Starting phenix.real_space_refine
on Wed Mar  5 16:07:45 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7q67_13854/03_2025/7q67_13854.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7q67_13854/03_2025/7q67_13854.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.37
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7q67_13854/03_2025/7q67_13854.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7q67_13854/03_2025/7q67_13854.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7q67_13854/03_2025/7q67_13854.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7q67_13854/03_2025/7q67_13854.cif"
  }
  resolution = 3.37
  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=   1.002
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: 3
    Type Number    sf(0)   Gaussians
     C    1639      2.51       5
     N     440      2.21       5
     O     539      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 2618
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 238
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 33, 238
          Classifications: {'peptide': 33}
          Link IDs: {'PTRANS': 1, 'TRANS': 31}
  Restraints were copied for chains:
    C, B, E, D, G, F, I, H, K, J
  Time building chain proxies: 1.26, per 1000 atoms: 0.48
  Number of scatterers: 2618
  At special positions: 0
  Unit cell: (88.2, 49.35, 44.1, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 3
    Type Number    sf(0)
     O     539      8.00
     N     440      7.00
     C    1639      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: 0.63
  Conformation dependent library (CDL) restraints added in 327.4 milliseconds
  

  682 Ramachandran restraints generated.
    341 Oldfield, 0 Emsley, 341 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  616

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 2 sheets defined
      0.0% alpha, 18.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.21
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 103 through 109
      removed outlier: 7.008A  pdb=" N   ALA A 107 " --> pdb=" O   PHE C 106 " (cutoff:3.500A)
      removed outlier: 7.012A  pdb=" N   GLN C 108 " --> pdb=" O   ALA A 107 " (cutoff:3.500A)
      removed outlier: 6.934A  pdb=" N   ASN A 109 " --> pdb=" O   GLN C 108 " (cutoff:3.500A)
      removed outlier: 7.008A  pdb=" N   ALA C 107 " --> pdb=" O   PHE E 106 " (cutoff:3.500A)
      removed outlier: 7.012A  pdb=" N   GLN E 108 " --> pdb=" O   ALA C 107 " (cutoff:3.500A)
      removed outlier: 6.934A  pdb=" N   ASN C 109 " --> pdb=" O   GLN E 108 " (cutoff:3.500A)
      removed outlier: 7.008A  pdb=" N   ALA E 107 " --> pdb=" O   PHE G 106 " (cutoff:3.500A)
      removed outlier: 7.012A  pdb=" N   GLN G 108 " --> pdb=" O   ALA E 107 " (cutoff:3.500A)
      removed outlier: 6.933A  pdb=" N   ASN E 109 " --> pdb=" O   GLN G 108 " (cutoff:3.500A)
      removed outlier: 7.008A  pdb=" N   ALA G 107 " --> pdb=" O   PHE I 106 " (cutoff:3.500A)
      removed outlier: 7.011A  pdb=" N   GLN I 108 " --> pdb=" O   ALA G 107 " (cutoff:3.500A)
      removed outlier: 6.934A  pdb=" N   ASN G 109 " --> pdb=" O   GLN I 108 " (cutoff:3.500A)
      removed outlier: 7.008A  pdb=" N   ALA I 107 " --> pdb=" O   PHE K 106 " (cutoff:3.500A)
      removed outlier: 7.012A  pdb=" N   GLN K 108 " --> pdb=" O   ALA I 107 " (cutoff:3.500A)
      removed outlier: 6.933A  pdb=" N   ASN I 109 " --> pdb=" O   GLN K 108 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 103 through 109
      removed outlier: 7.008A  pdb=" N   ALA B 107 " --> pdb=" O   PHE D 106 " (cutoff:3.500A)
      removed outlier: 7.012A  pdb=" N   GLN D 108 " --> pdb=" O   ALA B 107 " (cutoff:3.500A)
      removed outlier: 6.934A  pdb=" N   ASN B 109 " --> pdb=" O   GLN D 108 " (cutoff:3.500A)
      removed outlier: 7.008A  pdb=" N   ALA D 107 " --> pdb=" O   PHE F 106 " (cutoff:3.500A)
      removed outlier: 7.012A  pdb=" N   GLN F 108 " --> pdb=" O   ALA D 107 " (cutoff:3.500A)
      removed outlier: 6.934A  pdb=" N   ASN D 109 " --> pdb=" O   GLN F 108 " (cutoff:3.500A)
      removed outlier: 7.008A  pdb=" N   ALA F 107 " --> pdb=" O   PHE H 106 " (cutoff:3.500A)
      removed outlier: 7.012A  pdb=" N   GLN H 108 " --> pdb=" O   ALA F 107 " (cutoff:3.500A)
      removed outlier: 6.933A  pdb=" N   ASN F 109 " --> pdb=" O   GLN H 108 " (cutoff:3.500A)
      removed outlier: 7.008A  pdb=" N   ALA H 107 " --> pdb=" O   PHE J 106 " (cutoff:3.500A)
      removed outlier: 7.012A  pdb=" N   GLN J 108 " --> pdb=" O   ALA H 107 " (cutoff:3.500A)
      removed outlier: 6.934A  pdb=" N   ASN H 109 " --> pdb=" O   GLN J 108 " (cutoff:3.500A)

    27 hydrogen bonds defined for protein.
    81 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.49

