Starting phenix.real_space_refine
on Wed Jan 15 03:29:22 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9euy_19989/01_2025/9euy_19989_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9euy_19989/01_2025/9euy_19989.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.95
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9euy_19989/01_2025/9euy_19989.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9euy_19989/01_2025/9euy_19989.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9euy_19989/01_2025/9euy_19989_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9euy_19989/01_2025/9euy_19989_neut.cif"
  }
  resolution = 2.95
  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=  -0.001 sd=   0.022
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      38      5.16       5
     C    4942      2.51       5
     N    1400      2.21       5
     O    1466      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 7846
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3880
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 492, 3880
          Classifications: {'peptide': 492}
          Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 463}
    Chain: "B"
      Number of atoms: 3880
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 492, 3880
          Classifications: {'peptide': 492}
          Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 463}
    Chain: "A"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 43
          Unusual residues: {'LBV': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 43
          Unusual residues: {'LBV': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 6.25, per 1000 atoms: 0.80
  Number of scatterers: 7846
  At special positions: 0
  Unit cell: (85.284, 105.156, 119.232, 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      38     16.00
     O    1466      8.00
     N    1400      7.00
     C    4942      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: 2.26
  Conformation dependent library (CDL) restraints added in 876.7 milliseconds
  

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1824

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 6 sheets defined
      42.4% alpha, 19.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.94
  Creating SS restraints...
    Processing helix  chain 'A' and resid 11 through 15
    Processing helix  chain 'A' and resid 44 through 50
    Processing helix  chain 'A' and resid 60 through 78
      Proline residue:  A  66  - end of helix
    Processing helix  chain 'A' and resid 116 through 134
      removed outlier: 3.830A  pdb=" N   ILE A 120 " --> pdb=" O   ASP A 116 " (cutoff:3.500A)
      removed outlier: 6.023A  pdb=" N   SER A 122 " --> pdb=" O   LEU A 118 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 135 through 137
      No H-bonds generated for 'chain 'A' and resid 135 through 137'
    Processing helix  chain 'A' and resid 139 through 156
    Processing helix  chain 'A' and resid 191 through 195
    Processing helix  chain 'A' and resid 196 through 206
    Processing helix  chain 'A' and resid 244 through 254
    Processing helix  chain 'A' and resid 285 through 332
    Processing helix  chain 'A' and resid 334 through 340
    Processing helix  chain 'A' and resid 345 through 350
      removed outlier: 3.627A  pdb=" N   LEU A 349 " --> pdb=" O   GLY A 345 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   ILE A 350 " --> pdb=" O   ILE A 346 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 345 through 350'
    Processing helix  chain 'A' and resid 370 through 382
    Processing helix  chain 'A' and resid 430 through 437
      removed outlier: 3.934A  pdb=" N   TRP A 437 " --> pdb=" O   HIS A 433 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 455 through 468
    Processing helix  chain 'A' and resid 475 through 492
    Processing helix  chain 'B' and resid 11 through 15
    Processing helix  chain 'B' and resid 44 through 50
    Processing helix  chain 'B' and resid 64 through 77
      removed outlier: 4.351A  pdb=" N   VAL B  68 " --> pdb=" O   VAL B  64 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 116 through 134
    Processing helix  chain 'B' and resid 135 through 137
      No H-bonds generated for 'chain 'B' and resid 135 through 137'
    Processing helix  chain 'B' and resid 139 through 156
      removed outlier: 3.550A  pdb=" N   ASP B 149 " --> pdb=" O   SER B 145 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 191 through 195
    Processing helix  chain 'B' and resid 196 through 206
    Processing helix  chain 'B' and resid 244 through 254
    Processing helix  chain 'B' and resid 285 through 332
      removed outlier: 4.018A  pdb=" N   ARG B 330 " --> pdb=" O   ALA B 326 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 334 through 340
    Processing helix  chain 'B' and resid 345 through 349
    Processing helix  chain 'B' and resid 370 through 382
    Processing helix  chain 'B' and resid 418 through 421
      removed outlier: 4.045A  pdb=" N   SER B 421 " --> pdb=" O   ARG B 418 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 418 through 421'
    Processing helix  chain 'B' and resid 432 through 437
      removed outlier: 4.578A  pdb=" N   TRP B 437 " --> pdb=" O   HIS B 433 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 455 through 467
    Processing helix  chain 'B' and resid 475 through 490
    Processing sheet with id=AA1, first strand: chain 'A' and resid 22 through 23
      removed outlier: 3.548A  pdb=" N   ALA A  40 " --> pdb=" O   THR A  31 " (cutoff:3.500A)
      removed outlier: 6.076A  pdb=" N   LEU A  29 " --> pdb=" O   SER A  42 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 189 through 190
      removed outlier: 5.916A  pdb=" N   VAL A 173 " --> pdb=" O   ARG A 164 " (cutoff:3.500A)
      removed outlier: 6.961A  pdb=" N   ARG A 164 " --> pdb=" O   VAL A 173 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   ALA A 175 " --> pdb=" O   ALA A 162 " (cutoff:3.500A)
      removed outlier: 5.117A  pdb=" N   LEU A 270 " --> pdb=" O   VAL A 266 " (cutoff:3.500A)
      removed outlier: 6.310A  pdb=" N   VAL A 266 " --> pdb=" O   LEU A 270 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 362 through 366
      removed outlier: 6.196A  pdb=" N   GLY A 422 " --> pdb=" O   PHE A 416 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 22 through 23
      removed outlier: 3.561A  pdb=" N   ALA B  40 " --> pdb=" O   THR B  31 " (cutoff:3.500A)
      removed outlier: 6.640A  pdb=" N   LEU B  29 " --> pdb=" O   SER B  42 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 189 through 190
      removed outlier: 5.719A  pdb=" N   VAL B 173 " --> pdb=" O   ARG B 164 " (cutoff:3.500A)
      removed outlier: 6.814A  pdb=" N   ARG B 164 " --> pdb=" O   VAL B 173 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   ALA B 175 " --> pdb=" O   ALA B 162 " (cutoff:3.500A)
      removed outlier: 5.072A  pdb=" N   LEU B 270 " --> pdb=" O   VAL B 266 " (cutoff:3.500A)
      removed outlier: 6.319A  pdb=" N   VAL B 266 " --> pdb=" O   LEU B 270 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 362 through 366
      removed outlier: 7.162A  pdb=" N   ILE B 424 " --> pdb=" O   ARG B 415 " (cutoff:3.500A)
      removed outlier: 5.592A  pdb=" N   ARG B 415 " --> pdb=" O   ILE B 424 " (cutoff:3.500A)
      removed outlier: 7.324A  pdb=" N   TRP B 426 " --> pdb=" O   ALA B 413 " (cutoff:3.500A)
      removed outlier: 5.591A  pdb=" N   ALA B 413 " --> pdb=" O   TRP B 426 " (cutoff:3.500A)
      removed outlier: 7.543A  pdb=" N   ARG B 428 " --> pdb=" O   VAL B 411 " (cutoff:3.500A)
      removed outlier: 5.768A  pdb=" N   VAL B 411 " --> pdb=" O   ARG B 428 " (cutoff:3.500A)

