Starting phenix.real_space_refine
on Sun Apr 27 01:48:14 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6n3c_0334/04_2025/6n3c_0334.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6n3c_0334/04_2025/6n3c_0334.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6n3c_0334/04_2025/6n3c_0334.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6n3c_0334/04_2025/6n3c_0334.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6n3c_0334/04_2025/6n3c_0334.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6n3c_0334/04_2025/6n3c_0334.cif"
  }
  resolution = 3.3
  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
-------------------------------------------------------------------------------
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=   1.000
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      40      5.16       5
     C    2500      2.51       5
     N     840      2.21       5
     O     880      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 4260
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 213
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 32, 213
          Classifications: {'peptide': 32}
          Link IDs: {'TRANS': 31}
    Chain: "B"
      Number of atoms: 213
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 32, 213
          Classifications: {'peptide': 32}
          Link IDs: {'TRANS': 31}
  Restraints were copied for chains:
    C, E, G, I, K, M, O, Q, S, D, F, H, J, L, N, P, R, T
  Time building chain proxies: 1.66, per 1000 atoms: 0.39
  Number of scatterers: 4260
  At special positions: 0
  Unit cell: (86.92, 94.34, 47.7, 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      40     16.00
     O     880      8.00
     N     840      7.00
     C    2500      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.00
  Conformation dependent library (CDL) restraints added in 620.3 milliseconds
  

  1200 Ramachandran restraints generated.
    600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  800

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 12 sheets defined
      0.0% alpha, 29.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.69
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'E' and resid 292 through 293
      removed outlier: 6.461A  pdb=" N   SER A 292 " --> pdb=" O   ARG E 293 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'E' and resid 297 through 303
      removed outlier: 8.822A  pdb=" N   ALA A 297 " --> pdb=" O   GLY E 298 " (cutoff:3.500A)
      removed outlier: 10.331A  pdb=" N   GLY E 300 " --> pdb=" O   ALA A 297 " (cutoff:3.500A)
      removed outlier: 6.298A  pdb=" N   LEU A 299 " --> pdb=" O   GLY E 300 " (cutoff:3.500A)
      removed outlier: 7.692A  pdb=" N   ASN E 302 " --> pdb=" O   LEU A 299 " (cutoff:3.500A)
      removed outlier: 6.023A  pdb=" N   ASN A 301 " --> pdb=" O   ASN E 302 " (cutoff:3.500A)
      removed outlier: 6.833A  pdb=" N   GLY A 298 " --> pdb=" O   ALA K 297 " (cutoff:3.500A)
      removed outlier: 6.899A  pdb=" N   LEU K 299 " --> pdb=" O   GLY A 298 " (cutoff:3.500A)
      removed outlier: 6.945A  pdb=" N   GLY A 300 " --> pdb=" O   LEU K 299 " (cutoff:3.500A)
      removed outlier: 6.833A  pdb=" N   GLY K 298 " --> pdb=" O   ALA O 297 " (cutoff:3.500A)
      removed outlier: 6.899A  pdb=" N   LEU O 299 " --> pdb=" O   GLY K 298 " (cutoff:3.500A)
      removed outlier: 6.945A  pdb=" N   GLY K 300 " --> pdb=" O   LEU O 299 " (cutoff:3.500A)
      removed outlier: 6.833A  pdb=" N   GLY O 298 " --> pdb=" O   ALA S 297 " (cutoff:3.500A)
      removed outlier: 6.899A  pdb=" N   LEU S 299 " --> pdb=" O   GLY O 298 " (cutoff:3.500A)
      removed outlier: 6.946A  pdb=" N   GLY O 300 " --> pdb=" O   LEU S 299 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'E' and resid 306 through 308
      removed outlier: 6.125A  pdb=" N   ASN A 306 " --> pdb=" O   MET E 307 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'E' and resid 311 through 318
      removed outlier: 5.950A  pdb=" N   ASN A 312 " --> pdb=" O   PHE E 313 " (cutoff:3.500A)
      removed outlier: 6.937A  pdb=" N   GLU E 315 " --> pdb=" O   ASN A 312 " (cutoff:3.500A)
      removed outlier: 6.568A  pdb=" N   GLY A 314 " --> pdb=" O   GLU E 315 " (cutoff:3.500A)
      removed outlier: 8.141A  pdb=" N   SER E 317 " --> pdb=" O   GLY A 314 " (cutoff:3.500A)
      removed outlier: 6.414A  pdb=" N   PHE A 316 " --> pdb=" O   SER E 317 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'F' and resid 292 through 293
      removed outlier: 6.563A  pdb=" N   SER B 292 " --> pdb=" O   ARG F 293 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'F' and resid 312 through 314
      removed outlier: 6.179A  pdb=" N   PHE B 313 " --> pdb=" O   GLY L 314 " (cutoff:3.500A)
      removed outlier: 6.180A  pdb=" N   PHE L 313 " --> pdb=" O   GLY P 314 " (cutoff:3.500A)
      removed outlier: 6.179A  pdb=" N   PHE P 313 " --> pdb=" O   GLY T 314 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 292 through 293
    Processing sheet with id=AA8, first strand: chain 'C' and resid 297 through 303
      removed outlier: 6.833A  pdb=" N   GLY C 298 " --> pdb=" O   ALA G 297 " (cutoff:3.500A)
      removed outlier: 6.899A  pdb=" N   LEU G 299 " --> pdb=" O   GLY C 298 " (cutoff:3.500A)
      removed outlier: 6.945A  pdb=" N   GLY C 300 " --> pdb=" O   LEU G 299 " (cutoff:3.500A)
      removed outlier: 6.833A  pdb=" N   GLY G 298 " --> pdb=" O   ALA I 297 " (cutoff:3.500A)
      removed outlier: 6.899A  pdb=" N   LEU I 299 " --> pdb=" O   GLY G 298 " (cutoff:3.500A)
      removed outlier: 6.945A  pdb=" N   GLY G 300 " --> pdb=" O   LEU I 299 " (cutoff:3.500A)
      removed outlier: 6.833A  pdb=" N   GLY I 298 " --> pdb=" O   ALA M 297 " (cutoff:3.500A)
      removed outlier: 6.899A  pdb=" N   LEU M 299 " --> pdb=" O   GLY I 298 " (cutoff:3.500A)
      removed outlier: 6.945A  pdb=" N   GLY I 300 " --> pdb=" O   LEU M 299 " (cutoff:3.500A)
      removed outlier: 6.833A  pdb=" N   GLY M 298 " --> pdb=" O   ALA Q 297 " (cutoff:3.500A)
      removed outlier: 6.899A  pdb=" N   LEU Q 299 " --> pdb=" O   GLY M 298 " (cutoff:3.500A)
      removed outlier: 6.945A  pdb=" N   GLY M 300 " --> pdb=" O   LEU Q 299 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 306 through 308
    Processing sheet with id=AB1, first strand: chain 'C' and resid 311 through 318
    Processing sheet with id=AB2, first strand: chain 'D' and resid 292 through 293
    Processing sheet with id=AB3, first strand: chain 'D' and resid 312 through 314
      removed outlier: 6.180A  pdb=" N   PHE D 313 " --> pdb=" O   GLY H 314 " (cutoff:3.500A)
      removed outlier: 6.180A  pdb=" N   PHE H 313 " --> pdb=" O   GLY J 314 " (cutoff:3.500A)
      removed outlier: 6.180A  pdb=" N   PHE J 313 " --> pdb=" O   GLY N 314 " (cutoff:3.500A)
      removed outlier: 6.180A  pdb=" N   PHE N 313 " --> pdb=" O   GLY R 314 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB3