  Time building geometry restraints manager: 0.75 seconds

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

  Histogram of bond lengths:
        1.20 -     1.27: 429
        1.27 -     1.33: 382
        1.33 -     1.40: 379
        1.40 -     1.47: 522
        1.47 -     1.54: 961
  Bond restraints: 2673
  Sorted by residual:
  bond pdb=" CA  PHE I 114 "
       pdb=" CB  PHE I 114 "
    ideal  model  delta    sigma   weight residual
    1.530  1.485  0.045 1.58e-02 4.01e+03 8.10e+00
  bond pdb=" CA  PHE E 114 "
       pdb=" CB  PHE E 114 "
    ideal  model  delta    sigma   weight residual
    1.530  1.486  0.045 1.58e-02 4.01e+03 7.99e+00
  bond pdb=" CA  PHE K 114 "
       pdb=" CB  PHE K 114 "
    ideal  model  delta    sigma   weight residual
    1.530  1.486  0.045 1.58e-02 4.01e+03 7.98e+00
  bond pdb=" CA  PHE C 114 "
       pdb=" CB  PHE C 114 "
    ideal  model  delta    sigma   weight residual
    1.530  1.486  0.045 1.58e-02 4.01e+03 7.98e+00
  bond pdb=" CA  PHE B 114 "
       pdb=" CB  PHE B 114 "
    ideal  model  delta    sigma   weight residual
    1.530  1.486  0.044 1.58e-02 4.01e+03 7.91e+00
  ... (remaining 2668 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.19: 3241
        3.19 -     6.38: 268
        6.38 -     9.56: 88
        9.56 -    12.75: 0
       12.75 -    15.94: 11
  Bond angle restraints: 3608
  Sorted by residual:
  angle pdb=" N   PHE F 114 "
        pdb=" CA  PHE F 114 "
        pdb=" CB  PHE F 114 "
      ideal   model   delta    sigma   weight residual
     109.82  100.32    9.50 1.52e+00 4.33e-01 3.90e+01
  angle pdb=" N   PHE D 114 "
        pdb=" CA  PHE D 114 "
        pdb=" CB  PHE D 114 "
      ideal   model   delta    sigma   weight residual
     109.82  100.34    9.48 1.52e+00 4.33e-01 3.89e+01
  angle pdb=" N   PHE A 114 "
        pdb=" CA  PHE A 114 "
        pdb=" CB  PHE A 114 "
      ideal   model   delta    sigma   weight residual
     109.82  100.34    9.48 1.52e+00 4.33e-01 3.89e+01
  angle pdb=" N   PHE G 114 "
        pdb=" CA  PHE G 114 "
        pdb=" CB  PHE G 114 "
      ideal   model   delta    sigma   weight residual
     109.82  100.35    9.47 1.52e+00 4.33e-01 3.88e+01
  angle pdb=" N   PHE B 114 "
        pdb=" CA  PHE B 114 "
        pdb=" CB  PHE B 114 "
      ideal   model   delta    sigma   weight residual
     109.82  100.35    9.47 1.52e+00 4.33e-01 3.88e+01
  ... (remaining 3603 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.05 -     8.42: 1024
        8.42 -    16.80: 263
       16.80 -    25.17: 99
       25.17 -    33.54: 44
       33.54 -    41.92: 33
  Dihedral angle restraints: 1463
    sinusoidal: 495
      harmonic: 968
  Sorted by residual:
  dihedral pdb=" CA  GLY E 113 "
           pdb=" C   GLY E 113 "
           pdb=" N   PHE E 114 "
           pdb=" CA  PHE E 114 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -138.08  -41.92     0      5.00e+00 4.00e-02 7.03e+01
  dihedral pdb=" CA  GLY J 113 "
           pdb=" C   GLY J 113 "
           pdb=" N   PHE J 114 "
           pdb=" CA  PHE J 114 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -138.09  -41.91     0      5.00e+00 4.00e-02 7.03e+01
  dihedral pdb=" CA  GLY G 113 "
           pdb=" C   GLY G 113 "
           pdb=" N   PHE G 114 "
           pdb=" CA  PHE G 114 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -138.09  -41.91     0      5.00e+00 4.00e-02 7.03e+01
  ... (remaining 1460 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.068: 186
       0.068 -    0.135: 100
       0.135 -    0.203: 46
       0.203 -    0.270: 20
       0.270 -    0.338: 44
  Chirality restraints: 396
  Sorted by residual:
  chirality pdb=" CA  ASN H 103 "
            pdb=" N   ASN H 103 "
            pdb=" C   ASN H 103 "
            pdb=" CB  ASN H 103 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.17    0.34 2.00e-01 2.50e+01 2.85e+00
  chirality pdb=" CA  ASN G 103 "
            pdb=" N   ASN G 103 "
            pdb=" C   ASN G 103 "
            pdb=" CB  ASN G 103 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.17    0.34 2.00e-01 2.50e+01 2.85e+00
  chirality pdb=" CA  ASN A 103 "
            pdb=" N   ASN A 103 "
            pdb=" C   ASN A 103 "
            pdb=" CB  ASN A 103 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.17    0.34 2.00e-01 2.50e+01 2.85e+00
  ... (remaining 393 not shown)

  Planarity restraints: 484
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE E  99 "   -0.020 2.00e-02 2.50e+03   1.76e-02 5.40e+00
        pdb=" CG  PHE E  99 "    0.041 2.00e-02 2.50e+03
        pdb=" CD1 PHE E  99 "   -0.006 2.00e-02 2.50e+03
        pdb=" CD2 PHE E  99 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE1 PHE E  99 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE2 PHE E  99 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ  PHE E  99 "   -0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE D  99 "    0.020 2.00e-02 2.50e+03   1.75e-02 5.37e+00
        pdb=" CG  PHE D  99 "   -0.041 2.00e-02 2.50e+03
        pdb=" CD1 PHE D  99 "    0.007 2.00e-02 2.50e+03
        pdb=" CD2 PHE D  99 "    0.005 2.00e-02 2.50e+03
        pdb=" CE1 PHE D  99 "    0.003 2.00e-02 2.50e+03
        pdb=" CE2 PHE D  99 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ  PHE D  99 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE C  99 "   -0.020 2.00e-02 2.50e+03   1.75e-02 5.35e+00
        pdb=" CG  PHE C  99 "    0.041 2.00e-02 2.50e+03
        pdb=" CD1 PHE C  99 "   -0.006 2.00e-02 2.50e+03
        pdb=" CD2 PHE C  99 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE1 PHE C  99 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE2 PHE C  99 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ  PHE C  99 "   -0.003 2.00e-02 2.50e+03
  ... (remaining 481 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.80: 903
        2.80 -     3.33: 2451
        3.33 -     3.85: 4656
        3.85 -     4.38: 5350
        4.38 -     4.90: 9886
  Nonbonded interactions: 23246
  Sorted by model distance:
  nonbonded pdb=" O   SER K 101 "
            pdb=" OG  SER K 101 "
     model   vdw
     2.280 3.040
  nonbonded pdb=" O   SER D 101 "
            pdb=" OG  SER D 101 "
     model   vdw
     2.280 3.040
  nonbonded pdb=" O   SER H 101 "
            pdb=" OG  SER H 101 "
     model   vdw
     2.281 3.040
  nonbonded pdb=" O   SER F 101 "
            pdb=" OG  SER F 101 "
     model   vdw
     2.281 3.040
  nonbonded pdb=" O   SER B 101 "
            pdb=" OG  SER B 101 "
     model   vdw
     2.281 3.040
  ... (remaining 23241 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 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
  selection = chain 'G'
  selection = chain 'F'
  selection = chain 'I'
  selection = chain 'H'
  selection = chain 'K'
  selection = chain 'J'
}

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:             0.700
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     10.230
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.560
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.710
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7156
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      :  0.020   0.136   2673  Z= 1.490
  Angle     :  2.209  15.939   3608  Z= 1.304
  Chirality :  0.136   0.338    396
  Planarity :  0.009   0.019    484
  Dihedral  : 14.467  41.919    847
  Min Nonbonded Distance : 2.280

Molprobity Statistics.
  All-atom Clashscore : 12.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.13 %
    Favored  : 83.87 %
  Rotamer:
    Outliers :  8.00 %
    Allowed  : 12.00 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 3.23 %

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: -4.98 (0.33), residues: 341
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.79 (0.25), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.041   0.009   PHE E  99 

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

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

  682 Ramachandran restraints generated.
    341 Oldfield, 0 Emsley, 341 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  682 Ramachandran restraints generated.
    341 Oldfield, 0 Emsley, 341 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 143
  time to evaluate  : 0.284 
Fit side-chains
REVERT: A  104 ASN cc_start: 0.7201 (m110) cc_final: 0.6959 (m110)
  outliers start: 22
  outliers final: 11
  residues processed: 143
  average time/residue: 0.1104
  time to fit residues: 19.1834
Evaluate side-chains
  99 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 88
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 LEU
Chi-restraints excluded: chain B residue   88 LEU
Chi-restraints excluded: chain C residue   88 LEU
Chi-restraints excluded: chain D residue   88 LEU
Chi-restraints excluded: chain E residue   88 LEU
Chi-restraints excluded: chain F residue   88 LEU
Chi-restraints excluded: chain G residue   88 LEU
Chi-restraints excluded: chain H residue   88 LEU
Chi-restraints excluded: chain I residue   88 LEU
Chi-restraints excluded: chain J residue   88 LEU
Chi-restraints excluded: chain K residue   88 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 33
   random chunks:
   chunk 27 optimal weight:    6.9990
   chunk 25 optimal weight:    2.9990
   chunk 13 optimal weight:    5.9990
   chunk 8 optimal weight:    1.9990
   chunk 16 optimal weight:    2.9990
   chunk 10 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   chunk 19 optimal weight:    3.9990
   chunk 29 optimal weight:    1.9990
   chunk 9 optimal weight:    6.9990
   chunk 24 optimal weight:   10.0000
   overall best weight:    2.3990