    423 hydrogen bonds defined for protein.
    1185 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: 2.49

  Time building geometry restraints manager: 2.49 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1410
        1.32 -     1.44: 2081
        1.44 -     1.57: 4475
        1.57 -     1.69: 0
        1.69 -     1.81: 62
  Bond restraints: 8028
  Sorted by residual:
  bond pdb=" CB  MET B 154 "
       pdb=" CG  MET B 154 "
    ideal  model  delta    sigma   weight residual
    1.520  1.485  0.035 3.00e-02 1.11e+03 1.33e+00
  bond pdb=" CB  MET A 154 "
       pdb=" CG  MET A 154 "
    ideal  model  delta    sigma   weight residual
    1.520  1.486  0.034 3.00e-02 1.11e+03 1.26e+00
  bond pdb=" CB  ILE B 447 "
       pdb=" CG2 ILE B 447 "
    ideal  model  delta    sigma   weight residual
    1.521  1.485  0.036 3.30e-02 9.18e+02 1.20e+00
  bond pdb=" CG1 ILE A 294 "
       pdb=" CD1 ILE A 294 "
    ideal  model  delta    sigma   weight residual
    1.513  1.472  0.041 3.90e-02 6.57e+02 1.11e+00
  bond pdb=" CG1 ILE B 294 "
       pdb=" CD1 ILE B 294 "
    ideal  model  delta    sigma   weight residual
    1.513  1.474  0.039 3.90e-02 6.57e+02 9.93e-01
  ... (remaining 8023 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.62: 10415
        1.62 -     3.24: 430
        3.24 -     4.86: 54
        4.86 -     6.49: 9
        6.49 -     8.11: 4
  Bond angle restraints: 10912
  Sorted by residual:
  angle pdb=" CD  ARG A 453 "
        pdb=" NE  ARG A 453 "
        pdb=" CZ  ARG A 453 "
      ideal   model   delta    sigma   weight residual
     124.40  129.06   -4.66 1.40e+00 5.10e-01 1.11e+01
  angle pdb=" CB  ARG B 453 "
        pdb=" CG  ARG B 453 "
        pdb=" CD  ARG B 453 "
      ideal   model   delta    sigma   weight residual
     111.30  118.61   -7.31 2.30e+00 1.89e-01 1.01e+01
  angle pdb=" N   PRO B 452 "
        pdb=" CA  PRO B 452 "
        pdb=" C   PRO B 452 "
      ideal   model   delta    sigma   weight residual
     113.86  117.57   -3.71 1.25e+00 6.40e-01 8.83e+00
  angle pdb=" CG  ARG A 453 "
        pdb=" CD  ARG A 453 "
        pdb=" NE  ARG A 453 "
      ideal   model   delta    sigma   weight residual
     112.00  118.12   -6.12 2.20e+00 2.07e-01 7.75e+00
  angle pdb=" CB  MET A 154 "
        pdb=" CG  MET A 154 "
        pdb=" SD  MET A 154 "
      ideal   model   delta    sigma   weight residual
     112.70  104.59    8.11 3.00e+00 1.11e-01 7.30e+00
  ... (remaining 10907 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.15: 4513
       17.15 -    34.31: 239
       34.31 -    51.46: 51
       51.46 -    68.61: 14
       68.61 -    85.76: 9
  Dihedral angle restraints: 4826
    sinusoidal: 1994
      harmonic: 2832
  Sorted by residual:
  dihedral pdb=" CG  ARG A 453 "
           pdb=" CD  ARG A 453 "
           pdb=" NE  ARG A 453 "
           pdb=" CZ  ARG A 453 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00    5.38   84.62     2      1.50e+01 4.44e-03 2.11e+01
  dihedral pdb=" CA  ASP B  96 "
           pdb=" CB  ASP B  96 "
           pdb=" CG  ASP B  96 "
           pdb=" OD1 ASP B  96 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -83.23   53.23     1      2.00e+01 2.50e-03 9.63e+00
  dihedral pdb=" CG  ARG A 201 "
           pdb=" CD  ARG A 201 "
           pdb=" NE  ARG A 201 "
           pdb=" CZ  ARG A 201 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00 -132.08   42.08     2      1.50e+01 4.44e-03 9.58e+00
  ... (remaining 4823 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.038: 785
       0.038 -    0.075: 257
       0.075 -    0.113: 93
       0.113 -    0.150: 48
       0.150 -    0.188: 5
  Chirality restraints: 1188
  Sorted by residual:
  chirality pdb=" CA  PRO B 452 "
            pdb=" N   PRO B 452 "
            pdb=" C   PRO B 452 "
            pdb=" CB  PRO B 452 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.53    0.19 2.00e-01 2.50e+01 8.84e-01
  chirality pdb=" CA  PRO A 452 "
            pdb=" N   PRO A 452 "
            pdb=" C   PRO A 452 "
            pdb=" CB  PRO A 452 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.54    0.17 2.00e-01 2.50e+01 7.59e-01
  chirality pdb=" CA  ILE A 264 "
            pdb=" N   ILE A 264 "
            pdb=" C   ILE A 264 "
            pdb=" CB  ILE A 264 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.15 2.00e-01 2.50e+01 5.93e-01
  ... (remaining 1185 not shown)

  Planarity restraints: 1434
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 152 "    0.236 9.50e-02 1.11e+02   1.06e-01 8.43e+00
        pdb=" NE  ARG B 152 "   -0.021 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 152 "    0.019 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 152 "   -0.009 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 152 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 434 "    0.212 9.50e-02 1.11e+02   9.57e-02 7.46e+00
        pdb=" NE  ARG B 434 "   -0.021 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 434 "    0.022 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 434 "   -0.010 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 434 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 152 "   -0.211 9.50e-02 1.11e+02   9.49e-02 6.69e+00
        pdb=" NE  ARG A 152 "    0.019 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 152 "   -0.017 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 152 "    0.008 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 152 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 1431 not shown)

  Histogram of nonbonded interaction distances:
        2.31 -     2.83: 2280
        2.83 -     3.35: 7229
        3.35 -     3.86: 12967
        3.86 -     4.38: 15202
        4.38 -     4.90: 26273
  Nonbonded interactions: 63951
  Sorted by model distance:
  nonbonded pdb=" NH1 ARG A 178 "
            pdb=" O   LEU A 182 "
     model   vdw
     2.311 3.120
  nonbonded pdb=" NH1 ARG B 178 "
            pdb=" O   LEU B 182 "
     model   vdw
     2.339 3.120
  nonbonded pdb=" NH1 ARG A 322 "
            pdb=" OD2 ASP A 488 "
     model   vdw
     2.369 3.120
  nonbonded pdb=" OG  SER A 399 "
            pdb=" OD1 ASP A 401 "
     model   vdw
     2.406 3.040
  nonbonded pdb=" OD1 ASP B 234 "
            pdb=" OG  SER B 236 "
     model   vdw
     2.411 3.040
  ... (remaining 63946 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: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.720
  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:          0.350
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     22.810
  Find NCS groups from input model:        0.250
  Set up NCS constraints:                  0.040
  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:13.000
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   40.310
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8064
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      :  0.003   0.041   8028  Z= 0.226
  Angle     :  0.735   8.108  10912  Z= 0.419
  Chirality :  0.048   0.188   1188
  Planarity :  0.010   0.106   1434
  Dihedral  : 11.993  85.765   3002
  Min Nonbonded Distance : 2.311

