Starting phenix.real_space_refine
on Tue Jan 14 12:34:06 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xza_38791/01_2025/8xza_38791.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xza_38791/01_2025/8xza_38791.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.07
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xza_38791/01_2025/8xza_38791.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xza_38791/01_2025/8xza_38791.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xza_38791/01_2025/8xza_38791.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xza_38791/01_2025/8xza_38791.cif"
  }
  resolution = 4.07
  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=   0.040
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: 6
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     S      38      5.16       5
     Cl      1      4.86       5
     C    4202      2.51       5
     N    1083      2.21       5
     O    1240      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 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: 6565
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 1559
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 194, 1559
          Classifications: {'peptide': 194}
          Link IDs: {'PTRANS': 13, 'TRANS': 180}
    Chain: "A"
      Number of atoms: 4906
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 596, 4906
          Classifications: {'peptide': 596}
          Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 571}
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 72
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 72
          Unusual residues: {' CL': 1, ' ZN': 1, 'NAG': 5}
          Classifications: {'undetermined': 7}
          Link IDs: {None: 6}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 5
  Time building chain proxies: 4.67, per 1000 atoms: 0.71
  Number of scatterers: 6565
  At special positions: 0
  Unit cell: (79, 100, 109, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      1     29.99
     Cl      1     17.00
     S      38     16.00
     O    1240      8.00
     N    1083      7.00
     C    4202      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 336 " - pdb=" SG  CYS B 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 379 " - pdb=" SG  CYS B 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 391 " - pdb=" SG  CYS B 524 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 480 " - pdb=" SG  CYS B 487 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 343 " - pdb=" SG  CYS A 360 " distance=2.02

  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
  Links applied
    NAG-ASN
      " NAG A 902 " - " ASN A  53 "
      " NAG A 903 " - " ASN A  90 "
      " NAG A 904 " - " ASN A 298 "
      " NAG A 905 " - " ASN A 431 "
      " NAG A 906 " - " ASN A 545 "
      " NAG B1302 " - " ASN B 343 "
  Time building additional restraints: 2.02
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1494