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

Flipped N/Q/H residues before XYZ refinement:
** A 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4377 r_free = 0.4377 target = 0.182200 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.4166 r_free = 0.4166 target = 0.164020 restraints weight = 4041.593|
|-----------------------------------------------------------------------------|
r_work (start): 0.4169 rms_B_bonded: 3.33
r_work: 0.4050 rms_B_bonded: 4.22 restraints_weight: 0.5000
r_work (final): 0.4050
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7042
moved from start:          0.3203

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   2673  Z= 0.360
  Angle     :  1.113  10.344   3608  Z= 0.574
  Chirality :  0.063   0.213    396
  Planarity :  0.003   0.012    484
  Dihedral  :  9.148  27.489    374
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 21.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.84 %
    Favored  : 84.16 %
  Rotamer:
    Outliers : 15.64 %
    Allowed  : 17.82 %
    Favored  : 66.55 %
  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: -4.88 (0.31), residues: 341
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.72 (0.24), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.017   0.003   PHE E 114 

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

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

  682 Ramachandran restraints generated.
    341 Oldfield, 0 Emsley, 341 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  682 Ramachandran restraints generated.
    341 Oldfield, 0 Emsley, 341 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 116
  time to evaluate  : 0.295 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  110 LYS cc_start: 0.6603 (pttp) cc_final: 0.6207 (mmtt)
REVERT: C   87 THR cc_start: 0.5007 (p) cc_final: 0.4802 (p)
REVERT: C   91 THR cc_start: 0.8776 (p) cc_final: 0.8333 (t)
REVERT: F   91 THR cc_start: 0.8609 (p) cc_final: 0.8033 (t)
REVERT: G   94 THR cc_start: 0.8712 (p) cc_final: 0.8462 (m)
REVERT: H   91 THR cc_start: 0.8682 (p) cc_final: 0.8181 (t)
REVERT: J   91 THR cc_start: 0.8641 (p) cc_final: 0.8278 (t)
REVERT: K   94 THR cc_start: 0.8702 (p) cc_final: 0.8501 (m)
  outliers start: 43
  outliers final: 28
  residues processed: 139
  average time/residue: 0.0773
  time to fit residues: 14.0637
Evaluate side-chains
  113 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 85
  time to evaluate  : 0.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 LEU
Chi-restraints excluded: chain A residue  101 SER
Chi-restraints excluded: chain A residue  102 GLN
Chi-restraints excluded: chain B residue   88 LEU
Chi-restraints excluded: chain B residue  102 GLN
Chi-restraints excluded: chain C residue   88 LEU
Chi-restraints excluded: chain C residue   98 LEU
Chi-restraints excluded: chain C residue  101 SER
Chi-restraints excluded: chain C residue  102 GLN
Chi-restraints excluded: chain D residue   88 LEU
Chi-restraints excluded: chain D residue  101 SER
Chi-restraints excluded: chain E residue   88 LEU
Chi-restraints excluded: chain E residue   97 SER
Chi-restraints excluded: chain E residue   98 LEU
Chi-restraints excluded: chain F residue   88 LEU
Chi-restraints excluded: chain F residue   97 SER
Chi-restraints excluded: chain F residue   98 LEU
Chi-restraints excluded: chain F residue  100 SER
Chi-restraints excluded: chain G residue   88 LEU
Chi-restraints excluded: chain G residue   98 LEU
Chi-restraints excluded: chain H residue   88 LEU
Chi-restraints excluded: chain H residue   94 THR
Chi-restraints excluded: chain I residue   88 LEU
Chi-restraints excluded: chain I residue   98 LEU
Chi-restraints excluded: chain J residue   88 LEU
Chi-restraints excluded: chain J residue   94 THR
Chi-restraints excluded: chain J residue   98 LEU
Chi-restraints excluded: chain K residue   88 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 33
   random chunks:
   chunk 14 optimal weight:    5.9990
   chunk 5 optimal weight:    0.7980
   chunk 8 optimal weight:    0.9990
   chunk 27 optimal weight:    6.9990
   chunk 23 optimal weight:    7.9990
   chunk 18 optimal weight:   10.0000
   chunk 0 optimal weight:    9.9990
   chunk 4 optimal weight:    6.9990
   chunk 10 optimal weight:    0.9980
   chunk 20 optimal weight:    8.9990
   chunk 12 optimal weight:    2.9990
   overall best weight:    2.3586

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

Flipped N/Q/H residues before XYZ refinement:
** A 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4393 r_free = 0.4393 target = 0.183743 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4190 r_free = 0.4190 target = 0.165817 restraints weight = 3983.697|
|-----------------------------------------------------------------------------|
r_work (start): 0.4192 rms_B_bonded: 3.23
r_work: 0.4087 rms_B_bonded: 4.12 restraints_weight: 0.5000
r_work (final): 0.4087
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7011
moved from start:          0.3857

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033   2673  Z= 0.354
  Angle     :  1.052   9.969   3608  Z= 0.530
  Chirality :  0.061   0.208    396
  Planarity :  0.003   0.015    484
  Dihedral  :  7.831  20.880    374
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 19.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 18.77 %
    Favored  : 81.23 %
  Rotamer:
    Outliers : 15.64 %
    Allowed  : 19.27 %
    Favored  : 65.09 %
  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: -4.85 (0.31), residues: 341
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.69 (0.24), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.022   0.003   PHE I  99 