Molprobity Statistics.
  All-atom Clashscore : 3.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  0.24 %
    Allowed  :  2.03 %
    Favored  : 97.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    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:  0.41 (0.26), residues: 980
  helix:  0.76 (0.26), residues: 352
  sheet:  0.42 (0.40), residues: 166
  loop : -0.03 (0.28), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.003   TRP A  82 
 HIS   0.008   0.002   HIS A 167 
 PHE   0.020   0.003   PHE A 274 
 TYR   0.017   0.004   TYR B 163 
 ARG   0.024   0.003   ARG B 434 

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

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

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 178
  time to evaluate  : 0.910 
Fit side-chains
   revert: symmetry clash
REVERT: A  139 ASP cc_start: 0.7286 (t70) cc_final: 0.6880 (p0)
REVERT: A  394 ASN cc_start: 0.8018 (t0) cc_final: 0.7629 (t160)
REVERT: A  395 TRP cc_start: 0.7284 (t-100) cc_final: 0.7046 (t60)
REVERT: A  470 HIS cc_start: 0.7316 (m90) cc_final: 0.6840 (m90)
REVERT: B  228 GLU cc_start: 0.7553 (mt-10) cc_final: 0.7259 (mm-30)
REVERT: B  314 LEU cc_start: 0.7674 (mt) cc_final: 0.7435 (mp)
REVERT: B  353 ASP cc_start: 0.7189 (m-30) cc_final: 0.6969 (m-30)
REVERT: B  430 GLU cc_start: 0.3794 (tt0) cc_final: 0.3572 (tt0)
  outliers start: 2
  outliers final: 1
  residues processed: 180
  average time/residue: 1.3305
  time to fit residues: 252.2297
Evaluate side-chains
  112 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 111
  time to evaluate  : 0.807 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  393 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 82 optimal weight:    9.9990
   chunk 74 optimal weight:    0.5980
   chunk 41 optimal weight:    1.9990
   chunk 25 optimal weight:    2.9990
   chunk 50 optimal weight:    0.9990
   chunk 39 optimal weight:    0.6980
   chunk 76 optimal weight:    0.9990
   chunk 29 optimal weight:    0.7980
   chunk 46 optimal weight:    0.7980
   chunk 57 optimal weight:    0.6980
   chunk 88 optimal weight:    7.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A  61 GLN
A  79 ASN
A 137 HIS
** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 433 HIS
B 137 HIS
B 278 HIS
B 391 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4196 r_free = 0.4196 target = 0.189882 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.135394 restraints weight = 9255.296|
|-----------------------------------------------------------------------------|
r_work (start): 0.3570 rms_B_bonded: 2.27
r_work: 0.3442 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3309 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.3309
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8030
moved from start:          0.2135

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8028  Z= 0.222
  Angle     :  0.574   7.940  10912  Z= 0.305
  Chirality :  0.045   0.172   1188
  Planarity :  0.004   0.039   1434
  Dihedral  :  6.964  86.649   1142
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.02 %
    Favored  : 98.98 %
  Rotamer:
    Outliers :  3.34 %
    Allowed  :  9.55 %
    Favored  : 87.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.44 (0.27), residues: 980
  helix:  1.79 (0.27), residues: 360
  sheet:  0.59 (0.41), residues: 162
  loop :  0.55 (0.30), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 423 
 HIS   0.005   0.001   HIS B 391 
 PHE   0.013   0.002   PHE B 295 
 TYR   0.010   0.001   TYR B 163 
 ARG   0.004   0.001   ARG B  89 

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

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

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 121
  time to evaluate  : 0.930 
Fit side-chains
REVERT: A  394 ASN cc_start: 0.8038 (t0) cc_final: 0.7650 (t160)
REVERT: A  395 TRP cc_start: 0.7236 (t-100) cc_final: 0.6803 (t60)
REVERT: A  440 LYS cc_start: 0.7680 (mttt) cc_final: 0.7414 (mtpt)
REVERT: A  465 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.7150 (tt0)
REVERT: A  470 HIS cc_start: 0.7450 (m90) cc_final: 0.6962 (m170)
REVERT: B   43 GLU cc_start: 0.8109 (tt0) cc_final: 0.7719 (tp30)
REVERT: B   48 LEU cc_start: 0.7497 (OUTLIER) cc_final: 0.7217 (tt)
REVERT: B  220 ARG cc_start: 0.7715 (mtm180) cc_final: 0.7157 (mmt180)
REVERT: B  228 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7367 (mm-30)
REVERT: B  353 ASP cc_start: 0.7036 (m-30) cc_final: 0.6614 (m-30)
REVERT: B  430 GLU cc_start: 0.3891 (tt0) cc_final: 0.3620 (tt0)
  outliers start: 28
  outliers final: 13
  residues processed: 141
  average time/residue: 1.2510
  time to fit residues: 187.0021
Evaluate side-chains
  115 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 100
  time to evaluate  : 0.821 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 ILE
Chi-restraints excluded: chain A residue   79 ASN
Chi-restraints excluded: chain A residue  139 ASP
Chi-restraints excluded: chain A residue  230 ASN
Chi-restraints excluded: chain A residue  366 ILE
Chi-restraints excluded: chain A residue  393 ASP
Chi-restraints excluded: chain A residue  465 GLU
Chi-restraints excluded: chain B residue   31 THR
Chi-restraints excluded: chain B residue   48 LEU
Chi-restraints excluded: chain B residue   62 GLU
Chi-restraints excluded: chain B residue   67 GLU
Chi-restraints excluded: chain B residue   83 SER
Chi-restraints excluded: chain B residue  101 SER
Chi-restraints excluded: chain B residue  186 LEU
Chi-restraints excluded: chain B residue  392 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 36 optimal weight:    9.9990
   chunk 5 optimal weight:    1.9990
   chunk 14 optimal weight:    0.8980
   chunk 91 optimal weight:    4.9990
   chunk 44 optimal weight:    0.9980
   chunk 9 optimal weight:    0.5980
   chunk 78 optimal weight:    0.0980
   chunk 22 optimal weight:    2.9990
   chunk 37 optimal weight:    1.9990
   chunk 89 optimal weight:    0.9990
   chunk 16 optimal weight:    1.9990
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
A  79 ASN
A 206 ASN
** A 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 391 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4203 r_free = 0.4203 target = 0.190013 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.135062 restraints weight = 9335.354|
|-----------------------------------------------------------------------------|
r_work (start): 0.3565 rms_B_bonded: 2.31
r_work: 0.3448 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3318 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.3318
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8033
moved from start:          0.2478