    100 hydrogen bonds defined for protein.
    300 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: 1.19 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1606
        1.34 -     1.45: 742
        1.45 -     1.57: 1872
        1.57 -     1.68: 0
        1.68 -     1.80: 80
  Bond restraints: 4300
  Sorted by residual:
  bond pdb=" N   GLN S 303 "
       pdb=" CA  GLN S 303 "
    ideal  model  delta    sigma   weight residual
    1.457  1.491 -0.034 1.24e-02 6.50e+03 7.62e+00
  bond pdb=" N   GLN E 303 "
       pdb=" CA  GLN E 303 "
    ideal  model  delta    sigma   weight residual
    1.457  1.491 -0.034 1.24e-02 6.50e+03 7.54e+00
  bond pdb=" N   PHE C 289 "
       pdb=" CA  PHE C 289 "
    ideal  model  delta    sigma   weight residual
    1.457  1.493 -0.035 1.29e-02 6.01e+03 7.45e+00
  bond pdb=" N   PHE I 289 "
       pdb=" CA  PHE I 289 "
    ideal  model  delta    sigma   weight residual
    1.457  1.492 -0.035 1.29e-02 6.01e+03 7.40e+00
  bond pdb=" N   GLN G 303 "
       pdb=" CA  GLN G 303 "
    ideal  model  delta    sigma   weight residual
    1.457  1.490 -0.034 1.24e-02 6.50e+03 7.39e+00
  ... (remaining 4295 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.71: 4938
        1.71 -     3.42: 482
        3.42 -     5.13: 133
        5.13 -     6.84: 77
        6.84 -     8.55: 10
  Bond angle restraints: 5640
  Sorted by residual:
  angle pdb=" N   GLY D 294 "
        pdb=" CA  GLY D 294 "
        pdb=" C   GLY D 294 "
      ideal   model   delta    sigma   weight residual
     112.82  107.51    5.31 1.38e+00 5.25e-01 1.48e+01
  angle pdb=" N   GLY P 294 "
        pdb=" CA  GLY P 294 "
        pdb=" C   GLY P 294 "
      ideal   model   delta    sigma   weight residual
     112.82  107.52    5.30 1.38e+00 5.25e-01 1.47e+01
  angle pdb=" N   GLY F 294 "
        pdb=" CA  GLY F 294 "
        pdb=" C   GLY F 294 "
      ideal   model   delta    sigma   weight residual
     112.82  107.54    5.28 1.38e+00 5.25e-01 1.47e+01
  angle pdb=" N   GLY T 294 "
        pdb=" CA  GLY T 294 "
        pdb=" C   GLY T 294 "
      ideal   model   delta    sigma   weight residual
     112.82  107.55    5.27 1.38e+00 5.25e-01 1.46e+01
  angle pdb=" N   GLY B 294 "
        pdb=" CA  GLY B 294 "
        pdb=" C   GLY B 294 "
      ideal   model   delta    sigma   weight residual
     112.82  107.56    5.26 1.38e+00 5.25e-01 1.46e+01
  ... (remaining 5635 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    12.42: 1860
       12.42 -    24.84: 250
       24.84 -    37.25: 130
       37.25 -    49.67: 0
       49.67 -    62.09: 20
  Dihedral angle restraints: 2260
    sinusoidal: 840
      harmonic: 1420
  Sorted by residual:
  dihedral pdb=" CA  ASN B 312 "
           pdb=" C   ASN B 312 "
           pdb=" N   PHE B 313 "
           pdb=" CA  PHE B 313 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -162.66  -17.34     0      5.00e+00 4.00e-02 1.20e+01
  dihedral pdb=" CA  ASN P 312 "
           pdb=" C   ASN P 312 "
           pdb=" N   PHE P 313 "
           pdb=" CA  PHE P 313 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.66  -17.34     0      5.00e+00 4.00e-02 1.20e+01
  dihedral pdb=" CA  ASN D 312 "
           pdb=" C   ASN D 312 "
           pdb=" N   PHE D 313 "
           pdb=" CA  PHE D 313 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.69  -17.31     0      5.00e+00 4.00e-02 1.20e+01
  ... (remaining 2257 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.050: 310
       0.050 -    0.100: 60
       0.100 -    0.150: 47
       0.150 -    0.200: 13
       0.200 -    0.250: 10
  Chirality restraints: 440
  Sorted by residual:
  chirality pdb=" CA  SER M 305 "
            pdb=" N   SER M 305 "
            pdb=" C   SER M 305 "
            pdb=" CB  SER M 305 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.56e+00
  chirality pdb=" CA  SER E 305 "
            pdb=" N   SER E 305 "
            pdb=" C   SER E 305 "
            pdb=" CB  SER E 305 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.55e+00
  chirality pdb=" CA  SER I 305 "
            pdb=" N   SER I 305 "
            pdb=" C   SER I 305 "
            pdb=" CB  SER I 305 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.55e+00
  ... (remaining 437 not shown)

  Planarity restraints: 860
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY O 304 "   -0.010 2.00e-02 2.50e+03   2.05e-02 4.18e+00
        pdb=" C   GLY O 304 "    0.035 2.00e-02 2.50e+03
        pdb=" O   GLY O 304 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   SER O 305 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY G 304 "    0.010 2.00e-02 2.50e+03   2.04e-02 4.16e+00
        pdb=" C   GLY G 304 "   -0.035 2.00e-02 2.50e+03
        pdb=" O   GLY G 304 "    0.013 2.00e-02 2.50e+03
        pdb=" N   SER G 305 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY M 304 "    0.010 2.00e-02 2.50e+03   2.03e-02 4.11e+00
        pdb=" C   GLY M 304 "   -0.035 2.00e-02 2.50e+03
        pdb=" O   GLY M 304 "    0.013 2.00e-02 2.50e+03
        pdb=" N   SER M 305 "    0.012 2.00e-02 2.50e+03
  ... (remaining 857 not shown)

