): 0.3515
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8038
moved from start:          0.9005

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6396  Z= 0.120
  Angle     :  0.521   7.606   8698  Z= 0.263
  Chirality :  0.038   0.212   1032
  Planarity :  0.004   0.050   1042
  Dihedral  :  3.738  24.402    846
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 8.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.80 %
    Favored  : 99.20 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 24.48 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.39 (0.30), residues: 754
  helix:  2.83 (0.19), residues: 646
  sheet:  None (None), residues: 0
  loop : -1.75 (0.54), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 490 
 TYR   0.024   0.001   TYR A 548 
 PHE   0.014   0.001   PHE B  79 
 TRP   0.009   0.001   TRP A 509 
 HIS   0.003   0.000   HIS A 415 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 6396)
  covalent geometry    : angle       0.52057 ( 8698)
  hydrogen bonds       : bond        0.03841 (  528)
  hydrogen bonds       : angle       3.75667 ( 1584)

*********************** 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
  129 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 112
  time to evaluate  : 0.215 
Fit side-chains
REVERT: A   63 PHE cc_start: 0.8207 (m-10) cc_final: 0.7870 (m-80)
REVERT: A  124 TYR cc_start: 0.3628 (t80) cc_final: 0.2276 (t80)
REVERT: A  288 GLU cc_start: 0.3600 (OUTLIER) cc_final: 0.3031 (tp30)
REVERT: A  296 LEU cc_start: 0.8263 (mt) cc_final: 0.8051 (mp)
REVERT: A  519 HIS cc_start: 0.5679 (t70) cc_final: 0.5018 (m90)
REVERT: A  550 MET cc_start: 0.8264 (mtt) cc_final: 0.8006 (mtt)
REVERT: B  124 TYR cc_start: 0.3329 (t80) cc_final: 0.2175 (t80)
REVERT: B  125 TYR cc_start: 0.5599 (m-10) cc_final: 0.5352 (m-10)
REVERT: B  185 MET cc_start: 0.8359 (tpp) cc_final: 0.8114 (tpp)
REVERT: B  264 LYS cc_start: 0.8165 (ttmt) cc_final: 0.7705 (tptt)
REVERT: B  288 GLU cc_start: 0.3545 (OUTLIER) cc_final: 0.2991 (tp30)
REVERT: B  296 LEU cc_start: 0.8256 (mt) cc_final: 0.8028 (mp)
REVERT: B  374 MET cc_start: 0.8028 (OUTLIER) cc_final: 0.7510 (mpp)
REVERT: B  519 HIS cc_start: 0.5646 (t70) cc_final: 0.5089 (m90)
REVERT: B  550 MET cc_start: 0.8283 (mtt) cc_final: 0.8029 (mtt)
  outliers start: 17
  outliers final: 7
  residues processed: 128
  average time/residue: 0.0542
  time to fit residues: 10.1183
Evaluate side-chains
  119 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 109
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
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  180 ASN
Chi-restraints excluded: chain A residue  288 GLU
Chi-restraints excluded: chain A residue  389 VAL
Chi-restraints excluded: chain B residue   55 VAL
Chi-restraints excluded: chain B residue  165 HIS
Chi-restraints excluded: chain B residue  288 GLU
Chi-restraints excluded: chain B residue  374 MET
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 3 optimal weight:    2.9990
   chunk 66 optimal weight:    0.0000
   chunk 59 optimal weight:    6.9990
   chunk 51 optimal weight:    2.9990
   chunk 36 optimal weight:    2.9990
   chunk 57 optimal weight:    1.9990
   chunk 48 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9990
   chunk 53 optimal weight:    6.9990
   chunk 71 optimal weight:    6.9990
   chunk 12 optimal weight:    0.9990
   overall best weight:    1.1992

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4126 r_free = 0.4126 target = 0.167698 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.128315 restraints weight = 8924.774|
|-----------------------------------------------------------------------------|
r_work (start): 0.3623 rms_B_bonded: 2.33
r_work: 0.3449 rms_B_bonded: 3.81 restraints_weight: 0.5000
r_work (final): 0.3449
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8118
moved from start:          0.9409

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= 0.145
  Angle     :  0.576   9.134   8698  Z= 0.285
  Chirality :  0.040   0.242   1032
  Planarity :  0.004   0.051   1042
  Dihedral  :  3.964  27.666    846
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 7.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.93 %
    Favored  : 99.07 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 24.78 %
    Favored  : 73.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.36 (0.30), residues: 754
  helix:  2.78 (0.19), residues: 648
  sheet:  None (None), residues: 0
  loop : -1.71 (0.55), residues: 106