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8028  Z= 0.216
  Angle     :  0.523   5.336  10912  Z= 0.278
  Chirality :  0.044   0.172   1188
  Planarity :  0.004   0.042   1434
  Dihedral  :  6.815  89.699   1142
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 5.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  3.82 %
    Allowed  : 11.58 %
    Favored  : 84.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.59 (0.27), residues: 980
  helix:  2.13 (0.26), residues: 360
  sheet:  0.60 (0.42), residues: 162
  loop :  0.46 (0.30), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 423 
 HIS   0.008   0.001   HIS B 391 
 PHE   0.012   0.002   PHE B 295 
 TYR   0.009   0.001   TYR B 163 
 ARG   0.003   0.000   ARG A 328 

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

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

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 109
  time to evaluate  : 0.842 
Fit side-chains
REVERT: A    9 LEU cc_start: 0.8080 (OUTLIER) cc_final: 0.7729 (mp)
REVERT: A   37 MET cc_start: 0.7439 (ttp) cc_final: 0.7234 (ttp)
REVERT: A  219 MET cc_start: 0.6582 (OUTLIER) cc_final: 0.5942 (mmt)
REVERT: A  395 TRP cc_start: 0.7259 (t-100) cc_final: 0.6767 (t60)
REVERT: A  440 LYS cc_start: 0.7652 (mttt) cc_final: 0.7378 (mtpt)
REVERT: A  465 GLU cc_start: 0.7453 (OUTLIER) cc_final: 0.7169 (tt0)
REVERT: A  470 HIS cc_start: 0.7542 (m90) cc_final: 0.7332 (m170)
REVERT: B   43 GLU cc_start: 0.8133 (tt0) cc_final: 0.7758 (tp30)
REVERT: B   48 LEU cc_start: 0.7455 (OUTLIER) cc_final: 0.7232 (tt)
REVERT: B  135 GLN cc_start: 0.8489 (OUTLIER) cc_final: 0.8183 (mp10)
REVERT: B  220 ARG cc_start: 0.7700 (mtm180) cc_final: 0.7141 (mmt180)
REVERT: B  228 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7426 (mm-30)
REVERT: B  353 ASP cc_start: 0.7034 (m-30) cc_final: 0.6609 (m-30)
REVERT: B  430 GLU cc_start: 0.3996 (tt0) cc_final: 0.3720 (tt0)
REVERT: B  485 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.8143 (tt)
  outliers start: 32
  outliers final: 15
  residues processed: 131
  average time/residue: 1.0565
  time to fit residues: 147.5987
Evaluate side-chains
  121 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 100
  time to evaluate  : 0.854 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 LEU
Chi-restraints excluded: chain A residue   45 ILE
Chi-restraints excluded: chain A residue  219 MET
Chi-restraints excluded: chain A residue  230 ASN
Chi-restraints excluded: chain A residue  246 ILE
Chi-restraints excluded: chain A residue  280 SER
Chi-restraints excluded: chain A residue  366 ILE
Chi-restraints excluded: chain A residue  391 HIS
Chi-restraints excluded: chain A residue  393 ASP
Chi-restraints excluded: chain A residue  465 GLU
Chi-restraints excluded: chain A residue  492 LEU
Chi-restraints excluded: chain B residue   31 THR
Chi-restraints excluded: chain B residue   48 LEU
Chi-restraints excluded: chain B residue   62 GLU
Chi-restraints excluded: chain B residue   83 SER
Chi-restraints excluded: chain B residue  101 SER
Chi-restraints excluded: chain B residue  135 GLN
Chi-restraints excluded: chain B residue  186 LEU
Chi-restraints excluded: chain B residue  391 HIS
Chi-restraints excluded: chain B residue  392 THR
Chi-restraints excluded: chain B residue  485 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 5 optimal weight:    2.9990
   chunk 17 optimal weight:    2.9990
   chunk 75 optimal weight:    0.6980
   chunk 82 optimal weight:    5.9990
   chunk 36 optimal weight:    8.9990
   chunk 34 optimal weight:    0.8980
   chunk 43 optimal weight:    3.9990
   chunk 14 optimal weight:    0.9980
   chunk 55 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9990
   chunk 54 optimal weight:    0.0470
   overall best weight:    0.7280

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

Flipped N/Q/H residues before XYZ refinement:
A  79 ASN
A 206 ASN
A 394 ASN
B 391 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4239 r_free = 0.4239 target = 0.190635 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.140110 restraints weight = 9158.535|
|-----------------------------------------------------------------------------|
r_work (start): 0.3674 rms_B_bonded: 2.20
r_work: 0.3459 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.3325 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.3325
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8103
moved from start:          0.2673

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8028  Z= 0.217
  Angle     :  0.524  10.532  10912  Z= 0.273
  Chirality :  0.044   0.167   1188
  Planarity :  0.004   0.039   1434
  Dihedral  :  6.712  86.223   1142
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 5.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.12 %
    Favored  : 98.88 %
  Rotamer:
    Outliers :  4.06 %
    Allowed  : 13.48 %
    Favored  : 82.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.61 (0.27), residues: 980
  helix:  2.26 (0.26), residues: 360
  sheet:  0.54 (0.42), residues: 162
  loop :  0.41 (0.30), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 426 
 HIS   0.009   0.001   HIS B 391 
 PHE   0.012   0.002   PHE B 295 
 TYR   0.009   0.001   TYR B 286 
 ARG   0.002   0.000   ARG A 328 