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

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

  682 Ramachandran restraints generated.
    341 Oldfield, 0 Emsley, 341 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  682 Ramachandran restraints generated.
    341 Oldfield, 0 Emsley, 341 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 102
  time to evaluate  : 0.261 
Fit side-chains
   revert: symmetry clash
REVERT: A  110 LYS cc_start: 0.6475 (pttp) cc_final: 0.6037 (mmtt)
REVERT: B   91 THR cc_start: 0.8704 (p) cc_final: 0.8300 (t)
REVERT: C   91 THR cc_start: 0.8783 (p) cc_final: 0.8337 (t)
REVERT: F   91 THR cc_start: 0.8659 (p) cc_final: 0.8095 (t)
REVERT: G  106 PHE cc_start: 0.6959 (t80) cc_final: 0.6481 (t80)
REVERT: H   91 THR cc_start: 0.8664 (p) cc_final: 0.8121 (t)
REVERT: J   91 THR cc_start: 0.8613 (p) cc_final: 0.8234 (t)
  outliers start: 43
  outliers final: 37
  residues processed: 129
  average time/residue: 0.0790
  time to fit residues: 13.3047
Evaluate side-chains
  127 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 90
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 LEU
Chi-restraints excluded: chain A residue  101 SER
Chi-restraints excluded: chain B residue   88 LEU
Chi-restraints excluded: chain B residue  101 SER
Chi-restraints excluded: chain B residue  102 GLN
Chi-restraints excluded: chain C residue   88 LEU
Chi-restraints excluded: chain C residue   98 LEU
Chi-restraints excluded: chain C residue  101 SER
Chi-restraints excluded: chain C residue  102 GLN
Chi-restraints excluded: chain C residue  116 ASN
Chi-restraints excluded: chain D residue   88 LEU
Chi-restraints excluded: chain D residue   99 PHE
Chi-restraints excluded: chain D residue  101 SER
Chi-restraints excluded: chain E residue   88 LEU
Chi-restraints excluded: chain E residue   97 SER
Chi-restraints excluded: chain E residue   98 LEU
Chi-restraints excluded: chain E residue   99 PHE
Chi-restraints excluded: chain E residue  101 SER
Chi-restraints excluded: chain F residue   88 LEU
Chi-restraints excluded: chain F residue   98 LEU
Chi-restraints excluded: chain F residue   99 PHE
Chi-restraints excluded: chain G residue   88 LEU
Chi-restraints excluded: chain G residue   99 PHE
Chi-restraints excluded: chain G residue  101 SER
Chi-restraints excluded: chain H residue   88 LEU
Chi-restraints excluded: chain H residue   99 PHE
Chi-restraints excluded: chain H residue  101 SER
Chi-restraints excluded: chain I residue   88 LEU
Chi-restraints excluded: chain I residue   94 THR
Chi-restraints excluded: chain I residue   99 PHE
Chi-restraints excluded: chain I residue  101 SER
Chi-restraints excluded: chain J residue   88 LEU
Chi-restraints excluded: chain J residue   94 THR
Chi-restraints excluded: chain J residue   98 LEU
Chi-restraints excluded: chain J residue   99 PHE
Chi-restraints excluded: chain K residue   88 LEU
Chi-restraints excluded: chain K residue   99 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 33
   random chunks:
   chunk 17 optimal weight:    4.9990
   chunk 16 optimal weight:    2.9990
   chunk 27 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9980
   chunk 2 optimal weight:    0.3980
   chunk 25 optimal weight:    7.9990
   chunk 26 optimal weight:    1.9990
   chunk 7 optimal weight:    0.8980
   chunk 14 optimal weight:    8.9990
   chunk 28 optimal weight:    3.9990
   chunk 5 optimal weight:    0.1980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 104 ASN
B 102 GLN
B 104 ASN
C 104 ASN
C 108 GLN
** F 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 108 GLN
** J 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 103 ASN
** K 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4521 r_free = 0.4521 target = 0.196051 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4333 r_free = 0.4333 target = 0.178792 restraints weight = 3884.895|
|-----------------------------------------------------------------------------|
r_work (start): 0.4337 rms_B_bonded: 3.20
r_work: 0.4234 rms_B_bonded: 4.08 restraints_weight: 0.5000
r_work (final): 0.4234
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6828
moved from start:          0.4605

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   2673  Z= 0.228
  Angle     :  0.978  10.067   3608  Z= 0.471
  Chirality :  0.055   0.189    396
  Planarity :  0.003   0.014    484
  Dihedral  :  6.535  20.377    374
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 18.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.32 %
    Favored  : 87.68 %
  Rotamer:
    Outliers : 13.09 %
    Allowed  : 24.36 %
    Favored  : 62.55 %
  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: -4.76 (0.31), residues: 341
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.62 (0.24), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.020   0.002   PHE I  99 

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

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

  682 Ramachandran restraints generated.
    341 Oldfield, 0 Emsley, 341 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  682 Ramachandran restraints generated.
    341 Oldfield, 0 Emsley, 341 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 110
  time to evaluate  : 0.303 
Fit side-chains
REVERT: A   88 LEU cc_start: 0.7936 (OUTLIER) cc_final: 0.7235 (mt)
REVERT: A  110 LYS cc_start: 0.6349 (pttp) cc_final: 0.5989 (mmtt)
REVERT: B   88 LEU cc_start: 0.7879 (OUTLIER) cc_final: 0.7235 (mt)
REVERT: B   91 THR cc_start: 0.8783 (p) cc_final: 0.8300 (t)
REVERT: C   91 THR cc_start: 0.8796 (p) cc_final: 0.8223 (t)
REVERT: D   91 THR cc_start: 0.8654 (p) cc_final: 0.8167 (t)
REVERT: D  112 THR cc_start: 0.7676 (m) cc_final: 0.7469 (t)
REVERT: E   91 THR cc_start: 0.8781 (p) cc_final: 0.8298 (t)
REVERT: F   91 THR cc_start: 0.8821 (p) cc_final: 0.8382 (t)
REVERT: F  106 PHE cc_start: 0.6844 (t80) cc_final: 0.6220 (t80)
REVERT: G  106 PHE cc_start: 0.6523 (t80) cc_final: 0.6285 (t80)
REVERT: H   91 THR cc_start: 0.8751 (p) cc_final: 0.8258 (t)
REVERT: I  100 SER cc_start: 0.9042 (p) cc_final: 0.8798 (p)
REVERT: J   91 THR cc_start: 0.8661 (p) cc_final: 0.8331 (t)
REVERT: K  103 ASN cc_start: 0.7323 (OUTLIER) cc_final: 0.7022 (p0)
  outliers start: 36
  outliers final: 29
  residues processed: 128
  average time/residue: 0.0824
  time to fit residues: 13.8211
Evaluate side-chains
  127 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 95
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 LEU
Chi-restraints excluded: chain A residue   98 LEU
Chi-restraints excluded: chain A residue  101 SER
Chi-restraints excluded: chain B residue   88 LEU
Chi-restraints excluded: chain B residue  101 SER
Chi-restraints excluded: chain C residue   88 LEU
Chi-restraints excluded: chain C residue   98 LEU
Chi-restraints excluded: chain C residue   99 PHE
Chi-restraints excluded: chain C residue  101 SER
Chi-restraints excluded: chain C residue  102 GLN
Chi-restraints excluded: chain D residue   88 LEU
Chi-restraints excluded: chain D residue   99 PHE
Chi-restraints excluded: chain D residue  101 SER
Chi-restraints excluded: chain E residue   88 LEU
Chi-restraints excluded: chain E residue   98 LEU
Chi-restraints excluded: chain E residue   99 PHE
Chi-restraints excluded: chain F residue   88 LEU
Chi-restraints excluded: chain F residue   98 LEU
Chi-restraints excluded: chain F residue   99 PHE
Chi-restraints excluded: chain G residue   88 LEU
Chi-restraints excluded: chain G residue   99 PHE
Chi-restraints excluded: chain G residue  101 SER
Chi-restraints excluded: chain H residue   88 LEU
Chi-restraints excluded: chain H residue   99 PHE
Chi-restraints excluded: chain I residue   88 LEU
Chi-restraints excluded: chain I residue   99 PHE
Chi-restraints excluded: chain J residue   88 LEU
Chi-restraints excluded: chain J residue   98 LEU
Chi-restraints excluded: chain J residue   99 PHE
Chi-restraints excluded: chain K residue   88 LEU
Chi-restraints excluded: chain K residue   99 PHE
Chi-restraints excluded: chain K residue  103 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 33
   random chunks:
   chunk 12 optimal weight:   20.0000
   chunk 29 optimal weight:    0.1980
   chunk 3 optimal weight:    9.9990
   chunk 28 optimal weight:    0.9980
   chunk 25 optimal weight:    3.9990
   chunk 9 optimal weight:    9.9990
   chunk 4 optimal weight:    9.9990
   chunk 23 optimal weight:    3.9990
   chunk 14 optimal weight:    0.7980
   chunk 24 optimal weight:    9.9990
   chunk 32 optimal weight:    0.0050
   overall best weight:    1.1996