  Finding SS restraints...
    Secondary structure from input PDB file:
      37 helices and 4 sheets defined
      56.2% alpha, 3.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.66
  Creating SS restraints...
    Processing helix  chain 'B' and resid 337 through 343
    Processing helix  chain 'B' and resid 366 through 371
    Processing helix  chain 'B' and resid 403 through 410
      removed outlier: 3.770A  pdb=" N   SER B 408 " --> pdb=" O   GLY B 404 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 20 through 53
      removed outlier: 3.590A  pdb=" N   GLN A  24 " --> pdb=" O   THR A  20 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 55 through 81
    Processing helix  chain 'A' and resid 82 through 83
      No H-bonds generated for 'chain 'A' and resid 82 through 83'
    Processing helix  chain 'A' and resid 84 through 88
      removed outlier: 3.870A  pdb=" N   GLU A  87 " --> pdb=" O   SER A  84 " (cutoff:3.500A)
      removed outlier: 3.980A  pdb=" N   ILE A  88 " --> pdb=" O   LEU A  85 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 84 through 88'
    Processing helix  chain 'A' and resid 90 through 102
      removed outlier: 3.509A  pdb=" N   HIS A 102 " --> pdb=" O   LYS A  98 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 103 through 108
    Processing helix  chain 'A' and resid 109 through 130
    Processing helix  chain 'A' and resid 145 through 154
    Processing helix  chain 'A' and resid 156 through 193
      removed outlier: 3.519A  pdb=" N   ARG A 160 " --> pdb=" O   ASP A 156 " (cutoff:3.500A)
      removed outlier: 3.949A  pdb=" N   LYS A 173 " --> pdb=" O   ALA A 169 " (cutoff:3.500A)
      Proline residue:  A 177  - end of helix
    Processing helix  chain 'A' and resid 197 through 204
    Processing helix  chain 'A' and resid 205 through 207
      No H-bonds generated for 'chain 'A' and resid 205 through 207'
    Processing helix  chain 'A' and resid 219 through 251
      Proline residue:  A 234  - end of helix
    Processing helix  chain 'A' and resid 264 through 266
      No H-bonds generated for 'chain 'A' and resid 264 through 266'
    Processing helix  chain 'A' and resid 274 through 276
      No H-bonds generated for 'chain 'A' and resid 274 through 276'
    Processing helix  chain 'A' and resid 277 through 282
    Processing helix  chain 'A' and resid 292 through 300
    Processing helix  chain 'A' and resid 302 through 316
    Processing helix  chain 'A' and resid 323 through 330
      removed outlier: 3.895A  pdb=" N   TRP A 327 " --> pdb=" O   THR A 323 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 364 through 384
      removed outlier: 3.630A  pdb=" N   PHE A 368 " --> pdb=" O   THR A 364 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   TYR A 384 " --> pdb=" O   TYR A 380 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 388 through 392
    Processing helix  chain 'A' and resid 398 through 412
      removed outlier: 3.667A  pdb=" N   ALA A 402 " --> pdb=" O   GLY A 398 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   MET A 407 " --> pdb=" O   VAL A 403 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   SER A 408 " --> pdb=" O   GLY A 404 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 413 through 420
      removed outlier: 3.665A  pdb=" N   LEU A 417 " --> pdb=" O   THR A 413 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 430 through 444
    Processing helix  chain 'A' and resid 447 through 465
      removed outlier: 4.615A  pdb=" N   PHE A 451 " --> pdb=" O   GLY A 447 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 471 through 483
    Processing helix  chain 'A' and resid 497 through 501
    Processing helix  chain 'A' and resid 502 through 507
    Processing helix  chain 'A' and resid 511 through 532
      removed outlier: 3.602A  pdb=" N   TYR A 515 " --> pdb=" O   PHE A 511 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   PHE A 522 " --> pdb=" O   THR A 518 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 537 through 541
    Processing helix  chain 'A' and resid 546 through 558
      removed outlier: 3.872A  pdb=" N   MET A 556 " --> pdb=" O   ARG A 552 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 564 through 571
    Processing helix  chain 'A' and resid 580 through 587
      removed outlier: 3.795A  pdb=" N   PHE A 587 " --> pdb=" O   LEU A 583 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 587 through 598
    Processing helix  chain 'A' and resid 599 through 601
      No H-bonds generated for 'chain 'A' and resid 599 through 601'
    Processing sheet with id=AA1, first strand: chain 'B' and resid 355 through 358
    Processing sheet with id=AA2, first strand: chain 'B' and resid 452 through 454
    Processing sheet with id=AA3, first strand: chain 'A' and resid 132 through 133
      removed outlier: 3.534A  pdb=" N   LEU A 141 " --> pdb=" O   VAL A 132 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 261 through 262
      removed outlier: 6.710A  pdb=" N   LEU A 261 " --> pdb=" O   VAL A 487 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4

    299 hydrogen bonds defined for protein.
    864 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: 1.78