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 428 
 TYR   0.030   0.002   TYR A 548 
 PHE   0.017   0.001   PHE A 332 
 TRP   0.017   0.002   TRP B 509 
 HIS   0.004   0.001   HIS B 415 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 6396)
  covalent geometry    : angle       0.57577 ( 8698)
  hydrogen bonds       : bond        0.04040 (  528)
  hydrogen bonds       : angle       3.80032 ( 1584)

********************** 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
  138 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 125
  time to evaluate  : 0.183 
Fit side-chains
REVERT: A  120 PHE cc_start: 0.6921 (m-80) cc_final: 0.6525 (m-80)
REVERT: A  288 GLU cc_start: 0.3706 (OUTLIER) cc_final: 0.3050 (tp30)
REVERT: A  519 HIS cc_start: 0.5616 (t70) cc_final: 0.4985 (m90)
REVERT: A  550 MET cc_start: 0.8335 (mtt) cc_final: 0.8105 (mtt)
REVERT: B  120 PHE cc_start: 0.6860 (m-80) cc_final: 0.6506 (m-80)
REVERT: B  264 LYS cc_start: 0.8199 (ttmt) cc_final: 0.7734 (tptt)
REVERT: B  288 GLU cc_start: 0.3683 (OUTLIER) cc_final: 0.3100 (tp30)
REVERT: B  296 LEU cc_start: 0.8282 (mt) cc_final: 0.8045 (mp)
REVERT: B  374 MET cc_start: 0.7974 (OUTLIER) cc_final: 0.7437 (mpp)
REVERT: B  519 HIS cc_start: 0.5579 (t70) cc_final: 0.5053 (m90)
  outliers start: 13
  outliers final: 8
  residues processed: 136
  average time/residue: 0.0648
  time to fit residues: 12.5218
Evaluate side-chains
  129 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 118
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
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  180 ASN
Chi-restraints excluded: chain A residue  288 GLU
Chi-restraints excluded: chain A residue  389 VAL
Chi-restraints excluded: chain B residue   55 VAL
Chi-restraints excluded: chain B residue  288 GLU
Chi-restraints excluded: chain B residue  298 LEU
Chi-restraints excluded: chain B residue  374 MET
Chi-restraints excluded: chain B residue  389 VAL
Chi-restraints excluded: chain B residue  409 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 30 optimal weight:    0.8980
   chunk 41 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9980
   chunk 37 optimal weight:    0.6980
   chunk 13 optimal weight:    0.9980
   chunk 38 optimal weight:    0.7980
   chunk 31 optimal weight:    1.9990
   chunk 52 optimal weight:    2.9990
   chunk 8 optimal weight:    2.9990
   chunk 39 optimal weight:    3.9990
   chunk 64 optimal weight:   10.0000
   overall best weight:    0.8780

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4129 r_free = 0.4129 target = 0.167674 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.128937 restraints weight = 9009.167|
|-----------------------------------------------------------------------------|
r_work (start): 0.3632 rms_B_bonded: 2.34
r_work: 0.3459 rms_B_bonded: 3.80 restraints_weight: 0.5000
r_work (final): 0.3459
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8103
moved from start:          0.9715

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= 0.129
  Angle     :  0.544   7.647   8698  Z= 0.272
  Chirality :  0.040   0.267   1032
  Planarity :  0.004   0.050   1042
  Dihedral  :  3.923  26.075    846
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 8.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.66 %
    Favored  : 99.34 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 24.63 %
    Favored  : 73.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.46 (0.30), residues: 754
  helix:  2.87 (0.19), residues: 646
  sheet:  None (None), residues: 0
  loop : -1.72 (0.53), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 492 
 TYR   0.025   0.001   TYR B 548 
 PHE   0.026   0.001   PHE B 301 
 TRP   0.016   0.002   TRP B 509 
 HIS   0.003   0.001   HIS A 415 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 6396)
  covalent geometry    : angle       0.54394 ( 8698)
  hydrogen bonds       : bond        0.03829 (  528)
  hydrogen bonds       : angle       3.75303 ( 1584)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1456.72 seconds
wall clock time: 25 minutes 41.34 seconds (1541.34 seconds total)