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

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

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 104
  time to evaluate  : 0.991 
Fit side-chains
   revert: symmetry clash
REVERT: A    9 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7688 (mp)
REVERT: A   37 MET cc_start: 0.7505 (ttp) cc_final: 0.7032 (ttp)
REVERT: A  395 TRP cc_start: 0.7162 (t-100) cc_final: 0.6608 (t60)
REVERT: A  440 LYS cc_start: 0.7622 (mttt) cc_final: 0.7382 (mtpt)
REVERT: A  465 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.7347 (tt0)
REVERT: B   43 GLU cc_start: 0.8180 (tt0) cc_final: 0.7818 (tp30)
REVERT: B   88 THR cc_start: 0.8763 (t) cc_final: 0.8468 (p)
REVERT: B  135 GLN cc_start: 0.8547 (OUTLIER) cc_final: 0.8276 (mp10)
REVERT: B  220 ARG cc_start: 0.7808 (mtm180) cc_final: 0.7258 (mmt180)
REVERT: B  228 GLU cc_start: 0.7871 (mt-10) cc_final: 0.7477 (mm-30)
REVERT: B  353 ASP cc_start: 0.7158 (m-30) cc_final: 0.6728 (m-30)
REVERT: B  430 GLU cc_start: 0.4127 (tt0) cc_final: 0.3816 (tt0)
  outliers start: 34
  outliers final: 14
  residues processed: 124
  average time/residue: 1.1637
  time to fit residues: 153.3563
Evaluate side-chains
  117 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 100
  time to evaluate  : 0.911 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue    9 LEU
Chi-restraints excluded: chain A residue  230 ASN
Chi-restraints excluded: chain A residue  280 SER
Chi-restraints excluded: chain A residue  391 HIS
Chi-restraints excluded: chain A residue  393 ASP
Chi-restraints excluded: chain A residue  465 GLU
Chi-restraints excluded: chain A residue  477 THR
Chi-restraints excluded: chain A residue  492 LEU
Chi-restraints excluded: chain B residue   31 THR
Chi-restraints excluded: chain B residue   62 GLU
Chi-restraints excluded: chain B residue   67 GLU
Chi-restraints excluded: chain B residue   83 SER
Chi-restraints excluded: chain B residue  101 SER
Chi-restraints excluded: chain B residue  135 GLN
Chi-restraints excluded: chain B residue  186 LEU
Chi-restraints excluded: chain B residue  391 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 52 optimal weight:    1.9990
   chunk 90 optimal weight:    7.9990
   chunk 1 optimal weight:    0.0060
   chunk 54 optimal weight:    0.0870
   chunk 9 optimal weight:    0.5980
   chunk 95 optimal weight:    0.9980
   chunk 48 optimal weight:    0.9990
   chunk 59 optimal weight:    0.6980
   chunk 18 optimal weight:    0.6980
   chunk 96 optimal weight:    2.9990
   chunk 35 optimal weight:    4.9990
   overall best weight:    0.4174

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

Flipped N/Q/H residues before XYZ refinement:
A  79 ASN
B 188 GLN
B 391 HIS
** B 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4213 r_free = 0.4213 target = 0.191343 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.142713 restraints weight = 9235.122|
|-----------------------------------------------------------------------------|
r_work (start): 0.3666 rms_B_bonded: 2.17
r_work: 0.3464 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.3338 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.3338
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7999
moved from start:          0.2845

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   8028  Z= 0.162
  Angle     :  0.529  17.883  10912  Z= 0.265
  Chirality :  0.043   0.163   1188
  Planarity :  0.004   0.034   1434
  Dihedral  :  6.611  83.213   1142
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 5.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.92 %
    Favored  : 99.08 %
  Rotamer:
    Outliers :  3.82 %
    Allowed  : 14.56 %
    Favored  : 81.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.72 (0.27), residues: 980
  helix:  2.37 (0.26), residues: 360
  sheet:  0.56 (0.43), residues: 162
  loop :  0.46 (0.30), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 426 
 HIS   0.008   0.001   HIS B 391 
 PHE   0.009   0.001   PHE B 295 
 TYR   0.009   0.001   TYR B 286 
 ARG   0.002   0.000   ARG B 457 

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

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

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 95
  time to evaluate  : 0.857 
Fit side-chains
REVERT: A    9 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7612 (mp)
REVERT: A   73 GLU cc_start: 0.7287 (mm-30) cc_final: 0.7057 (tm-30)
REVERT: A  219 MET cc_start: 0.6690 (OUTLIER) cc_final: 0.5979 (mmt)
REVERT: A  395 TRP cc_start: 0.7120 (t-100) cc_final: 0.6527 (t60)
REVERT: A  440 LYS cc_start: 0.7795 (mttt) cc_final: 0.7467 (mtpt)
REVERT: A  465 GLU cc_start: 0.7462 (OUTLIER) cc_final: 0.7138 (tt0)
REVERT: B   43 GLU cc_start: 0.8055 (tt0) cc_final: 0.7626 (tp30)
REVERT: B   88 THR cc_start: 0.8712 (t) cc_final: 0.8427 (p)
REVERT: B  135 GLN cc_start: 0.8410 (OUTLIER) cc_final: 0.8171 (mp10)
REVERT: B  220 ARG cc_start: 0.7633 (mtm180) cc_final: 0.7105 (mmt180)
REVERT: B  228 GLU cc_start: 0.7778 (mt-10) cc_final: 0.7405 (mm-30)
REVERT: B  353 ASP cc_start: 0.7214 (m-30) cc_final: 0.6749 (m-30)
  outliers start: 32
  outliers final: 13
  residues processed: 118
  average time/residue: 1.1655
  time to fit residues: 146.4783
Evaluate side-chains
  108 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 91
  time to evaluate  : 0.808 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue    9 LEU
Chi-restraints excluded: chain A residue   79 ASN
Chi-restraints excluded: chain A residue  219 MET
Chi-restraints excluded: chain A residue  230 ASN
Chi-restraints excluded: chain A residue  280 SER
Chi-restraints excluded: chain A residue  391 HIS
Chi-restraints excluded: chain A residue  393 ASP
Chi-restraints excluded: chain A residue  465 GLU
Chi-restraints excluded: chain A residue  477 THR
Chi-restraints excluded: chain A residue  492 LEU
Chi-restraints excluded: chain B residue   31 THR
Chi-restraints excluded: chain B residue   62 GLU
Chi-restraints excluded: chain B residue  101 SER
Chi-restraints excluded: chain B residue  135 GLN
Chi-restraints excluded: chain B residue  186 LEU
Chi-restraints excluded: chain B residue  391 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 69 optimal weight:    0.5980
   chunk 76 optimal weight:    0.9990
   chunk 73 optimal weight:    0.9980
   chunk 48 optimal weight:    0.9980
   chunk 51 optimal weight:    0.4980
   chunk 84 optimal weight:    4.9990
   chunk 47 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9990
   chunk 82 optimal weight:    5.9990
   chunk 91 optimal weight:    0.7980
   chunk 19 optimal weight:    0.7980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A  79 ASN
A 226 ASN
B 188 GLN
B 391 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4238 r_free = 0.4238 target = 0.190762 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.141153 restraints weight = 9169.007|
|-----------------------------------------------------------------------------|
r_work (start): 0.3689 rms_B_bonded: 2.09
r_work: 0.3472 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3343 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.3343
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8092
moved from start:          0.2963

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8028  Z= 0.223
  Angle     :  0.541  14.092  10912  Z= 0.276
  Chirality :  0.044   0.166   1188
  Planarity :  0.004   0.043   1434
  Dihedral  :  6.573  79.015   1142
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.43 %
    Favored  : 98.57 %
  Rotamer:
    Outliers :  3.94 %
    Allowed  : 15.16 %
    Favored  : 80.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.69 (0.27), residues: 980
  helix:  2.34 (0.27), residues: 360
  sheet:  0.59 (0.41), residues: 172
  loop :  0.42 (0.30), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 426 
 HIS   0.008   0.001   HIS B 391 
 PHE   0.011   0.001   PHE B 295 
 TYR   0.010   0.001   TYR B 286 
 ARG   0.003   0.000   ARG B 457 