  Time building geometry restraints manager: 2.32 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: 1198
        1.32 -     1.45: 1924
        1.45 -     1.57: 3570
        1.57 -     1.70: 0
        1.70 -     1.82: 60
  Bond restraints: 6752
  Sorted by residual:
  bond pdb=" CA  SER B 438 "
       pdb=" C   SER B 438 "
    ideal  model  delta    sigma   weight residual
    1.522  1.419  0.103 1.08e-02 8.57e+03 9.10e+01
  bond pdb=" CA  ALA B 352 "
       pdb=" C   ALA B 352 "
    ideal  model  delta    sigma   weight residual
    1.530  1.476  0.055 1.08e-02 8.57e+03 2.58e+01
  bond pdb=" CA  ASN B 439 "
       pdb=" C   ASN B 439 "
    ideal  model  delta    sigma   weight residual
    1.522  1.475  0.047 9.30e-03 1.16e+04 2.52e+01
  bond pdb=" CA  ARG B 466 "
       pdb=" C   ARG B 466 "
    ideal  model  delta    sigma   weight residual
    1.524  1.464  0.060 1.25e-02 6.40e+03 2.31e+01
  bond pdb=" CA  SER B 443 "
       pdb=" C   SER B 443 "
    ideal  model  delta    sigma   weight residual
    1.528  1.466  0.061 1.37e-02 5.33e+03 2.00e+01
  ... (remaining 6747 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.03: 8906
        3.03 -     6.07: 220
        6.07 -     9.10: 31
        9.10 -    12.13: 3
       12.13 -    15.17: 4
  Bond angle restraints: 9164
  Sorted by residual:
  angle pdb=" N   GLY B 447 "
        pdb=" CA  GLY B 447 "
        pdb=" C   GLY B 447 "
      ideal   model   delta    sigma   weight residual
     111.95  125.46  -13.51 9.50e-01 1.11e+00 2.02e+02
  angle pdb=" N   GLY B 482 "
        pdb=" CA  GLY B 482 "
        pdb=" C   GLY B 482 "
      ideal   model   delta    sigma   weight residual
     110.60  123.34  -12.74 1.46e+00 4.69e-01 7.62e+01
  angle pdb=" N   LYS B 481 "
        pdb=" CA  LYS B 481 "
        pdb=" C   LYS B 481 "
      ideal   model   delta    sigma   weight residual
     111.11  100.80   10.31 1.20e+00 6.94e-01 7.38e+01
  angle pdb=" N   ALA B 352 "
        pdb=" CA  ALA B 352 "
        pdb=" C   ALA B 352 "
      ideal   model   delta    sigma   weight residual
     107.32   93.57   13.75 1.65e+00 3.67e-01 6.94e+01
  angle pdb=" N   PHE B 400 "
        pdb=" CA  PHE B 400 "
        pdb=" C   PHE B 400 "
      ideal   model   delta    sigma   weight residual
     109.63  121.74  -12.11 1.49e+00 4.50e-01 6.61e+01
  ... (remaining 9159 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.80: 3803
       23.80 -    47.59: 221
       47.59 -    71.38: 28
       71.38 -    95.18: 9
       95.18 -   118.97: 14
  Dihedral angle restraints: 4075
    sinusoidal: 1746
      harmonic: 2329
  Sorted by residual:
  dihedral pdb=" CB  CYS B 480 "
           pdb=" SG  CYS B 480 "
           pdb=" SG  CYS B 487 "
           pdb=" CB  CYS B 487 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -158.70   72.70     1      1.00e+01 1.00e-02 6.75e+01
  dihedral pdb=" CB  CYS B 336 "
           pdb=" SG  CYS B 336 "
           pdb=" SG  CYS B 361 "
           pdb=" CB  CYS B 361 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   44.40   48.60     1      1.00e+01 1.00e-02 3.25e+01
  dihedral pdb=" CA  MET A  62 "
           pdb=" C   MET A  62 "
           pdb=" N   ASN A  63 "
           pdb=" CA  ASN A  63 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.82   26.18     0      5.00e+00 4.00e-02 2.74e+01
  ... (remaining 4072 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.075: 822
       0.075 -    0.150: 124
       0.150 -    0.225: 16
       0.225 -    0.300: 3
       0.300 -    0.375: 3
  Chirality restraints: 968
  Sorted by residual:
  chirality pdb=" C1  NAG A 902 "
            pdb=" ND2 ASN A  53 "
            pdb=" C2  NAG A 902 "
            pdb=" O5  NAG A 902 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.02   -0.38 2.00e-01 2.50e+01 3.52e+00
  chirality pdb=" C1  NAG A 904 "
            pdb=" ND2 ASN A 298 "
            pdb=" C2  NAG A 904 "
            pdb=" O5  NAG A 904 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.04   -0.36 2.00e-01 2.50e+01 3.28e+00
  chirality pdb=" CA  TRP B 353 "
            pdb=" N   TRP B 353 "
            pdb=" C   TRP B 353 "
            pdb=" CB  TRP B 353 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.20    0.31 2.00e-01 2.50e+01 2.34e+00
  ... (remaining 965 not shown)