  Histogram of nonbonded interaction distances:
        2.39 -     2.89: 1842
        2.89 -     3.39: 3758
        3.39 -     3.89: 7085
        3.89 -     4.40: 8792
        4.40 -     4.90: 17058
  Nonbonded interactions: 38535
  Sorted by model distance:
  nonbonded pdb=" ND2 ASN A 302 "
            pdb=" OG  SER A 305 "
     model   vdw
     2.387 3.120
  nonbonded pdb=" ND2 ASN C 302 "
            pdb=" OG  SER C 305 "
     model   vdw
     2.387 3.120
  nonbonded pdb=" ND2 ASN K 302 "
            pdb=" OG  SER K 305 "
     model   vdw
     2.388 3.120
  nonbonded pdb=" ND2 ASN I 302 "
            pdb=" OG  SER I 305 "
     model   vdw
     2.388 3.120
  nonbonded pdb=" ND2 ASN S 302 "
            pdb=" OG  SER S 305 "
     model   vdw
     2.388 3.120
  ... (remaining 38530 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'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
  selection = chain 'I'
  selection = chain 'J'
  selection = chain 'K'
  selection = chain 'L'
  selection = chain 'M'
  selection = chain 'N'
  selection = chain 'O'
  selection = chain 'P'
  selection = chain 'Q'
  selection = chain 'R'
  selection = chain 'S'
  selection = chain 'T'
}

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:             0.220
  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:          0.170
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     13.720
  Find NCS groups from input model:        0.260
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.890
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.360
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8095
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      :  0.009   0.035   4300  Z= 0.507
  Angle     :  1.311   8.550   5640  Z= 0.786
  Chirality :  0.073   0.250    440
  Planarity :  0.004   0.020    860
  Dihedral  : 14.000  62.088   1460
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 18.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.50 %
    Favored  : 88.50 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  7.89 %
    Favored  : 92.11 %
  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 (0.17), residues: 600
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.82 (0.13), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.015   0.001   PHE M 313 
 ARG   0.001   0.000   ARG N 293 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14059 (  100)
  hydrogen bonds       : angle       9.80604 (  300)
  covalent geometry    : bond        0.00932 ( 4300)
  covalent geometry    : angle       1.31051 ( 5640)

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

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

  1200 Ramachandran restraints generated.
    600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1200 Ramachandran restraints generated.
    600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.464 
Fit side-chains
REVERT: C  291 ASN cc_start: 0.8565 (p0) cc_final: 0.7128 (m-40)
REVERT: C  305 SER cc_start: 0.7761 (p) cc_final: 0.7471 (m)
REVERT: C  315 GLU cc_start: 0.8507 (tt0) cc_final: 0.8251 (tt0)
REVERT: E  311 MET cc_start: 0.8956 (ttt) cc_final: 0.8665 (ttm)
REVERT: F  307 MET cc_start: 0.7926 (mmt) cc_final: 0.7668 (mmt)
REVERT: G  311 MET cc_start: 0.8909 (ttt) cc_final: 0.8596 (ttm)
  outliers start: 0
  outliers final: 0
  residues processed: 87
  average time/residue: 0.1104
  time to fit residues: 13.3647
Evaluate side-chains
  70 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 70
  time to evaluate  : 0.450 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 50 optimal weight:    3.9990
   chunk 45 optimal weight:   30.0000
   chunk 25 optimal weight:    6.9990
   chunk 15 optimal weight:    9.9990
   chunk 30 optimal weight:   20.0000
   chunk 24 optimal weight:    9.9990
   chunk 47 optimal weight:   10.0000
   chunk 18 optimal weight:   10.0000
   chunk 28 optimal weight:    9.9990
   chunk 35 optimal weight:    9.9990
   chunk 54 optimal weight:    4.9990
   overall best weight:    7.1990

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

Flipped N/Q/H residues before XYZ refinement:
A 302 ASN
** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 302 ASN
** D 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 302 ASN
** F 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 302 ASN
I 302 ASN
K 302 ASN
M 302 ASN
N 306 ASN
O 302 ASN
Q 302 ASN
S 302 ASN
T 306 ASN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4218 r_free = 0.4218 target = 0.147493 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4097 r_free = 0.4097 target = 0.134989 restraints weight = 6320.778|
|-----------------------------------------------------------------------------|
r_work (start): 0.4069 rms_B_bonded: 2.14
r_work: 0.4009 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3906 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.3906
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8232
moved from start:          0.1695

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.026   4300  Z= 0.210
  Angle     :  0.608   8.329   5640  Z= 0.307
  Chirality :  0.045   0.135    440
  Planarity :  0.002   0.010    860
  Dihedral  :  5.702  17.004    640
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 8.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.33 %
    Favored  : 88.67 %
  Rotamer:
    Outliers :  4.74 %
    Allowed  : 21.58 %
    Favored  : 73.68 %
  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: -4.44 (0.21), residues: 600
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.37 (0.16), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.017   0.002   PHE G 313 
 ARG   0.002   0.000   ARG S 293 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04234 (  100)
  hydrogen bonds       : angle       6.64642 (  300)
  covalent geometry    : bond        0.00474 ( 4300)
  covalent geometry    : angle       0.60802 ( 5640)

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

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

  1200 Ramachandran restraints generated.
    600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1200 Ramachandran restraints generated.
    600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 78
  time to evaluate  : 0.423 
Fit side-chains
   revert: symmetry clash
REVERT: C  291 ASN cc_start: 0.8691 (p0) cc_final: 0.6981 (m-40)
REVERT: E  291 ASN cc_start: 0.8770 (p0) cc_final: 0.6932 (m-40)
REVERT: G  311 MET cc_start: 0.9137 (ttt) cc_final: 0.8911 (ttm)
  outliers start: 18
  outliers final: 12
  residues processed: 88
  average time/residue: 0.1054
  time to fit residues: 13.0183
Evaluate side-chains
  80 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 68
  time to evaluate  : 0.475 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  305 SER
Chi-restraints excluded: chain D residue  306 ASN
Chi-restraints excluded: chain G residue  305 SER
Chi-restraints excluded: chain G residue  318 ILE
Chi-restraints excluded: chain I residue  305 SER
Chi-restraints excluded: chain K residue  291 ASN
Chi-restraints excluded: chain K residue  305 SER
Chi-restraints excluded: chain K residue  318 ILE
Chi-restraints excluded: chain M residue  305 SER
Chi-restraints excluded: chain M residue  318 ILE
Chi-restraints excluded: chain O residue  305 SER
Chi-restraints excluded: chain S residue  305 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 48 optimal weight:   30.0000
   chunk 19 optimal weight:   30.0000
   chunk 38 optimal weight:    4.9990
   chunk 31 optimal weight:   20.0000
   chunk 50 optimal weight:    7.9990
   chunk 17 optimal weight:   20.0000
   chunk 32 optimal weight:    9.9990
   chunk 14 optimal weight:    9.9990
   chunk 55 optimal weight:    7.9990
   chunk 57 optimal weight:   20.0000
   chunk 18 optimal weight:   30.0000
   overall best weight:    8.1990

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

Flipped N/Q/H residues before XYZ refinement:
** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
J 312 ASN
R 312 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4242 r_free = 0.4242 target = 0.147148 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4107 r_free = 0.4107 target = 0.134063 restraints weight = 6204.911|
|-----------------------------------------------------------------------------|
r_work (start): 0.4172 rms_B_bonded: 2.21
r_work: 0.4104 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.4006 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.4006
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8261
moved from start:          0.2065