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

Flipped N/Q/H residues before XYZ refinement:
** G 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4524 r_free = 0.4524 target = 0.195890 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4340 r_free = 0.4340 target = 0.178678 restraints weight = 3855.622|
|-----------------------------------------------------------------------------|
r_work (start): 0.4340 rms_B_bonded: 3.16
r_work: 0.4236 rms_B_bonded: 4.07 restraints_weight: 0.5000
r_work (final): 0.4236
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6850
moved from start:          0.4791

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   2673  Z= 0.231
  Angle     :  0.931   9.953   3608  Z= 0.448
  Chirality :  0.054   0.186    396
  Planarity :  0.003   0.019    484
  Dihedral  :  6.331  21.057    374
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 17.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 17.30 %
    Favored  : 82.70 %
  Rotamer:
    Outliers : 11.64 %
    Allowed  : 24.00 %
    Favored  : 64.36 %
  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: -4.94 (0.31), residues: 341
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.76 (0.23), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.019   0.002   PHE I  99 

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

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

  682 Ramachandran restraints generated.
    341 Oldfield, 0 Emsley, 341 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  682 Ramachandran restraints generated.
    341 Oldfield, 0 Emsley, 341 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 106
  time to evaluate  : 0.305 
Fit side-chains
REVERT: A   88 LEU cc_start: 0.7767 (OUTLIER) cc_final: 0.7055 (mt)
REVERT: A  110 LYS cc_start: 0.6333 (pttp) cc_final: 0.5976 (mmtt)
REVERT: B   88 LEU cc_start: 0.7990 (OUTLIER) cc_final: 0.7340 (mt)
REVERT: B   91 THR cc_start: 0.8798 (p) cc_final: 0.8301 (t)
REVERT: B  104 ASN cc_start: 0.6898 (m-40) cc_final: 0.6555 (t0)
REVERT: C   91 THR cc_start: 0.8802 (p) cc_final: 0.8245 (t)
REVERT: D   91 THR cc_start: 0.8664 (p) cc_final: 0.8199 (t)
REVERT: D  112 THR cc_start: 0.7562 (m) cc_final: 0.7348 (t)
REVERT: E   91 THR cc_start: 0.8807 (p) cc_final: 0.8324 (t)
REVERT: F   91 THR cc_start: 0.8841 (p) cc_final: 0.8412 (t)
REVERT: F  106 PHE cc_start: 0.6886 (t80) cc_final: 0.6323 (t80)
REVERT: H   91 THR cc_start: 0.8771 (p) cc_final: 0.8245 (t)
REVERT: I  100 SER cc_start: 0.9069 (p) cc_final: 0.8816 (p)
REVERT: J   91 THR cc_start: 0.8632 (p) cc_final: 0.8283 (t)
  outliers start: 32
  outliers final: 28
  residues processed: 121
  average time/residue: 0.0731
  time to fit residues: 11.7528
Evaluate side-chains
  128 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 98
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 LEU
Chi-restraints excluded: chain A residue   98 LEU
Chi-restraints excluded: chain B residue   88 LEU
Chi-restraints excluded: chain B residue   98 LEU
Chi-restraints excluded: chain B residue  101 SER
Chi-restraints excluded: chain C residue   88 LEU
Chi-restraints excluded: chain C residue   98 LEU
Chi-restraints excluded: chain C residue  102 GLN
Chi-restraints excluded: chain D residue   88 LEU
Chi-restraints excluded: chain D residue   94 THR
Chi-restraints excluded: chain D residue   99 PHE
Chi-restraints excluded: chain D residue  101 SER
Chi-restraints excluded: chain E residue   88 LEU
Chi-restraints excluded: chain E residue   99 PHE
Chi-restraints excluded: chain F residue   88 LEU
Chi-restraints excluded: chain F residue   98 LEU
Chi-restraints excluded: chain F residue   99 PHE
Chi-restraints excluded: chain G residue   88 LEU
Chi-restraints excluded: chain G residue   99 PHE
Chi-restraints excluded: chain G residue  100 SER
Chi-restraints excluded: chain H residue   88 LEU
Chi-restraints excluded: chain H residue   99 PHE
Chi-restraints excluded: chain I residue   88 LEU
Chi-restraints excluded: chain I residue   99 PHE
Chi-restraints excluded: chain J residue   88 LEU
Chi-restraints excluded: chain J residue   94 THR
Chi-restraints excluded: chain J residue   98 LEU
Chi-restraints excluded: chain J residue   99 PHE
Chi-restraints excluded: chain K residue   88 LEU
Chi-restraints excluded: chain K residue   99 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 33
   random chunks:
   chunk 27 optimal weight:    8.9990
   chunk 14 optimal weight:    0.0050
   chunk 10 optimal weight:    3.9990
   chunk 28 optimal weight:    2.9990
   chunk 32 optimal weight:    7.9990
   chunk 15 optimal weight:    8.9990
   chunk 18 optimal weight:   10.0000
   chunk 20 optimal weight:    0.9980
   chunk 8 optimal weight:    0.7980
   chunk 21 optimal weight:    8.9990
   chunk 30 optimal weight:   10.0000
   overall best weight:    1.7598

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

Flipped N/Q/H residues before XYZ refinement:
** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 102 GLN
K 103 ASN
K 104 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4524 r_free = 0.4524 target = 0.194243 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4337 r_free = 0.4337 target = 0.176532 restraints weight = 3954.296|
|-----------------------------------------------------------------------------|
r_work (start): 0.4340 rms_B_bonded: 3.20
r_work: 0.4229 rms_B_bonded: 4.16 restraints_weight: 0.5000
r_work (final): 0.4229
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6906
moved from start:          0.4920

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   2673  Z= 0.267
  Angle     :  0.930   9.969   3608  Z= 0.447
  Chirality :  0.054   0.190    396
  Planarity :  0.003   0.013    484
  Dihedral  :  6.302  22.058    374
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 18.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 18.48 %
    Favored  : 81.52 %
  Rotamer:
    Outliers : 13.09 %
    Allowed  : 24.00 %
    Favored  : 62.91 %
  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: -4.91 (0.30), residues: 341
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.74 (0.23), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.018   0.002   PHE G  99 