  Planarity restraints: 1174
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG B1301 "    0.297 2.00e-02 2.50e+03   2.53e-01 8.02e+02
        pdb=" C7  NAG B1301 "   -0.069 2.00e-02 2.50e+03
        pdb=" C8  NAG B1301 "   -0.018 2.00e-02 2.50e+03
        pdb=" N2  NAG B1301 "   -0.425 2.00e-02 2.50e+03
        pdb=" O7  NAG B1301 "    0.215 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL B 350 "   -0.043 2.00e-02 2.50e+03   8.82e-02 7.78e+01
        pdb=" C   VAL B 350 "    0.152 2.00e-02 2.50e+03
        pdb=" O   VAL B 350 "   -0.059 2.00e-02 2.50e+03
        pdb=" N   TYR B 351 "   -0.050 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR B 345 "    0.031 2.00e-02 2.50e+03   6.23e-02 3.88e+01
        pdb=" C   THR B 345 "   -0.108 2.00e-02 2.50e+03
        pdb=" O   THR B 345 "    0.040 2.00e-02 2.50e+03
        pdb=" N   ARG B 346 "    0.037 2.00e-02 2.50e+03
  ... (remaining 1171 not shown)

  Histogram of nonbonded interaction distances:
        1.21 -     1.95: 4
        1.95 -     2.69: 278
        2.69 -     3.42: 10143
        3.42 -     4.16: 16088
        4.16 -     4.90: 27724
  Nonbonded interactions: 54237
  Sorted by model distance:
  nonbonded pdb=" CD2 TYR B 351 "
            pdb=" O   TRP B 452 "
     model   vdw
     1.212 3.340
  nonbonded pdb=" CZ3 TRP B 353 "
            pdb=" CB  ARG B 355 "
     model   vdw
     1.659 3.740
  nonbonded pdb=" CE2 TYR B 351 "
            pdb=" O   TRP B 452 "
     model   vdw
     1.746 3.340
  nonbonded pdb=" OH  TYR A 242 "
            pdb=" O   LEU A 594 "
     model   vdw
     1.927 3.040
  nonbonded pdb=" OG  SER B 349 "
            pdb=" CE2 TYR B 351 "
     model   vdw
     1.982 3.340
  ... (remaining 54232 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: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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 group one per residue
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:             3.730
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.300
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     19.470
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.030
  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:3.110
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.840
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7286
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      :  0.007   0.103   6752  Z= 0.440
  Angle     :  1.099  15.168   9164  Z= 0.641
  Chirality :  0.058   0.375    968
  Planarity :  0.010   0.253   1168
  Dihedral  : 16.313 118.973   2566
  Min Nonbonded Distance : 1.212

Molprobity Statistics.
  All-atom Clashscore : 30.95
  Ramachandran Plot:
    Outliers :  0.89 %
    Allowed  :  8.02 %
    Favored  : 91.09 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  2.02 %
    Favored  : 97.84 %
  Cbeta Deviations :  0.13 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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: -1.65 (0.28), residues: 786
  helix: -0.42 (0.25), residues: 393
  sheet: -0.89 (0.99), residues: 31
  loop : -1.85 (0.31), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.003   TRP A 164 
 HIS   0.008   0.001   HIS A 264 
 PHE   0.030   0.003   PHE A 437 
 TYR   0.055   0.003   TYR A 453 
 ARG   0.004   0.001   ARG A 558 