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.027   4300  Z= 0.230
  Angle     :  0.616   8.378   5640  Z= 0.308
  Chirality :  0.043   0.136    440
  Planarity :  0.002   0.010    860
  Dihedral  :  5.620  17.772    640
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 9.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.17 %
    Favored  : 90.83 %
  Rotamer:
    Outliers :  5.79 %
    Allowed  : 26.05 %
    Favored  : 68.16 %
  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: -4.01 (0.25), residues: 600
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.05 (0.19), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.017   0.002   PHE G 313 
 ARG   0.002   0.000   ARG O 293 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04126 (  100)
  hydrogen bonds       : angle       6.51782 (  300)
  covalent geometry    : bond        0.00523 ( 4300)
  covalent geometry    : angle       0.61648 ( 5640)

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

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

  1200 Ramachandran restraints generated.
    600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1200 Ramachandran restraints generated.
    600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 75
  time to evaluate  : 0.486 
Fit side-chains
REVERT: C  291 ASN cc_start: 0.8795 (p0) cc_final: 0.6825 (m-40)
REVERT: D  307 MET cc_start: 0.8507 (OUTLIER) cc_final: 0.8288 (ttm)
REVERT: E  291 ASN cc_start: 0.8811 (p0) cc_final: 0.6791 (m-40)
REVERT: F  311 MET cc_start: 0.8097 (ptm) cc_final: 0.7841 (ttm)
REVERT: G  311 MET cc_start: 0.9174 (ttt) cc_final: 0.8948 (ttm)
  outliers start: 22
  outliers final: 17
  residues processed: 86
  average time/residue: 0.1044
  time to fit residues: 12.6754
Evaluate side-chains
  88 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 70
  time to evaluate  : 0.797 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  305 SER
Chi-restraints excluded: chain C residue  305 SER
Chi-restraints excluded: chain D residue  307 MET
Chi-restraints excluded: chain E residue  305 SER
Chi-restraints excluded: chain E residue  311 MET
Chi-restraints excluded: chain G residue  305 SER
Chi-restraints excluded: chain G residue  318 ILE
Chi-restraints excluded: chain I residue  305 SER
Chi-restraints excluded: chain K residue  305 SER
Chi-restraints excluded: chain K residue  318 ILE
Chi-restraints excluded: chain M residue  291 ASN
Chi-restraints excluded: chain M residue  305 SER
Chi-restraints excluded: chain M residue  318 ILE
Chi-restraints excluded: chain O residue  291 ASN
Chi-restraints excluded: chain O residue  305 SER
Chi-restraints excluded: chain S residue  291 ASN
Chi-restraints excluded: chain S residue  305 SER
Chi-restraints excluded: chain T residue  292 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 2 optimal weight:   20.0000
   chunk 1 optimal weight:   10.0000
   chunk 13 optimal weight:    6.9990
   chunk 47 optimal weight:   20.0000
   chunk 42 optimal weight:   30.0000
   chunk 52 optimal weight:   20.0000
   chunk 20 optimal weight:   20.0000
   chunk 53 optimal weight:   10.0000
   chunk 48 optimal weight:   30.0000
   chunk 26 optimal weight:    6.9990
   chunk 51 optimal weight:   30.0000
   overall best weight:   10.7996

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

Flipped N/Q/H residues before XYZ refinement:
** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 312 ASN
** P 312 ASN ** 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 = 0.4242 r_free = 0.4242 target = 0.144467 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4085 r_free = 0.4085 target = 0.131633 restraints weight = 6288.111|
|-----------------------------------------------------------------------------|
r_work (start): 0.4123 rms_B_bonded: 2.25
r_work: 0.4069 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3966 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.3966
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8318
moved from start:          0.2228

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.034   4300  Z= 0.291
  Angle     :  0.656   8.765   5640  Z= 0.329
  Chirality :  0.044   0.157    440
  Planarity :  0.002   0.012    860
  Dihedral  :  5.774  18.351    640
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 10.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.83 %
    Favored  : 87.17 %
  Rotamer:
    Outliers :  8.68 %
    Allowed  : 22.63 %
    Favored  : 68.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.99 (0.25), residues: 600
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.03 (0.19), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.018   0.002   PHE G 313 
 ARG   0.002   0.000   ARG S 293 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04188 (  100)
  hydrogen bonds       : angle       6.58756 (  300)
  covalent geometry    : bond        0.00665 ( 4300)
  covalent geometry    : angle       0.65595 ( 5640)

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

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

  1200 Ramachandran restraints generated.
    600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1200 Ramachandran restraints generated.
    600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 71
  time to evaluate  : 0.809 
Fit side-chains
REVERT: C  311 MET cc_start: 0.8818 (OUTLIER) cc_final: 0.8365 (ttm)
REVERT: E  291 ASN cc_start: 0.8847 (p0) cc_final: 0.6697 (m-40)
REVERT: F  307 MET cc_start: 0.8290 (mtt) cc_final: 0.7991 (ttm)
REVERT: G  311 MET cc_start: 0.9165 (ttt) cc_final: 0.8952 (ttm)
REVERT: Q  303 GLN cc_start: 0.8872 (OUTLIER) cc_final: 0.7649 (mt0)
REVERT: S  303 GLN cc_start: 0.8856 (OUTLIER) cc_final: 0.7854 (mt0)
  outliers start: 33
  outliers final: 24
  residues processed: 85
  average time/residue: 0.1462
  time to fit residues: 17.2780
Evaluate side-chains
  95 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 68
  time to evaluate  : 0.593 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  291 ASN
Chi-restraints excluded: chain A residue  305 SER
Chi-restraints excluded: chain C residue  305 SER
Chi-restraints excluded: chain C residue  311 MET
Chi-restraints excluded: chain D residue  306 ASN
Chi-restraints excluded: chain E residue  305 SER
Chi-restraints excluded: chain E residue  311 MET
Chi-restraints excluded: chain G residue  291 ASN
Chi-restraints excluded: chain G residue  305 SER
Chi-restraints excluded: chain G residue  318 ILE
Chi-restraints excluded: chain I residue  291 ASN
Chi-restraints excluded: chain I residue  305 SER
Chi-restraints excluded: chain K residue  291 ASN
Chi-restraints excluded: chain K residue  305 SER
Chi-restraints excluded: chain K residue  318 ILE
Chi-restraints excluded: chain M residue  291 ASN
Chi-restraints excluded: chain M residue  305 SER
Chi-restraints excluded: chain M residue  318 ILE
Chi-restraints excluded: chain N residue  311 MET
Chi-restraints excluded: chain O residue  291 ASN
Chi-restraints excluded: chain O residue  305 SER
Chi-restraints excluded: chain Q residue  303 GLN
Chi-restraints excluded: chain S residue  291 ASN
Chi-restraints excluded: chain S residue  303 GLN
Chi-restraints excluded: chain S residue  305 SER
Chi-restraints excluded: chain S residue  318 ILE
Chi-restraints excluded: chain T residue  292 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 21 optimal weight:   30.0000
   chunk 17 optimal weight:   10.0000
   chunk 50 optimal weight:   10.0000
   chunk 53 optimal weight:    3.9990
   chunk 30 optimal weight:   30.0000
   chunk 2 optimal weight:   10.0000
   chunk 10 optimal weight:    4.9990
   chunk 51 optimal weight:    6.9990
   chunk 44 optimal weight:   10.0000
   chunk 36 optimal weight:   20.0000
   chunk 29 optimal weight:   10.0000
   overall best weight:    7.1994