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

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

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 92
  time to evaluate  : 0.792 
Fit side-chains
REVERT: A    9 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7686 (mp)
REVERT: A   46 GLN cc_start: 0.8341 (OUTLIER) cc_final: 0.7574 (tp40)
REVERT: A   73 GLU cc_start: 0.7300 (mm-30) cc_final: 0.7061 (tm-30)
REVERT: A  219 MET cc_start: 0.6632 (OUTLIER) cc_final: 0.5904 (mmt)
REVERT: A  395 TRP cc_start: 0.7197 (t-100) cc_final: 0.6666 (t60)
REVERT: A  465 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.7323 (tt0)
REVERT: B   43 GLU cc_start: 0.8062 (tt0) cc_final: 0.7673 (tp30)
REVERT: B   88 THR cc_start: 0.8657 (t) cc_final: 0.8396 (p)
REVERT: B  135 GLN cc_start: 0.8472 (OUTLIER) cc_final: 0.8234 (mp10)
REVERT: B  220 ARG cc_start: 0.7713 (mtm180) cc_final: 0.7214 (mmt180)
REVERT: B  228 GLU cc_start: 0.7883 (mt-10) cc_final: 0.7478 (mm-30)
REVERT: B  353 ASP cc_start: 0.7245 (m-30) cc_final: 0.6793 (m-30)
REVERT: B  485 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.8156 (tt)
  outliers start: 33
  outliers final: 17
  residues processed: 115
  average time/residue: 1.1388
  time to fit residues: 139.5559
Evaluate side-chains
  114 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 91
  time to evaluate  : 0.859 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue    9 LEU
Chi-restraints excluded: chain A residue   43 GLU
Chi-restraints excluded: chain A residue   46 GLN
Chi-restraints excluded: chain A residue  219 MET
Chi-restraints excluded: chain A residue  230 ASN
Chi-restraints excluded: chain A residue  280 SER
Chi-restraints excluded: chain A residue  349 LEU
Chi-restraints excluded: chain A residue  391 HIS
Chi-restraints excluded: chain A residue  393 ASP
Chi-restraints excluded: chain A residue  465 GLU
Chi-restraints excluded: chain A residue  477 THR
Chi-restraints excluded: chain A residue  492 LEU
Chi-restraints excluded: chain B residue   31 THR
Chi-restraints excluded: chain B residue   54 SER
Chi-restraints excluded: chain B residue   62 GLU
Chi-restraints excluded: chain B residue   67 GLU
Chi-restraints excluded: chain B residue   83 SER
Chi-restraints excluded: chain B residue  101 SER
Chi-restraints excluded: chain B residue  135 GLN
Chi-restraints excluded: chain B residue  186 LEU
Chi-restraints excluded: chain B residue  391 HIS
Chi-restraints excluded: chain B residue  485 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 44 optimal weight:    6.9990
   chunk 66 optimal weight:    0.7980
   chunk 43 optimal weight:    0.9990
   chunk 75 optimal weight:    0.9980
   chunk 35 optimal weight:    4.9990
   chunk 3 optimal weight:    2.9990
   chunk 34 optimal weight:   10.0000
   chunk 59 optimal weight:    1.9990
   chunk 12 optimal weight:    0.8980
   chunk 13 optimal weight:    0.7980
   chunk 86 optimal weight:    3.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
** A 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 188 GLN
B 391 HIS

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 = 0.190548 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.132681 restraints weight = 9146.901|
|-----------------------------------------------------------------------------|
r_work (start): 0.3590 rms_B_bonded: 2.30
r_work: 0.3458 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.3323 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.3323
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8143
moved from start:          0.3053

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8028  Z= 0.253
  Angle     :  0.545  11.976  10912  Z= 0.279
  Chirality :  0.044   0.177   1188
  Planarity :  0.004   0.036   1434
  Dihedral  :  6.590  74.046   1142
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 5.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.63 %
    Favored  : 98.37 %
  Rotamer:
    Outliers :  3.82 %
    Allowed  : 15.63 %
    Favored  : 80.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.60 (0.27), residues: 980
  helix:  2.29 (0.27), residues: 360
  sheet:  0.53 (0.41), residues: 172
  loop :  0.35 (0.30), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 426 
 HIS   0.009   0.001   HIS B 391 
 PHE   0.012   0.001   PHE B 295 
 TYR   0.010   0.002   TYR A  58 
 ARG   0.006   0.000   ARG B 321 

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

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

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 89
  time to evaluate  : 0.937 
Fit side-chains
REVERT: A    9 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7678 (mp)
REVERT: A   73 GLU cc_start: 0.7252 (mm-30) cc_final: 0.7034 (tm-30)
REVERT: A  219 MET cc_start: 0.6628 (OUTLIER) cc_final: 0.5866 (mmt)
REVERT: A  395 TRP cc_start: 0.7234 (t-100) cc_final: 0.6707 (t60)
REVERT: A  465 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.7352 (tt0)
REVERT: B   43 GLU cc_start: 0.8132 (tt0) cc_final: 0.7727 (tp30)
REVERT: B   88 THR cc_start: 0.8691 (t) cc_final: 0.8427 (p)
REVERT: B  135 GLN cc_start: 0.8483 (OUTLIER) cc_final: 0.8213 (mp10)
REVERT: B  220 ARG cc_start: 0.7784 (mtm180) cc_final: 0.7291 (mmt180)
REVERT: B  353 ASP cc_start: 0.7368 (m-30) cc_final: 0.6962 (m-30)
REVERT: B  485 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.8146 (tt)
  outliers start: 32
  outliers final: 18
  residues processed: 112
  average time/residue: 1.1852
  time to fit residues: 142.1062
Evaluate side-chains
  110 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 87
  time to evaluate  : 0.892 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue    9 LEU
Chi-restraints excluded: chain A residue   45 ILE
Chi-restraints excluded: chain A residue  219 MET
Chi-restraints excluded: chain A residue  230 ASN
Chi-restraints excluded: chain A residue  243 VAL
Chi-restraints excluded: chain A residue  280 SER
Chi-restraints excluded: chain A residue  349 LEU
Chi-restraints excluded: chain A residue  391 HIS
Chi-restraints excluded: chain A residue  393 ASP
Chi-restraints excluded: chain A residue  465 GLU
Chi-restraints excluded: chain A residue  477 THR
Chi-restraints excluded: chain B residue   31 THR
Chi-restraints excluded: chain B residue   54 SER
Chi-restraints excluded: chain B residue   62 GLU
Chi-restraints excluded: chain B residue   67 GLU
Chi-restraints excluded: chain B residue   83 SER
Chi-restraints excluded: chain B residue  101 SER
Chi-restraints excluded: chain B residue  135 GLN
Chi-restraints excluded: chain B residue  186 LEU
Chi-restraints excluded: chain B residue  391 HIS
Chi-restraints excluded: chain B residue  477 THR
Chi-restraints excluded: chain B residue  485 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 27 optimal weight:    1.9990
   chunk 79 optimal weight:    0.7980
   chunk 96 optimal weight:    3.9990
   chunk 4 optimal weight:    0.9990
   chunk 68 optimal weight:    0.5980
   chunk 59 optimal weight:    0.7980
   chunk 28 optimal weight:    0.7980
   chunk 31 optimal weight:    0.5980
   chunk 72 optimal weight:    0.5980
   chunk 93 optimal weight:    5.9990
   chunk 63 optimal weight:    0.9980
   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 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 391 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4253 r_free = 0.4253 target = 0.191575 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.133411 restraints weight = 9153.433|
|-----------------------------------------------------------------------------|
r_work (start): 0.3600 rms_B_bonded: 2.32
r_work: 0.3468 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.3334 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.3334
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8132
moved from start:          0.3129