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 151
  time to evaluate  : 0.774 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  340 GLU cc_start: 0.7243 (mp0) cc_final: 0.6369 (tp30)
REVERT: B  514 PHE cc_start: 0.6054 (m-80) cc_final: 0.5758 (m-10)
REVERT: A  100 LEU cc_start: 0.8461 (mt) cc_final: 0.8260 (mt)
REVERT: A  248 MET cc_start: 0.7022 (ptm) cc_final: 0.6781 (ppp)
REVERT: A  455 LEU cc_start: 0.9450 (mt) cc_final: 0.9067 (mt)
REVERT: A  458 TRP cc_start: 0.7185 (m100) cc_final: 0.6846 (m100)
REVERT: A  557 LEU cc_start: 0.8950 (mt) cc_final: 0.8523 (mt)
  outliers start: 1
  outliers final: 0
  residues processed: 152
  average time/residue: 0.2011
  time to fit residues: 39.6805
Evaluate side-chains
  98 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.770 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 65 optimal weight:    0.8980
   chunk 59 optimal weight:    0.0770
   chunk 32 optimal weight:    6.9990
   chunk 20 optimal weight:    0.8980
   chunk 39 optimal weight:    5.9990
   chunk 31 optimal weight:    1.9990
   chunk 61 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   chunk 37 optimal weight:    0.8980
   chunk 45 optimal weight:    1.9990
   chunk 70 optimal weight:    8.9990
   overall best weight:    0.9540

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

Flipped N/Q/H residues before XYZ refinement:
B 354 ASN
** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 448 ASN
B 474 GLN
B 492 GLN
A  33 ASN
A  42 GLN
** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4178 r_free = 0.4178 target = 0.125572 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.101999 restraints weight = 21162.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.105123 restraints weight = 11791.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.107236 restraints weight = 7711.360|
|-----------------------------------------------------------------------------|
r_work (final): 0.3878
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7399
moved from start:          0.2053

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   6752  Z= 0.252
  Angle     :  0.765   7.915   9164  Z= 0.390
  Chirality :  0.050   0.385    968
  Planarity :  0.005   0.044   1168
  Dihedral  : 10.262 108.064   1016
  Min Nonbonded Distance : 2.367

Molprobity Statistics.
  All-atom Clashscore : 18.95
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.47 %
    Favored  : 94.40 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  6.64 %
    Favored  : 93.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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: -1.30 (0.29), residues: 786
  helix: -0.17 (0.25), residues: 397
  sheet: -0.35 (0.93), residues: 31
  loop : -1.68 (0.31), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.047   0.003   TRP B 353 
 HIS   0.006   0.001   HIS A 264 
 PHE   0.017   0.002   PHE B 347 
 TYR   0.047   0.003   TYR A 453 
 ARG   0.004   0.001   ARG B 466 

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 139
  time to evaluate  : 0.747 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  403 LYS cc_start: 0.7796 (mtmt) cc_final: 0.7299 (mtpt)
REVERT: B  499 THR cc_start: 0.8586 (p) cc_final: 0.8334 (p)
REVERT: A   79 MET cc_start: 0.8819 (tpp) cc_final: 0.8331 (tpp)
REVERT: A  100 LEU cc_start: 0.8722 (mt) cc_final: 0.8458 (mt)
REVERT: A  123 MET cc_start: 0.8248 (mtm) cc_final: 0.8006 (mtm)
REVERT: A  167 TRP cc_start: 0.4146 (m-90) cc_final: 0.3937 (t-100)
REVERT: A  248 MET cc_start: 0.7158 (ptm) cc_final: 0.6878 (ppp)
REVERT: A  455 LEU cc_start: 0.9567 (mt) cc_final: 0.9151 (mt)
REVERT: A  458 TRP cc_start: 0.7273 (m100) cc_final: 0.6810 (m100)
REVERT: A  479 MET cc_start: 0.8975 (ppp) cc_final: 0.8704 (ppp)
REVERT: A  516 THR cc_start: 0.8998 (p) cc_final: 0.8500 (p)
REVERT: A  557 LEU cc_start: 0.8958 (mt) cc_final: 0.8566 (mt)
REVERT: A  567 LEU cc_start: 0.9031 (tp) cc_final: 0.8815 (tp)
  outliers start: 1
  outliers final: 1
  residues processed: 140
  average time/residue: 0.1776
  time to fit residues: 33.3987
Evaluate side-chains
  108 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 107
  time to evaluate  : 0.724 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 8 optimal weight:    2.9990
   chunk 36 optimal weight:    8.9990
   chunk 24 optimal weight:    3.9990
   chunk 17 optimal weight:    1.9990
   chunk 61 optimal weight:    3.9990
   chunk 13 optimal weight:    3.9990
   chunk 48 optimal weight:    0.8980
   chunk 43 optimal weight:    4.9990
   chunk 42 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9990
   chunk 54 optimal weight:    4.9990
   overall best weight:    1.9788