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

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

  682 Ramachandran restraints generated.
    341 Oldfield, 0 Emsley, 341 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  682 Ramachandran restraints generated.
    341 Oldfield, 0 Emsley, 341 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 106
  time to evaluate  : 0.290 
Fit side-chains
REVERT: A   88 LEU cc_start: 0.7870 (OUTLIER) cc_final: 0.7139 (mt)
REVERT: A  110 LYS cc_start: 0.6139 (pttp) cc_final: 0.5823 (mmtt)
REVERT: B   88 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7292 (mt)
REVERT: B  104 ASN cc_start: 0.6695 (OUTLIER) cc_final: 0.6429 (t0)
REVERT: C   91 THR cc_start: 0.8809 (p) cc_final: 0.8401 (t)
REVERT: D  112 THR cc_start: 0.7644 (m) cc_final: 0.7368 (t)
REVERT: F   91 THR cc_start: 0.8861 (p) cc_final: 0.8380 (t)
REVERT: F  106 PHE cc_start: 0.6469 (t80) cc_final: 0.6112 (t80)
REVERT: H   91 THR cc_start: 0.8780 (p) cc_final: 0.8211 (t)
REVERT: I  100 SER cc_start: 0.9092 (p) cc_final: 0.8832 (p)
REVERT: J   91 THR cc_start: 0.8676 (p) cc_final: 0.8329 (t)
REVERT: J   99 PHE cc_start: 0.7529 (OUTLIER) cc_final: 0.6760 (m-80)
  outliers start: 36
  outliers final: 31
  residues processed: 125
  average time/residue: 0.0783
  time to fit residues: 12.9255
Evaluate side-chains
  136 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 101
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 LEU
Chi-restraints excluded: chain A residue   98 LEU
Chi-restraints excluded: chain A residue  101 SER
Chi-restraints excluded: chain B residue   88 LEU
Chi-restraints excluded: chain B residue   98 LEU
Chi-restraints excluded: chain B residue  101 SER
Chi-restraints excluded: chain B residue  104 ASN
Chi-restraints excluded: chain C residue   88 LEU
Chi-restraints excluded: chain C residue   98 LEU
Chi-restraints excluded: chain C residue   99 PHE
Chi-restraints excluded: chain C residue  102 GLN
Chi-restraints excluded: chain D residue   88 LEU
Chi-restraints excluded: chain D residue   94 THR
Chi-restraints excluded: chain D residue   99 PHE
Chi-restraints excluded: chain D residue  101 SER
Chi-restraints excluded: chain E residue   88 LEU
Chi-restraints excluded: chain E residue   99 PHE
Chi-restraints excluded: chain F residue   88 LEU
Chi-restraints excluded: chain F residue   94 THR
Chi-restraints excluded: chain F residue   98 LEU
Chi-restraints excluded: chain F residue   99 PHE
Chi-restraints excluded: chain G residue   88 LEU
Chi-restraints excluded: chain G residue   99 PHE
Chi-restraints excluded: chain G residue  100 SER
Chi-restraints excluded: chain H residue   88 LEU
Chi-restraints excluded: chain H residue   99 PHE
Chi-restraints excluded: chain I residue   88 LEU
Chi-restraints excluded: chain I residue   94 THR
Chi-restraints excluded: chain I residue   99 PHE
Chi-restraints excluded: chain J residue   88 LEU
Chi-restraints excluded: chain J residue   94 THR
Chi-restraints excluded: chain J residue   98 LEU
Chi-restraints excluded: chain J residue   99 PHE
Chi-restraints excluded: chain K residue   88 LEU
Chi-restraints excluded: chain K residue   99 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 33
   random chunks:
   chunk 17 optimal weight:    6.9990
   chunk 15 optimal weight:   10.0000
   chunk 27 optimal weight:   10.0000
   chunk 3 optimal weight:    9.9990
   chunk 7 optimal weight:    7.9990
   chunk 19 optimal weight:    7.9990
   chunk 18 optimal weight:   10.0000
   chunk 12 optimal weight:    6.9990
   chunk 11 optimal weight:    0.9980
   chunk 30 optimal weight:   10.0000
   chunk 25 optimal weight:    0.9980
   overall best weight:    4.7986

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

Flipped N/Q/H residues before XYZ refinement:
** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
J 102 GLN
** J 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4379 r_free = 0.4379 target = 0.179431 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4182 r_free = 0.4182 target = 0.161422 restraints weight = 4292.863|
|-----------------------------------------------------------------------------|
r_work (start): 0.4182 rms_B_bonded: 3.22
r_work: 0.4064 rms_B_bonded: 4.23 restraints_weight: 0.5000
r_work (final): 0.4064
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7100
moved from start:          0.4625

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.051   2673  Z= 0.562
  Angle     :  1.019   9.686   3608  Z= 0.527
  Chirality :  0.063   0.222    396
  Planarity :  0.004   0.013    484
  Dihedral  :  7.863  26.074    374
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 22.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 20.23 %
    Favored  : 79.77 %
  Rotamer:
    Outliers : 14.18 %
    Allowed  : 25.82 %
    Favored  : 60.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.14 (0.28), residues: 341
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.91 (0.21), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.029   0.004   PHE K 114 

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

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

  682 Ramachandran restraints generated.
    341 Oldfield, 0 Emsley, 341 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  682 Ramachandran restraints generated.
    341 Oldfield, 0 Emsley, 341 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 98
  time to evaluate  : 0.295 
Fit side-chains
REVERT: A   88 LEU cc_start: 0.7855 (OUTLIER) cc_final: 0.6952 (mt)
REVERT: B   88 LEU cc_start: 0.7861 (OUTLIER) cc_final: 0.7144 (mt)
REVERT: B  104 ASN cc_start: 0.6810 (OUTLIER) cc_final: 0.6602 (t0)
REVERT: D  112 THR cc_start: 0.8159 (m) cc_final: 0.7881 (t)
REVERT: F  106 PHE cc_start: 0.6781 (t80) cc_final: 0.6457 (t80)
REVERT: I  100 SER cc_start: 0.9087 (p) cc_final: 0.8816 (p)
REVERT: K  114 PHE cc_start: 0.7886 (m-80) cc_final: 0.7482 (m-10)
  outliers start: 39
  outliers final: 31
  residues processed: 123
  average time/residue: 0.0786
  time to fit residues: 12.8095
Evaluate side-chains
  129 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 95
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 LEU
Chi-restraints excluded: chain A residue   98 LEU
Chi-restraints excluded: chain A residue  101 SER
Chi-restraints excluded: chain B residue   88 LEU
Chi-restraints excluded: chain B residue  104 ASN
Chi-restraints excluded: chain C residue   88 LEU
Chi-restraints excluded: chain C residue   98 LEU
Chi-restraints excluded: chain C residue   99 PHE
Chi-restraints excluded: chain C residue  102 GLN
Chi-restraints excluded: chain D residue   88 LEU
Chi-restraints excluded: chain D residue   94 THR
Chi-restraints excluded: chain D residue   99 PHE
Chi-restraints excluded: chain D residue  101 SER
Chi-restraints excluded: chain E residue   88 LEU
Chi-restraints excluded: chain E residue   99 PHE
Chi-restraints excluded: chain F residue   88 LEU
Chi-restraints excluded: chain F residue   94 THR
Chi-restraints excluded: chain F residue   98 LEU
Chi-restraints excluded: chain F residue   99 PHE
Chi-restraints excluded: chain G residue   88 LEU
Chi-restraints excluded: chain G residue  100 SER
Chi-restraints excluded: chain H residue   88 LEU
Chi-restraints excluded: chain H residue   99 PHE
Chi-restraints excluded: chain H residue  101 SER
Chi-restraints excluded: chain I residue   88 LEU
Chi-restraints excluded: chain I residue   94 THR
Chi-restraints excluded: chain I residue   99 PHE
Chi-restraints excluded: chain J residue   88 LEU
Chi-restraints excluded: chain J residue   94 THR
Chi-restraints excluded: chain J residue   98 LEU
Chi-restraints excluded: chain J residue   99 PHE
Chi-restraints excluded: chain K residue   88 LEU
Chi-restraints excluded: chain K residue   94 THR
Chi-restraints excluded: chain K residue   99 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 33
   random chunks:
   chunk 10 optimal weight:    2.9990
   chunk 26 optimal weight:    4.9990
   chunk 8 optimal weight:    0.9990
   chunk 28 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 9 optimal weight:    7.9990
   chunk 30 optimal weight:   10.0000
   chunk 16 optimal weight:    3.9990
   chunk 22 optimal weight:    2.9990
   chunk 19 optimal weight:    3.9990
   chunk 31 optimal weight:    1.9990
   overall best weight:    2.3990