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8028  Z= 0.208
  Angle     :  0.521  10.630  10912  Z= 0.268
  Chirality :  0.043   0.196   1188
  Planarity :  0.004   0.034   1434
  Dihedral  :  6.552  69.486   1142
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 5.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.43 %
    Favored  : 98.57 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 16.59 %
    Favored  : 79.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.61 (0.27), residues: 980
  helix:  2.35 (0.27), residues: 360
  sheet:  0.48 (0.42), residues: 172
  loop :  0.35 (0.30), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 426 
 HIS   0.007   0.001   HIS B 391 
 PHE   0.010   0.001   PHE B 295 
 TYR   0.010   0.001   TYR B 286 
 ARG   0.006   0.000   ARG B 321 

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

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

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 89
  time to evaluate  : 0.946 
Fit side-chains
REVERT: A    9 LEU cc_start: 0.8066 (OUTLIER) cc_final: 0.7634 (mp)
REVERT: A   46 GLN cc_start: 0.8344 (OUTLIER) cc_final: 0.7614 (tp40)
REVERT: A   73 GLU cc_start: 0.7287 (mm-30) cc_final: 0.7043 (tm-30)
REVERT: A  219 MET cc_start: 0.6645 (OUTLIER) cc_final: 0.5887 (mmt)
REVERT: A  395 TRP cc_start: 0.7160 (t-100) cc_final: 0.6647 (t60)
REVERT: A  465 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7357 (tt0)
REVERT: B   43 GLU cc_start: 0.8112 (tt0) cc_final: 0.7702 (tp30)
REVERT: B   88 THR cc_start: 0.8706 (t) cc_final: 0.8436 (p)
REVERT: B  135 GLN cc_start: 0.8462 (OUTLIER) cc_final: 0.8207 (mp10)
REVERT: B  220 ARG cc_start: 0.7774 (mtm180) cc_final: 0.7344 (mmt180)
REVERT: B  353 ASP cc_start: 0.7364 (m-30) cc_final: 0.6964 (m-30)
  outliers start: 31
  outliers final: 15
  residues processed: 113
  average time/residue: 1.1365
  time to fit residues: 137.0011
Evaluate side-chains
  109 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 89
  time to evaluate  : 0.860 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue    9 LEU
Chi-restraints excluded: chain A residue   45 ILE
Chi-restraints excluded: chain A residue   46 GLN
Chi-restraints excluded: chain A residue  219 MET
Chi-restraints excluded: chain A residue  230 ASN
Chi-restraints excluded: chain A residue  243 VAL
Chi-restraints excluded: chain A residue  280 SER
Chi-restraints excluded: chain A residue  349 LEU
Chi-restraints excluded: chain A residue  391 HIS
Chi-restraints excluded: chain A residue  393 ASP
Chi-restraints excluded: chain A residue  465 GLU
Chi-restraints excluded: chain A residue  477 THR
Chi-restraints excluded: chain B residue   31 THR
Chi-restraints excluded: chain B residue   54 SER
Chi-restraints excluded: chain B residue   83 SER
Chi-restraints excluded: chain B residue  101 SER
Chi-restraints excluded: chain B residue  135 GLN
Chi-restraints excluded: chain B residue  186 LEU
Chi-restraints excluded: chain B residue  391 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 74 optimal weight:    1.9990
   chunk 69 optimal weight:    0.5980
   chunk 10 optimal weight:    0.7980
   chunk 16 optimal weight:    0.4980
   chunk 71 optimal weight:    0.4980
   chunk 11 optimal weight:    0.5980
   chunk 59 optimal weight:    0.7980
   chunk 2 optimal weight:    0.6980
   chunk 78 optimal weight:    0.5980
   chunk 28 optimal weight:    0.0570
   chunk 86 optimal weight:    2.9990
   overall best weight:    0.4498

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

Flipped N/Q/H residues before XYZ refinement:
A 277 HIS
** A 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 188 GLN
B 391 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4266 r_free = 0.4266 target = 0.192157 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.132877 restraints weight = 9266.090|
|-----------------------------------------------------------------------------|
r_work (start): 0.3629 rms_B_bonded: 2.40
r_work: 0.3503 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3369 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.3369
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8130
moved from start:          0.3284

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   8028  Z= 0.173
  Angle     :  0.535   9.701  10912  Z= 0.272
  Chirality :  0.043   0.213   1188
  Planarity :  0.004   0.051   1434
  Dihedral  :  6.490  64.730   1142
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 6.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.53 %
    Favored  : 98.47 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 17.66 %
    Favored  : 79.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.68 (0.28), residues: 980
  helix:  2.41 (0.27), residues: 362
  sheet:  0.57 (0.42), residues: 172
  loop :  0.33 (0.31), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 423 
 HIS   0.009   0.001   HIS B 391 
 PHE   0.008   0.001   PHE B 295 
 TYR   0.014   0.001   TYR A  58 
 ARG   0.006   0.000   ARG B 321 