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

Flipped N/Q/H residues before XYZ refinement:
** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 474 GLN
A  33 ASN
A  42 GLN
** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 299 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.118332 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.094275 restraints weight = 21660.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.097296 restraints weight = 11973.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.099305 restraints weight = 7845.473|
|-----------------------------------------------------------------------------|
r_work (final): 0.3739
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7605
moved from start:          0.3239

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.056   6752  Z= 0.354
  Angle     :  0.805  10.661   9164  Z= 0.414
  Chirality :  0.051   0.327    968
  Planarity :  0.005   0.045   1168
  Dihedral  :  9.539  98.811   1016
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 22.30
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  6.23 %
    Favored  : 93.64 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  5.63 %
    Favored  : 94.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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: -1.32 (0.29), residues: 786
  helix: -0.35 (0.25), residues: 408
  sheet: -0.26 (0.98), residues: 29
  loop : -1.49 (0.33), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.003   TRP B 353 
 HIS   0.008   0.001   HIS A 264 
 PHE   0.023   0.002   PHE B 347 
 TYR   0.075   0.003   TYR A 453 
 ARG   0.005   0.001   ARG B 457 

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 126
  time to evaluate  : 0.889 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  403 LYS cc_start: 0.7764 (mtmt) cc_final: 0.7132 (mtpt)
REVERT: B  499 THR cc_start: 0.8629 (p) cc_final: 0.8376 (p)
REVERT: A  100 LEU cc_start: 0.8714 (mt) cc_final: 0.8443 (mt)
REVERT: A  151 MET cc_start: 0.6401 (tpt) cc_final: 0.5826 (tpp)
REVERT: A  189 MET cc_start: 0.8845 (tmm) cc_final: 0.8412 (tmm)
REVERT: A  248 MET cc_start: 0.7448 (ptm) cc_final: 0.7206 (ppp)
REVERT: A  382 MET cc_start: 0.8776 (mtp) cc_final: 0.8502 (mtm)
REVERT: A  458 TRP cc_start: 0.7231 (m100) cc_final: 0.6771 (m100)
REVERT: A  479 MET cc_start: 0.9036 (ppp) cc_final: 0.8816 (ppp)
REVERT: A  516 THR cc_start: 0.9063 (p) cc_final: 0.8522 (p)
REVERT: A  567 LEU cc_start: 0.9042 (tp) cc_final: 0.8786 (tp)
REVERT: A  588 GLU cc_start: 0.8669 (mt-10) cc_final: 0.8119 (mm-30)
  outliers start: 1
  outliers final: 0
  residues processed: 127
  average time/residue: 0.2115
  time to fit residues: 36.9517
Evaluate side-chains
  96 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 0.644 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 0 optimal weight:    4.9990
   chunk 23 optimal weight:    0.7980
   chunk 49 optimal weight:    1.9990
   chunk 61 optimal weight:    0.8980
   chunk 14 optimal weight:    0.0370
   chunk 9 optimal weight:    0.8980
   chunk 47 optimal weight:    0.9990
   chunk 40 optimal weight:    0.7980
   chunk 41 optimal weight:    0.9990
   chunk 37 optimal weight:    4.9990
   chunk 65 optimal weight:    2.9990
   overall best weight:    0.6858