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

Flipped N/Q/H residues before XYZ refinement:
** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
S 291 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4265 r_free = 0.4265 target = 0.150618 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4142 r_free = 0.4142 target = 0.137002 restraints weight = 6341.237|
|-----------------------------------------------------------------------------|
r_work (start): 0.4164 rms_B_bonded: 2.18
r_work: 0.4116 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.4015 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.4015
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8270
moved from start:          0.2446

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.027   4300  Z= 0.204
  Angle     :  0.592   8.079   5640  Z= 0.298
  Chirality :  0.042   0.155    440
  Planarity :  0.002   0.008    860
  Dihedral  :  5.550  16.842    640
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 9.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.83 %
    Favored  : 89.17 %
  Rotamer:
    Outliers :  8.42 %
    Allowed  : 23.68 %
    Favored  : 67.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.85 (0.26), residues: 600
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.93 (0.20), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.017   0.002   PHE G 313 
 ARG   0.002   0.000   ARG Q 293 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03713 (  100)
  hydrogen bonds       : angle       6.36888 (  300)
  covalent geometry    : bond        0.00469 ( 4300)
  covalent geometry    : angle       0.59215 ( 5640)

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

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

  1200 Ramachandran restraints generated.
    600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1200 Ramachandran restraints generated.
    600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 78
  time to evaluate  : 0.423 
Fit side-chains
REVERT: C  311 MET cc_start: 0.8814 (OUTLIER) cc_final: 0.8298 (ttm)
REVERT: E  291 ASN cc_start: 0.8832 (p0) cc_final: 0.6784 (m-40)
REVERT: G  311 MET cc_start: 0.9153 (ttt) cc_final: 0.8907 (ttm)
REVERT: Q  303 GLN cc_start: 0.8878 (OUTLIER) cc_final: 0.7624 (mt0)
REVERT: S  303 GLN cc_start: 0.8843 (OUTLIER) cc_final: 0.7892 (mt0)
  outliers start: 32
  outliers final: 22
  residues processed: 95
  average time/residue: 0.1045
  time to fit residues: 13.9553
Evaluate side-chains
  102 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 77
  time to evaluate  : 0.467 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  305 SER
Chi-restraints excluded: chain A residue  318 ILE
Chi-restraints excluded: chain C residue  305 SER
Chi-restraints excluded: chain C residue  311 MET
Chi-restraints excluded: chain D residue  306 ASN
Chi-restraints excluded: chain E residue  305 SER
Chi-restraints excluded: chain E residue  311 MET
Chi-restraints excluded: chain G residue  305 SER
Chi-restraints excluded: chain G residue  318 ILE
Chi-restraints excluded: chain I residue  305 SER
Chi-restraints excluded: chain K residue  305 SER
Chi-restraints excluded: chain K residue  318 ILE
Chi-restraints excluded: chain M residue  291 ASN
Chi-restraints excluded: chain M residue  305 SER
Chi-restraints excluded: chain M residue  318 ILE
Chi-restraints excluded: chain N residue  311 MET
Chi-restraints excluded: chain O residue  291 ASN
Chi-restraints excluded: chain O residue  305 SER
Chi-restraints excluded: chain O residue  318 ILE
Chi-restraints excluded: chain Q residue  303 GLN
Chi-restraints excluded: chain S residue  291 ASN
Chi-restraints excluded: chain S residue  303 GLN
Chi-restraints excluded: chain S residue  305 SER
Chi-restraints excluded: chain S residue  318 ILE
Chi-restraints excluded: chain T residue  292 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 23 optimal weight:    8.9990
   chunk 12 optimal weight:    0.0870
   chunk 33 optimal weight:   30.0000
   chunk 40 optimal weight:    5.9990
   chunk 16 optimal weight:   20.0000
   chunk 13 optimal weight:    6.9990
   chunk 43 optimal weight:   20.0000
   chunk 18 optimal weight:   30.0000
   chunk 31 optimal weight:    5.9990
   chunk 0 optimal weight:   20.0000
   chunk 14 optimal weight:   10.0000
   overall best weight:    5.6166

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

Flipped N/Q/H residues before XYZ refinement:
** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 312 ASN
N 306 ASN
** P 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** S 291 ASN ** 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 = 0.4288 r_free = 0.4288 target = 0.150644 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4150 r_free = 0.4150 target = 0.137337 restraints weight = 6158.317|
|-----------------------------------------------------------------------------|
r_work (start): 0.4193 rms_B_bonded: 2.24
r_work: 0.4141 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.4036 rms_B_bonded: 4.09 restraints_weight: 0.2500
r_work (final): 0.4036
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8254
moved from start:          0.2593

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.023   4300  Z= 0.166
  Angle     :  0.571   8.332   5640  Z= 0.288
  Chirality :  0.040   0.152    440
  Planarity :  0.002   0.009    860
  Dihedral  :  5.380  16.947    640
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 11.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.33 %
    Favored  : 87.67 %
  Rotamer:
    Outliers :  7.37 %
    Allowed  : 23.68 %
    Favored  : 68.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.73 (0.27), residues: 600
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.84 (0.21), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.015   0.001   PHE G 313 
 ARG   0.004   0.000   ARG S 293 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03395 (  100)
  hydrogen bonds       : angle       6.27838 (  300)
  covalent geometry    : bond        0.00383 ( 4300)
  covalent geometry    : angle       0.57134 ( 5640)