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

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

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 93
  time to evaluate  : 0.834 
Fit side-chains
REVERT: A    9 LEU cc_start: 0.8027 (OUTLIER) cc_final: 0.7630 (mp)
REVERT: A   46 GLN cc_start: 0.8323 (OUTLIER) cc_final: 0.7608 (tp40)
REVERT: A   73 GLU cc_start: 0.7314 (mm-30) cc_final: 0.7089 (tm-30)
REVERT: A  219 MET cc_start: 0.6638 (OUTLIER) cc_final: 0.5917 (mmt)
REVERT: A  395 TRP cc_start: 0.6973 (t-100) cc_final: 0.6554 (t60)
REVERT: A  465 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7374 (tt0)
REVERT: B   43 GLU cc_start: 0.8029 (tt0) cc_final: 0.7691 (tp30)
REVERT: B   88 THR cc_start: 0.8672 (t) cc_final: 0.8427 (p)
REVERT: B  135 GLN cc_start: 0.8494 (OUTLIER) cc_final: 0.8264 (mp10)
REVERT: B  220 ARG cc_start: 0.7685 (mtm180) cc_final: 0.7301 (mmt180)
  outliers start: 24
  outliers final: 16
  residues processed: 112
  average time/residue: 1.1888
  time to fit residues: 141.6865
Evaluate side-chains
  106 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 85
  time to evaluate  : 0.979 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue    9 LEU
Chi-restraints excluded: chain A residue   46 GLN
Chi-restraints excluded: chain A residue  219 MET
Chi-restraints excluded: chain A residue  230 ASN
Chi-restraints excluded: chain A residue  243 VAL
Chi-restraints excluded: chain A residue  280 SER
Chi-restraints excluded: chain A residue  349 LEU
Chi-restraints excluded: chain A residue  391 HIS
Chi-restraints excluded: chain A residue  393 ASP
Chi-restraints excluded: chain A residue  465 GLU
Chi-restraints excluded: chain A residue  477 THR
Chi-restraints excluded: chain B residue   31 THR
Chi-restraints excluded: chain B residue   54 SER
Chi-restraints excluded: chain B residue   67 GLU
Chi-restraints excluded: chain B residue   83 SER
Chi-restraints excluded: chain B residue  101 SER
Chi-restraints excluded: chain B residue  135 GLN
Chi-restraints excluded: chain B residue  186 LEU
Chi-restraints excluded: chain B residue  392 THR
Chi-restraints excluded: chain B residue  477 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 33 optimal weight:    3.9990
   chunk 66 optimal weight:    0.8980
   chunk 55 optimal weight:    0.8980
   chunk 64 optimal weight:    0.7980
   chunk 60 optimal weight:    3.9990
   chunk 74 optimal weight:    1.9990
   chunk 10 optimal weight:    2.9990
   chunk 68 optimal weight:    0.7980
   chunk 52 optimal weight:    0.9980
   chunk 22 optimal weight:    0.0570
   chunk 30 optimal weight:    0.8980
   overall best weight:    0.6898

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

Flipped N/Q/H residues before XYZ refinement:
A 226 ASN
** A 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 188 GLN
B 308 GLN
B 391 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4279 r_free = 0.4279 target = 0.191804 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.133371 restraints weight = 9160.333|
|-----------------------------------------------------------------------------|
r_work (start): 0.3625 rms_B_bonded: 2.32
r_work: 0.3498 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.3369 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.3369
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8147
moved from start:          0.3314

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8028  Z= 0.214
  Angle     :  0.534   9.169  10912  Z= 0.274
  Chirality :  0.044   0.208   1188
  Planarity :  0.004   0.046   1434
  Dihedral  :  6.512  62.209   1142
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 5.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.73 %
    Favored  : 98.27 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 18.02 %
    Favored  : 79.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.60 (0.27), residues: 980
  helix:  2.34 (0.27), residues: 362
  sheet:  0.53 (0.42), residues: 172
  loop :  0.30 (0.30), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 395 
 HIS   0.008   0.001   HIS B 391 
 PHE   0.010   0.001   PHE B 295 
 TYR   0.010   0.001   TYR B 286 
 ARG   0.016   0.000   ARG A  33 

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

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

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 89
  time to evaluate  : 0.855 
Fit side-chains
REVERT: A   46 GLN cc_start: 0.8329 (OUTLIER) cc_final: 0.7613 (tp40)
REVERT: A   73 GLU cc_start: 0.7346 (mm-30) cc_final: 0.7112 (tm-30)
REVERT: A  219 MET cc_start: 0.6626 (OUTLIER) cc_final: 0.5900 (mmt)
REVERT: A  395 TRP cc_start: 0.7017 (t-100) cc_final: 0.6621 (t60)
REVERT: A  465 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.7375 (tt0)
REVERT: B   88 THR cc_start: 0.8687 (t) cc_final: 0.8446 (p)
REVERT: B  135 GLN cc_start: 0.8471 (OUTLIER) cc_final: 0.8232 (mp10)
REVERT: B  220 ARG cc_start: 0.7663 (mtm180) cc_final: 0.7307 (mmt180)
REVERT: B  485 LEU cc_start: 0.8394 (tt) cc_final: 0.8181 (tt)
  outliers start: 23
  outliers final: 15
  residues processed: 108
  average time/residue: 1.1943
  time to fit residues: 137.2344
Evaluate side-chains
  106 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 87
  time to evaluate  : 0.969 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue   45 ILE
Chi-restraints excluded: chain A residue   46 GLN
Chi-restraints excluded: chain A residue  219 MET
Chi-restraints excluded: chain A residue  230 ASN
Chi-restraints excluded: chain A residue  243 VAL
Chi-restraints excluded: chain A residue  280 SER
Chi-restraints excluded: chain A residue  391 HIS
Chi-restraints excluded: chain A residue  393 ASP
Chi-restraints excluded: chain A residue  465 GLU
Chi-restraints excluded: chain A residue  477 THR
Chi-restraints excluded: chain B residue   31 THR
Chi-restraints excluded: chain B residue   54 SER
Chi-restraints excluded: chain B residue   83 SER
Chi-restraints excluded: chain B residue  101 SER
Chi-restraints excluded: chain B residue  135 GLN
Chi-restraints excluded: chain B residue  186 LEU
Chi-restraints excluded: chain B residue  391 HIS
Chi-restraints excluded: chain B residue  477 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 69 optimal weight:    0.2980
   chunk 96 optimal weight:    0.0570
   chunk 19 optimal weight:    0.0870
   chunk 60 optimal weight:    0.9990
   chunk 63 optimal weight:    0.8980
   chunk 6 optimal weight:    0.9980
   chunk 90 optimal weight:    0.9980
   chunk 21 optimal weight:    0.6980
   chunk 13 optimal weight:    0.7980
   chunk 45 optimal weight:    0.7980
   chunk 62 optimal weight:    0.0020
   overall best weight:    0.2284

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

Flipped N/Q/H residues before XYZ refinement:
B 188 GLN
B 391 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4263 r_free = 0.4263 target = 0.194474 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.143950 restraints weight = 9163.694|
|-----------------------------------------------------------------------------|
r_work (start): 0.3716 rms_B_bonded: 2.15
r_work: 0.3507 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.3376 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.3376
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8057
moved from start:          0.3470

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.047   8028  Z= 0.140
  Angle     :  0.503   7.535  10912  Z= 0.260
  Chirality :  0.042   0.201   1188
  Planarity :  0.004   0.029   1434
  Dihedral  :  6.442  58.333   1142
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 5.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.53 %
    Favored  : 98.47 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 18.74 %
    Favored  : 79.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.80 (0.28), residues: 980
  helix:  2.53 (0.26), residues: 362
  sheet:  0.71 (0.43), residues: 168
  loop :  0.36 (0.31), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 423 
 HIS   0.011   0.001   HIS B 391 
 PHE   0.009   0.001   PHE B 274 
 TYR   0.026   0.001   TYR A 190 
 ARG   0.007   0.000   ARG B 321 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6505.22 seconds
wall clock time: 115 minutes 20.15 seconds (6920.15 seconds total)