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

Flipped N/Q/H residues before XYZ refinement:
** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 102 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4427 r_free = 0.4427 target = 0.183845 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4245 r_free = 0.4245 target = 0.166252 restraints weight = 4056.404|
|-----------------------------------------------------------------------------|
r_work (start): 0.4247 rms_B_bonded: 3.16
r_work: 0.4133 rms_B_bonded: 4.10 restraints_weight: 0.5000
r_work (final): 0.4133
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7020
moved from start:          0.4867

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033   2673  Z= 0.327
  Angle     :  0.957   9.960   3608  Z= 0.474
  Chirality :  0.059   0.215    396
  Planarity :  0.003   0.014    484
  Dihedral  :  7.268  24.493    374
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 22.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 19.65 %
    Favored  : 80.35 %
  Rotamer:
    Outliers : 13.45 %
    Allowed  : 28.73 %
    Favored  : 57.82 %
  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: -5.14 (0.27), residues: 341
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.91 (0.21), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.023   0.002   PHE G  99 

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

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

  682 Ramachandran restraints generated.
    341 Oldfield, 0 Emsley, 341 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  682 Ramachandran restraints generated.
    341 Oldfield, 0 Emsley, 341 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 104
  time to evaluate  : 0.266 
Fit side-chains
REVERT: A   88 LEU cc_start: 0.7802 (OUTLIER) cc_final: 0.6888 (mt)
REVERT: A   99 PHE cc_start: 0.7626 (OUTLIER) cc_final: 0.7165 (t80)
REVERT: B   88 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7156 (mt)
REVERT: D  112 THR cc_start: 0.8103 (m) cc_final: 0.7787 (t)
REVERT: F  106 PHE cc_start: 0.6740 (t80) cc_final: 0.6376 (t80)
REVERT: I  100 SER cc_start: 0.9109 (p) cc_final: 0.8828 (p)
REVERT: K  114 PHE cc_start: 0.7588 (m-80) cc_final: 0.7111 (m-10)
  outliers start: 37
  outliers final: 32
  residues processed: 127
  average time/residue: 0.0749
  time to fit residues: 12.5292
Evaluate side-chains
  131 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 96
  time to evaluate  : 0.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 LEU
Chi-restraints excluded: chain A residue   98 LEU
Chi-restraints excluded: chain A residue   99 PHE
Chi-restraints excluded: chain A residue  101 SER
Chi-restraints excluded: chain B residue   88 LEU
Chi-restraints excluded: chain C residue   88 LEU
Chi-restraints excluded: chain C residue   98 LEU
Chi-restraints excluded: chain C residue  101 SER
Chi-restraints excluded: chain C residue  102 GLN
Chi-restraints excluded: chain D residue   88 LEU
Chi-restraints excluded: chain D residue   94 THR
Chi-restraints excluded: chain D residue   99 PHE
Chi-restraints excluded: chain D residue  101 SER
Chi-restraints excluded: chain E residue   88 LEU
Chi-restraints excluded: chain E residue   99 PHE
Chi-restraints excluded: chain F residue   88 LEU
Chi-restraints excluded: chain F residue   94 THR
Chi-restraints excluded: chain F residue   98 LEU
Chi-restraints excluded: chain F residue   99 PHE
Chi-restraints excluded: chain G residue   88 LEU
Chi-restraints excluded: chain G residue   99 PHE
Chi-restraints excluded: chain G residue  100 SER
Chi-restraints excluded: chain H residue   88 LEU
Chi-restraints excluded: chain H residue   99 PHE
Chi-restraints excluded: chain I residue   88 LEU
Chi-restraints excluded: chain I residue   94 THR
Chi-restraints excluded: chain I residue   99 PHE
Chi-restraints excluded: chain J residue   88 LEU
Chi-restraints excluded: chain J residue   94 THR
Chi-restraints excluded: chain J residue   98 LEU
Chi-restraints excluded: chain J residue   99 PHE
Chi-restraints excluded: chain K residue   88 LEU
Chi-restraints excluded: chain K residue   94 THR
Chi-restraints excluded: chain K residue   99 PHE
Chi-restraints excluded: chain K residue  102 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 33
   random chunks:
   chunk 26 optimal weight:    7.9990
   chunk 13 optimal weight:    6.9990
   chunk 12 optimal weight:    9.9990
   chunk 31 optimal weight:    0.9980
   chunk 4 optimal weight:   10.0000
   chunk 7 optimal weight:    3.9990
   chunk 20 optimal weight:    0.9980
   chunk 17 optimal weight:    4.9990
   chunk 11 optimal weight:    0.9990
   chunk 6 optimal weight:    4.9990
   chunk 19 optimal weight:    1.9990
   overall best weight:    1.7986

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

Flipped N/Q/H residues before XYZ refinement:
** G 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 102 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4443 r_free = 0.4443 target = 0.185776 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4271 r_free = 0.4271 target = 0.168904 restraints weight = 3988.442|
|-----------------------------------------------------------------------------|
r_work (start): 0.4278 rms_B_bonded: 3.13
r_work: 0.4165 rms_B_bonded: 4.01 restraints_weight: 0.5000
r_work (final): 0.4165
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6975
moved from start:          0.5065

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   2673  Z= 0.285
  Angle     :  0.941  10.016   3608  Z= 0.465
  Chirality :  0.056   0.189    396
  Planarity :  0.003   0.015    484
  Dihedral  :  7.037  24.114    374
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 21.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 18.77 %
    Favored  : 81.23 %
  Rotamer:
    Outliers : 12.73 %
    Allowed  : 30.18 %
    Favored  : 57.09 %
  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: -5.05 (0.28), residues: 341
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.84 (0.21), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.021   0.002   PHE G  99 