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

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

  1200 Ramachandran restraints generated.
    600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1200 Ramachandran restraints generated.
    600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 79
  time to evaluate  : 0.460 
Fit side-chains
REVERT: C  311 MET cc_start: 0.8774 (OUTLIER) cc_final: 0.8108 (ttm)
REVERT: E  291 ASN cc_start: 0.8784 (p0) cc_final: 0.6810 (m-40)
REVERT: E  302 ASN cc_start: 0.8656 (t0) cc_final: 0.8195 (t0)
REVERT: G  311 MET cc_start: 0.9147 (ttt) cc_final: 0.8905 (ttt)
REVERT: Q  303 GLN cc_start: 0.8857 (OUTLIER) cc_final: 0.7605 (mt0)
REVERT: S  303 GLN cc_start: 0.8854 (OUTLIER) cc_final: 0.7900 (mt0)
  outliers start: 28
  outliers final: 22
  residues processed: 94
  average time/residue: 0.1050
  time to fit residues: 13.8254
Evaluate side-chains
  103 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 78
  time to evaluate  : 0.461 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  305 SER
Chi-restraints excluded: chain A residue  318 ILE
Chi-restraints excluded: chain B residue  311 MET
Chi-restraints excluded: chain C residue  305 SER
Chi-restraints excluded: chain C residue  311 MET
Chi-restraints excluded: chain E residue  305 SER
Chi-restraints excluded: chain E residue  311 MET
Chi-restraints excluded: chain G residue  305 SER
Chi-restraints excluded: chain G residue  318 ILE
Chi-restraints excluded: chain H residue  306 ASN
Chi-restraints excluded: chain I residue  305 SER
Chi-restraints excluded: chain K residue  305 SER
Chi-restraints excluded: chain K residue  318 ILE
Chi-restraints excluded: chain M residue  291 ASN
Chi-restraints excluded: chain M residue  305 SER
Chi-restraints excluded: chain M residue  318 ILE
Chi-restraints excluded: chain N residue  318 ILE
Chi-restraints excluded: chain O residue  291 ASN
Chi-restraints excluded: chain O residue  305 SER
Chi-restraints excluded: chain O residue  318 ILE
Chi-restraints excluded: chain Q residue  303 GLN
Chi-restraints excluded: chain S residue  291 ASN
Chi-restraints excluded: chain S residue  303 GLN
Chi-restraints excluded: chain S residue  305 SER
Chi-restraints excluded: chain S residue  318 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 50 optimal weight:    5.9990
   chunk 16 optimal weight:   20.0000
   chunk 39 optimal weight:   30.0000
   chunk 23 optimal weight:    8.9990
   chunk 24 optimal weight:   30.0000
   chunk 34 optimal weight:    9.9990
   chunk 28 optimal weight:   30.0000
   chunk 13 optimal weight:   20.0000
   chunk 4 optimal weight:    5.9990
   chunk 33 optimal weight:   50.0000
   chunk 47 optimal weight:   10.0000
   overall best weight:    8.1992

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

Flipped N/Q/H residues before XYZ refinement:
** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P 312 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 = 0.4257 r_free = 0.4257 target = 0.148130 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4112 r_free = 0.4112 target = 0.134665 restraints weight = 6287.126|
|-----------------------------------------------------------------------------|
r_work (start): 0.4212 rms_B_bonded: 2.35
r_work: 0.4143 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.4043 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.4043
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8235
moved from start:          0.2597

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.029   4300  Z= 0.226
  Angle     :  0.609   8.389   5640  Z= 0.306
  Chirality :  0.041   0.151    440
  Planarity :  0.002   0.008    860
  Dihedral  :  5.553  17.996    640
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 10.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.50 %
    Favored  : 89.50 %
  Rotamer:
    Outliers :  7.89 %
    Allowed  : 23.42 %
    Favored  : 68.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.73 (0.27), residues: 600
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.84 (0.21), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.016   0.002   PHE M 313 
 ARG   0.002   0.000   ARG S 293 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03720 (  100)
  hydrogen bonds       : angle       6.39342 (  300)
  covalent geometry    : bond        0.00520 ( 4300)
  covalent geometry    : angle       0.60904 ( 5640)

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

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

  1200 Ramachandran restraints generated.
    600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1200 Ramachandran restraints generated.
    600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 77
  time to evaluate  : 0.423 
Fit side-chains
REVERT: C  311 MET cc_start: 0.8799 (OUTLIER) cc_final: 0.8164 (ttm)
REVERT: E  291 ASN cc_start: 0.8867 (p0) cc_final: 0.6681 (m-40)
REVERT: E  302 ASN cc_start: 0.8712 (t0) cc_final: 0.8190 (t0)
REVERT: G  311 MET cc_start: 0.9214 (ttt) cc_final: 0.8933 (ttt)
REVERT: Q  303 GLN cc_start: 0.8889 (OUTLIER) cc_final: 0.7607 (mt0)
REVERT: S  303 GLN cc_start: 0.8845 (OUTLIER) cc_final: 0.7818 (mt0)
  outliers start: 30
  outliers final: 24
  residues processed: 93
  average time/residue: 0.0992
  time to fit residues: 12.9774
Evaluate side-chains
  104 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 77
  time to evaluate  : 0.415 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  305 SER
Chi-restraints excluded: chain A residue  318 ILE
Chi-restraints excluded: chain C residue  291 ASN
Chi-restraints excluded: chain C residue  305 SER
Chi-restraints excluded: chain C residue  311 MET
Chi-restraints excluded: chain E residue  305 SER
Chi-restraints excluded: chain E residue  311 MET
Chi-restraints excluded: chain G residue  305 SER
Chi-restraints excluded: chain G residue  318 ILE
Chi-restraints excluded: chain I residue  305 SER
Chi-restraints excluded: chain I residue  311 MET
Chi-restraints excluded: chain J residue  311 MET
Chi-restraints excluded: chain K residue  305 SER
Chi-restraints excluded: chain K residue  318 ILE
Chi-restraints excluded: chain M residue  291 ASN
Chi-restraints excluded: chain M residue  305 SER
Chi-restraints excluded: chain M residue  318 ILE
Chi-restraints excluded: chain O residue  291 ASN
Chi-restraints excluded: chain O residue  305 SER
Chi-restraints excluded: chain O residue  318 ILE
Chi-restraints excluded: chain P residue  311 MET
Chi-restraints excluded: chain Q residue  303 GLN
Chi-restraints excluded: chain Q residue  305 SER
Chi-restraints excluded: chain S residue  291 ASN
Chi-restraints excluded: chain S residue  303 GLN
Chi-restraints excluded: chain S residue  305 SER
Chi-restraints excluded: chain S residue  318 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 7 optimal weight:   30.0000
   chunk 56 optimal weight:   10.0000
   chunk 58 optimal weight:    0.9980
   chunk 52 optimal weight:   20.0000
   chunk 45 optimal weight:    8.9990
   chunk 44 optimal weight:    5.9990
   chunk 15 optimal weight:   20.0000
   chunk 36 optimal weight:   20.0000
   chunk 37 optimal weight:    8.9990
   chunk 33 optimal weight:    6.9990
   chunk 49 optimal weight:    6.9990
   overall best weight:    5.9988

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

Flipped N/Q/H residues before XYZ refinement:
** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
S 291 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4297 r_free = 0.4297 target = 0.153003 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4167 r_free = 0.4167 target = 0.139646 restraints weight = 6064.147|
|-----------------------------------------------------------------------------|
r_work (start): 0.4212 rms_B_bonded: 2.17
r_work: 0.4159 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.4056 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.4056
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8266
moved from start:          0.2733

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.022   4300  Z= 0.172
  Angle     :  0.567   7.835   5640  Z= 0.286
  Chirality :  0.040   0.148    440
  Planarity :  0.001   0.007    860
  Dihedral  :  5.376  19.293    640
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 9.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.67 %
    Favored  : 89.33 %
  Rotamer:
    Outliers :  8.16 %
    Allowed  : 23.16 %
    Favored  : 68.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.62 (0.28), residues: 600
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.75 (0.21), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.015   0.001   PHE M 313 
 ARG   0.001   0.000   ARG S 293 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03356 (  100)
  hydrogen bonds       : angle       6.22924 (  300)
  covalent geometry    : bond        0.00396 ( 4300)
  covalent geometry    : angle       0.56666 ( 5640)

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

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

  1200 Ramachandran restraints generated.
    600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1200 Ramachandran restraints generated.
    600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 81
  time to evaluate  : 0.488 
Fit side-chains
REVERT: C  311 MET cc_start: 0.8788 (OUTLIER) cc_final: 0.8084 (ttm)
REVERT: E  291 ASN cc_start: 0.8735 (p0) cc_final: 0.6689 (m-40)
REVERT: E  302 ASN cc_start: 0.8612 (t0) cc_final: 0.8195 (t0)
REVERT: G  311 MET cc_start: 0.9141 (ttt) cc_final: 0.8897 (ttt)
REVERT: I  311 MET cc_start: 0.9032 (OUTLIER) cc_final: 0.8525 (ttt)
REVERT: J  307 MET cc_start: 0.8444 (tpp) cc_final: 0.7731 (tpt)
REVERT: Q  303 GLN cc_start: 0.8828 (OUTLIER) cc_final: 0.7589 (mt0)
REVERT: S  303 GLN cc_start: 0.8821 (OUTLIER) cc_final: 0.7892 (mt0)
  outliers start: 31
  outliers final: 23
  residues processed: 95
  average time/residue: 0.1230
  time to fit residues: 15.9831
Evaluate side-chains
  106 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 79
  time to evaluate  : 0.428 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  305 SER
Chi-restraints excluded: chain A residue  318 ILE
Chi-restraints excluded: chain C residue  305 SER
Chi-restraints excluded: chain C residue  311 MET
Chi-restraints excluded: chain E residue  305 SER
Chi-restraints excluded: chain E residue  311 MET
Chi-restraints excluded: chain F residue  311 MET
Chi-restraints excluded: chain G residue  305 SER
Chi-restraints excluded: chain G residue  318 ILE
Chi-restraints excluded: chain I residue  305 SER
Chi-restraints excluded: chain I residue  311 MET
Chi-restraints excluded: chain K residue  305 SER
Chi-restraints excluded: chain K residue  318 ILE
Chi-restraints excluded: chain M residue  291 ASN
Chi-restraints excluded: chain M residue  305 SER
Chi-restraints excluded: chain M residue  318 ILE
Chi-restraints excluded: chain N residue  318 ILE
Chi-restraints excluded: chain O residue  291 ASN
Chi-restraints excluded: chain O residue  305 SER
Chi-restraints excluded: chain O residue  318 ILE
Chi-restraints excluded: chain P residue  311 MET
Chi-restraints excluded: chain Q residue  303 GLN
Chi-restraints excluded: chain R residue  311 MET
Chi-restraints excluded: chain S residue  291 ASN
Chi-restraints excluded: chain S residue  303 GLN
Chi-restraints excluded: chain S residue  305 SER
Chi-restraints excluded: chain S residue  318 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 7 optimal weight:   30.0000
   chunk 8 optimal weight:    4.9990
   chunk 20 optimal weight:    5.9990
   chunk 6 optimal weight:   20.0000
   chunk 12 optimal weight:    8.9990
   chunk 54 optimal weight:   30.0000
   chunk 45 optimal weight:   40.0000
   chunk 0 optimal weight:   20.0000
   chunk 5 optimal weight:    7.9990
   chunk 57 optimal weight:    5.9990
   chunk 39 optimal weight:   40.0000
   overall best weight:    6.7990

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

Flipped N/Q/H residues before XYZ refinement:
** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P 312 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 = 0.4286 r_free = 0.4286 target = 0.151995 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4153 r_free = 0.4153 target = 0.138510 restraints weight = 6221.657|
|-----------------------------------------------------------------------------|
r_work (start): 0.4192 rms_B_bonded: 2.19
r_work: 0.4135 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.4031 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.4031
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8254
moved from start:          0.2760

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   4300  Z= 0.192
  Angle     :  0.579   7.997   5640  Z= 0.293
  Chirality :  0.040   0.149    440
  Planarity :  0.002   0.008    860
  Dihedral  :  5.436  17.921    640
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 9.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.33 %
    Favored  : 90.67 %
  Rotamer:
    Outliers :  8.95 %
    Allowed  : 22.37 %
    Favored  : 68.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.56 (0.28), residues: 600
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.70 (0.21), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.015   0.001   PHE M 313 
 ARG   0.002   0.000   ARG S 293 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03482 (  100)
  hydrogen bonds       : angle       6.26918 (  300)
  covalent geometry    : bond        0.00443 ( 4300)
  covalent geometry    : angle       0.57858 ( 5640)

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

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

  1200 Ramachandran restraints generated.
    600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1200 Ramachandran restraints generated.
    600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 81
  time to evaluate  : 0.457 
Fit side-chains
REVERT: C  291 ASN cc_start: 0.8944 (OUTLIER) cc_final: 0.6707 (m-40)
REVERT: C  311 MET cc_start: 0.8782 (OUTLIER) cc_final: 0.8080 (ttm)
REVERT: E  291 ASN cc_start: 0.8834 (p0) cc_final: 0.6693 (m-40)
REVERT: E  302 ASN cc_start: 0.8641 (t0) cc_final: 0.8139 (t0)
REVERT: G  311 MET cc_start: 0.9173 (ttt) cc_final: 0.8927 (ttt)
REVERT: J  307 MET cc_start: 0.8469 (tpp) cc_final: 0.7931 (tpt)
REVERT: Q  303 GLN cc_start: 0.8868 (OUTLIER) cc_final: 0.7618 (mt0)
REVERT: S  303 GLN cc_start: 0.8841 (OUTLIER) cc_final: 0.7890 (mt0)
  outliers start: 34
  outliers final: 27
  residues processed: 98
  average time/residue: 0.1491
  time to fit residues: 20.9603
Evaluate side-chains
  111 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 80
  time to evaluate  : 0.472 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  305 SER
Chi-restraints excluded: chain A residue  318 ILE
Chi-restraints excluded: chain B residue  318 ILE
Chi-restraints excluded: chain C residue  291 ASN
Chi-restraints excluded: chain C residue  305 SER
Chi-restraints excluded: chain C residue  311 MET
Chi-restraints excluded: chain D residue  311 MET
Chi-restraints excluded: chain E residue  305 SER
Chi-restraints excluded: chain E residue  311 MET
Chi-restraints excluded: chain G residue  305 SER
Chi-restraints excluded: chain G residue  318 ILE
Chi-restraints excluded: chain I residue  305 SER
Chi-restraints excluded: chain I residue  311 MET
Chi-restraints excluded: chain K residue  305 SER
Chi-restraints excluded: chain K residue  318 ILE
Chi-restraints excluded: chain M residue  291 ASN
Chi-restraints excluded: chain M residue  305 SER
Chi-restraints excluded: chain M residue  318 ILE
Chi-restraints excluded: chain N residue  318 ILE
Chi-restraints excluded: chain O residue  291 ASN
Chi-restraints excluded: chain O residue  305 SER
Chi-restraints excluded: chain O residue  318 ILE
Chi-restraints excluded: chain P residue  311 MET
Chi-restraints excluded: chain Q residue  303 GLN
Chi-restraints excluded: chain Q residue  305 SER
Chi-restraints excluded: chain R residue  311 MET
Chi-restraints excluded: chain S residue  291 ASN
Chi-restraints excluded: chain S residue  303 GLN
Chi-restraints excluded: chain S residue  305 SER
Chi-restraints excluded: chain S residue  318 ILE
Chi-restraints excluded: chain T residue  292 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 35 optimal weight:   20.0000
   chunk 55 optimal weight:    9.9990
   chunk 6 optimal weight:   30.0000
   chunk 33 optimal weight:   40.0000
   chunk 11 optimal weight:    6.9990
   chunk 19 optimal weight:   20.0000
   chunk 58 optimal weight:    5.9990
   chunk 25 optimal weight:    5.9990
   chunk 8 optimal weight:    8.9990
   chunk 47 optimal weight:    5.9990
   chunk 53 optimal weight:    9.9990
   overall best weight:    6.7990