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

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

  682 Ramachandran restraints generated.
    341 Oldfield, 0 Emsley, 341 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  682 Ramachandran restraints generated.
    341 Oldfield, 0 Emsley, 341 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 97
  time to evaluate  : 0.266 
Fit side-chains
REVERT: A   88 LEU cc_start: 0.7840 (OUTLIER) cc_final: 0.6894 (mt)
REVERT: A   99 PHE cc_start: 0.7716 (OUTLIER) cc_final: 0.7156 (t80)
REVERT: B   88 LEU cc_start: 0.7941 (OUTLIER) cc_final: 0.7160 (mt)
REVERT: D  112 THR cc_start: 0.8026 (m) cc_final: 0.7727 (t)
REVERT: F  106 PHE cc_start: 0.6632 (t80) cc_final: 0.6235 (t80)
REVERT: I  100 SER cc_start: 0.9097 (p) cc_final: 0.8808 (p)
REVERT: K  114 PHE cc_start: 0.7517 (m-80) cc_final: 0.6997 (m-10)
  outliers start: 35
  outliers final: 32
  residues processed: 120
  average time/residue: 0.0745
  time to fit residues: 11.7956
Evaluate side-chains
  126 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 91
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 LEU
Chi-restraints excluded: chain A residue   98 LEU
Chi-restraints excluded: chain A residue   99 PHE
Chi-restraints excluded: chain A residue  101 SER
Chi-restraints excluded: chain B residue   88 LEU
Chi-restraints excluded: chain C residue   88 LEU
Chi-restraints excluded: chain C residue   98 LEU
Chi-restraints excluded: chain C residue   99 PHE
Chi-restraints excluded: chain C residue  101 SER
Chi-restraints excluded: chain C residue  102 GLN
Chi-restraints excluded: chain D residue   88 LEU
Chi-restraints excluded: chain D residue   94 THR
Chi-restraints excluded: chain D residue   99 PHE
Chi-restraints excluded: chain D residue  101 SER
Chi-restraints excluded: chain E residue   88 LEU
Chi-restraints excluded: chain E residue   99 PHE
Chi-restraints excluded: chain F residue   88 LEU
Chi-restraints excluded: chain F residue   94 THR
Chi-restraints excluded: chain F residue   98 LEU
Chi-restraints excluded: chain F residue   99 PHE
Chi-restraints excluded: chain G residue   88 LEU
Chi-restraints excluded: chain G residue   99 PHE
Chi-restraints excluded: chain G residue  100 SER
Chi-restraints excluded: chain H residue   88 LEU
Chi-restraints excluded: chain H residue   99 PHE
Chi-restraints excluded: chain I residue   88 LEU
Chi-restraints excluded: chain I residue   94 THR
Chi-restraints excluded: chain I residue   99 PHE
Chi-restraints excluded: chain J residue   88 LEU
Chi-restraints excluded: chain J residue   98 LEU
Chi-restraints excluded: chain J residue   99 PHE
Chi-restraints excluded: chain K residue   88 LEU
Chi-restraints excluded: chain K residue   94 THR
Chi-restraints excluded: chain K residue   99 PHE
Chi-restraints excluded: chain K residue  102 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 33
   random chunks:
   chunk 20 optimal weight:    3.9990
   chunk 26 optimal weight:    0.6980
   chunk 22 optimal weight:    5.9990
   chunk 13 optimal weight:    0.9990
   chunk 0 optimal weight:    9.9990
   chunk 30 optimal weight:    9.9990
   chunk 28 optimal weight:    0.9980
   chunk 2 optimal weight:    0.5980
   chunk 27 optimal weight:    2.9990
   chunk 21 optimal weight:    7.9990
   chunk 7 optimal weight:    1.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
** G 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 102 GLN
** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 102 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4472 r_free = 0.4472 target = 0.189488 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4308 r_free = 0.4308 target = 0.172747 restraints weight = 3977.611|
|-----------------------------------------------------------------------------|
r_work (start): 0.4302 rms_B_bonded: 3.11
r_work: 0.4196 rms_B_bonded: 3.94 restraints_weight: 0.5000
r_work (final): 0.4196
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6915
moved from start:          0.5267

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   2673  Z= 0.232
  Angle     :  0.925  10.112   3608  Z= 0.452
  Chirality :  0.053   0.186    396
  Planarity :  0.003   0.017    484
  Dihedral  :  6.689  24.310    374
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 19.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 18.77 %
    Favored  : 81.23 %
  Rotamer:
    Outliers : 11.64 %
    Allowed  : 30.91 %
    Favored  : 57.45 %
  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: -5.01 (0.28), residues: 341
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.81 (0.22), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.020   0.002   PHE G  99 

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

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

  682 Ramachandran restraints generated.
    341 Oldfield, 0 Emsley, 341 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  682 Ramachandran restraints generated.
    341 Oldfield, 0 Emsley, 341 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 98
  time to evaluate  : 0.292 
Fit side-chains
REVERT: A   88 LEU cc_start: 0.7666 (OUTLIER) cc_final: 0.6798 (mt)
REVERT: A  110 LYS cc_start: 0.5956 (pttp) cc_final: 0.5692 (mmtt)
REVERT: B   88 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7405 (mt)
REVERT: B   91 THR cc_start: 0.8837 (p) cc_final: 0.8442 (t)
REVERT: D  112 THR cc_start: 0.7792 (m) cc_final: 0.7561 (t)
REVERT: F  106 PHE cc_start: 0.6367 (t80) cc_final: 0.5966 (t80)
REVERT: I  100 SER cc_start: 0.9004 (p) cc_final: 0.8689 (p)
REVERT: J   99 PHE cc_start: 0.7698 (OUTLIER) cc_final: 0.7085 (m-80)
REVERT: K  102 GLN cc_start: 0.7953 (OUTLIER) cc_final: 0.7562 (pp30)
  outliers start: 32
  outliers final: 27
  residues processed: 117
  average time/residue: 0.0759
  time to fit residues: 11.8530
Evaluate side-chains
  126 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 95
  time to evaluate  : 0.310 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 LEU
Chi-restraints excluded: chain A residue   98 LEU
Chi-restraints excluded: chain A residue  101 SER
Chi-restraints excluded: chain B residue   88 LEU
Chi-restraints excluded: chain C residue   88 LEU
Chi-restraints excluded: chain C residue   98 LEU
Chi-restraints excluded: chain C residue  101 SER
Chi-restraints excluded: chain C residue  102 GLN
Chi-restraints excluded: chain D residue   88 LEU
Chi-restraints excluded: chain D residue   94 THR
Chi-restraints excluded: chain D residue   99 PHE
Chi-restraints excluded: chain E residue   88 LEU
Chi-restraints excluded: chain E residue   99 PHE
Chi-restraints excluded: chain F residue   88 LEU
Chi-restraints excluded: chain F residue   98 LEU
Chi-restraints excluded: chain F residue   99 PHE
Chi-restraints excluded: chain G residue   88 LEU
Chi-restraints excluded: chain G residue   99 PHE
Chi-restraints excluded: chain G residue  100 SER
Chi-restraints excluded: chain H residue   88 LEU
Chi-restraints excluded: chain H residue   99 PHE
Chi-restraints excluded: chain I residue   88 LEU
Chi-restraints excluded: chain I residue   94 THR
Chi-restraints excluded: chain I residue   99 PHE
Chi-restraints excluded: chain I residue  102 GLN
Chi-restraints excluded: chain J residue   88 LEU
Chi-restraints excluded: chain J residue   98 LEU
Chi-restraints excluded: chain J residue   99 PHE
Chi-restraints excluded: chain K residue   88 LEU
Chi-restraints excluded: chain K residue   99 PHE
Chi-restraints excluded: chain K residue  102 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 33
   random chunks:
   chunk 7 optimal weight:    6.9990
   chunk 6 optimal weight:   10.0000
   chunk 2 optimal weight:    5.9990
   chunk 24 optimal weight:   10.0000
   chunk 30 optimal weight:    4.9990
   chunk 31 optimal weight:    0.5980
   chunk 9 optimal weight:   20.0000
   chunk 22 optimal weight:    4.9990
   chunk 25 optimal weight:    0.9980
   chunk 5 optimal weight:    0.3980
   chunk 12 optimal weight:    7.9990
   overall best weight:    2.3984

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

Flipped N/Q/H residues before XYZ refinement:
** G 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 102 GLN
** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 102 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4457 r_free = 0.4457 target = 0.187091 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4287 r_free = 0.4287 target = 0.170315 restraints weight = 4042.982|
|-----------------------------------------------------------------------------|
r_work (start): 0.4295 rms_B_bonded: 3.14
r_work: 0.4179 rms_B_bonded: 4.01 restraints_weight: 0.5000
r_work (final): 0.4179
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7022
moved from start:          0.5235

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035   2673  Z= 0.316
  Angle     :  0.931   9.975   3608  Z= 0.462
  Chirality :  0.055   0.190    396
  Planarity :  0.003   0.016    484
  Dihedral  :  6.875  24.442    374
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 19.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 18.77 %
    Favored  : 81.23 %
  Rotamer:
    Outliers : 11.64 %
    Allowed  : 31.64 %
    Favored  : 56.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -5.01 (0.29), residues: 341
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.81 (0.22), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.019   0.002   PHE G  99 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1404.76 seconds
wall clock time: 24 minutes 55.61 seconds (1495.61 seconds total)