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

Flipped N/Q/H residues before XYZ refinement:
** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
S 291 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4290 r_free = 0.4290 target = 0.150765 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4149 r_free = 0.4149 target = 0.137383 restraints weight = 6136.211|
|-----------------------------------------------------------------------------|
r_work (start): 0.4237 rms_B_bonded: 2.31
r_work: 0.4170 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.4071 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.4071
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8217
moved from start:          0.2843

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   4300  Z= 0.192
  Angle     :  0.587   8.047   5640  Z= 0.297
  Chirality :  0.041   0.149    440
  Planarity :  0.002   0.007    860
  Dihedral  :  5.436  18.786    640
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 10.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.33 %
    Favored  : 89.67 %
  Rotamer:
    Outliers :  8.16 %
    Allowed  : 23.16 %
    Favored  : 68.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.54 (0.28), residues: 600
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.69 (0.21), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.016   0.001   PHE M 313 
 ARG   0.002   0.000   ARG S 293 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03486 (  100)
  hydrogen bonds       : angle       6.26443 (  300)
  covalent geometry    : bond        0.00444 ( 4300)
  covalent geometry    : angle       0.58669 ( 5640)

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

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

  1200 Ramachandran restraints generated.
    600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1200 Ramachandran restraints generated.
    600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 78
  time to evaluate  : 0.711 
Fit side-chains
REVERT: C  291 ASN cc_start: 0.8982 (OUTLIER) cc_final: 0.6733 (m-40)
REVERT: C  311 MET cc_start: 0.8782 (OUTLIER) cc_final: 0.8079 (ttm)
REVERT: E  291 ASN cc_start: 0.8845 (p0) cc_final: 0.6657 (m-40)
REVERT: E  302 ASN cc_start: 0.8660 (t0) cc_final: 0.8115 (t0)
REVERT: F  307 MET cc_start: 0.8192 (tpp) cc_final: 0.7823 (tpt)
REVERT: G  311 MET cc_start: 0.9199 (ttt) cc_final: 0.8933 (ttt)
REVERT: J  307 MET cc_start: 0.8419 (tpp) cc_final: 0.7772 (tpt)
REVERT: Q  303 GLN cc_start: 0.8883 (OUTLIER) cc_final: 0.7601 (mt0)
REVERT: R  307 MET cc_start: 0.8568 (tpp) cc_final: 0.8219 (tpt)
REVERT: S  303 GLN cc_start: 0.8820 (OUTLIER) cc_final: 0.7845 (mt0)
  outliers start: 31
  outliers final: 26
  residues processed: 94
  average time/residue: 0.1418
  time to fit residues: 19.3007
Evaluate side-chains
  108 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 78
  time to evaluate  : 1.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  305 SER
Chi-restraints excluded: chain A residue  318 ILE
Chi-restraints excluded: chain C residue  291 ASN
Chi-restraints excluded: chain C residue  305 SER
Chi-restraints excluded: chain C residue  311 MET
Chi-restraints excluded: chain D residue  311 MET
Chi-restraints excluded: chain E residue  305 SER
Chi-restraints excluded: chain E residue  311 MET
Chi-restraints excluded: chain G residue  305 SER
Chi-restraints excluded: chain G residue  318 ILE
Chi-restraints excluded: chain I residue  305 SER
Chi-restraints excluded: chain I residue  311 MET
Chi-restraints excluded: chain K residue  305 SER
Chi-restraints excluded: chain K residue  318 ILE
Chi-restraints excluded: chain M residue  291 ASN
Chi-restraints excluded: chain M residue  305 SER
Chi-restraints excluded: chain M residue  318 ILE
Chi-restraints excluded: chain N residue  318 ILE
Chi-restraints excluded: chain O residue  291 ASN
Chi-restraints excluded: chain O residue  305 SER
Chi-restraints excluded: chain O residue  318 ILE
Chi-restraints excluded: chain P residue  311 MET
Chi-restraints excluded: chain Q residue  303 GLN
Chi-restraints excluded: chain Q residue  305 SER
Chi-restraints excluded: chain R residue  311 MET
Chi-restraints excluded: chain S residue  291 ASN
Chi-restraints excluded: chain S residue  303 GLN
Chi-restraints excluded: chain S residue  305 SER
Chi-restraints excluded: chain S residue  318 ILE
Chi-restraints excluded: chain T residue  292 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 46 optimal weight:   20.0000
   chunk 33 optimal weight:   40.0000
   chunk 0 optimal weight:   40.0000
   chunk 39 optimal weight:   30.0000
   chunk 17 optimal weight:    0.6980
   chunk 37 optimal weight:    9.9990
   chunk 26 optimal weight:   20.0000
   chunk 41 optimal weight:    7.9990
   chunk 42 optimal weight:   20.0000
   chunk 6 optimal weight:   30.0000
   chunk 1 optimal weight:    6.9990
   overall best weight:    9.1390

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

Flipped N/Q/H residues before XYZ refinement:
** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
S 291 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4285 r_free = 0.4285 target = 0.152756 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4160 r_free = 0.4160 target = 0.138030 restraints weight = 6375.478|
|-----------------------------------------------------------------------------|
r_work (start): 0.4190 rms_B_bonded: 2.28
r_work: 0.4129 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.4029 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.4029
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8276
moved from start:          0.2817

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.030   4300  Z= 0.248
  Angle     :  0.636   8.280   5640  Z= 0.320
  Chirality :  0.042   0.151    440
  Planarity :  0.002   0.009    860
  Dihedral  :  5.619  19.471    640
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 10.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.00 %
    Favored  : 90.00 %
  Rotamer:
    Outliers :  8.42 %
    Allowed  : 22.63 %
    Favored  : 68.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.55 (0.27), residues: 600
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.70 (0.21), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.017   0.002   PHE M 313 
 ARG   0.003   0.000   ARG S 293 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03761 (  100)
  hydrogen bonds       : angle       6.37771 (  300)
  covalent geometry    : bond        0.00572 ( 4300)
  covalent geometry    : angle       0.63619 ( 5640)

===============================================================================
Job complete
usr+sys time: 2536.65 seconds
wall clock time: 47 minutes 29.70 seconds (2849.70 seconds total)