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

Flipped N/Q/H residues before XYZ refinement:
** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 492 GLN
** A  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 193 ASN
** A 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 264 HIS
A 525 HIS
A 551 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4122 r_free = 0.4122 target = 0.121748 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.098013 restraints weight = 21560.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.101094 restraints weight = 11951.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.103177 restraints weight = 7763.563|
|-----------------------------------------------------------------------------|
r_work (final): 0.3806
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7492
moved from start:          0.3729

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6752  Z= 0.223
  Angle     :  0.728   8.973   9164  Z= 0.368
  Chirality :  0.049   0.348    968
  Planarity :  0.005   0.049   1168
  Dihedral  :  8.660  91.059   1016
  Min Nonbonded Distance : 2.379

Molprobity Statistics.
  All-atom Clashscore : 16.30
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.71 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  2.60 %
    Favored  : 97.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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: -1.19 (0.29), residues: 786
  helix: -0.24 (0.25), residues: 402
  sheet: -0.37 (0.94), residues: 29
  loop : -1.41 (0.32), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.002   TRP B 353 
 HIS   0.008   0.001   HIS A 264 
 PHE   0.024   0.002   PHE B 456 
 TYR   0.043   0.002   TYR A 453 
 ARG   0.007   0.001   ARG A 305 

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 127
  time to evaluate  : 0.803 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  499 THR cc_start: 0.8480 (p) cc_final: 0.8190 (p)
REVERT: A  151 MET cc_start: 0.6715 (tpt) cc_final: 0.6353 (tpp)
REVERT: A  164 TRP cc_start: 0.6311 (m-90) cc_final: 0.5827 (m-90)
REVERT: A  248 MET cc_start: 0.7449 (ptm) cc_final: 0.7191 (ppp)
REVERT: A  322 MET cc_start: 0.7733 (mtt) cc_final: 0.7252 (mtt)
REVERT: A  453 TYR cc_start: 0.6018 (m-80) cc_final: 0.5682 (m-80)
REVERT: A  522 PHE cc_start: 0.8825 (m-10) cc_final: 0.8538 (m-10)
REVERT: A  557 LEU cc_start: 0.8997 (mm) cc_final: 0.8715 (mm)
REVERT: A  567 LEU cc_start: 0.9065 (tp) cc_final: 0.8838 (tp)
REVERT: A  588 GLU cc_start: 0.8589 (mt-10) cc_final: 0.8023 (mm-30)
  outliers start: 1
  outliers final: 0
  residues processed: 128
  average time/residue: 0.2019
  time to fit residues: 34.7082
Evaluate side-chains
  96 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 0.855 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 45 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9980
   chunk 41 optimal weight:    1.9990
   chunk 71 optimal weight:    1.9990
   chunk 21 optimal weight:    4.9990
   chunk 46 optimal weight:    0.0070
   chunk 14 optimal weight:    0.9980
   chunk 25 optimal weight:    3.9990
   chunk 26 optimal weight:    0.6980
   chunk 31 optimal weight:    0.9990
   chunk 34 optimal weight:    0.7980
   overall best weight:    0.6998

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

Flipped N/Q/H residues before XYZ refinement:
** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 379 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4130 r_free = 0.4130 target = 0.122564 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.098694 restraints weight = 21526.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.101822 restraints weight = 11651.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.103971 restraints weight = 7509.006|
|-----------------------------------------------------------------------------|
r_work (final): 0.3813
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7485
moved from start:          0.4053

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   6752  Z= 0.232
  Angle     :  0.741   8.965   9164  Z= 0.371
  Chirality :  0.051   0.457    968
  Planarity :  0.005   0.048   1168
  Dihedral  :  8.458  88.718   1016
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 18.79
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.96 %
    Favored  : 94.91 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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: -0.99 (0.29), residues: 786
  helix: -0.08 (0.25), residues: 393
  sheet: -0.45 (0.94), residues: 29
  loop : -1.26 (0.33), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.002   TRP A 460 
 HIS   0.003   0.001   HIS A 264 
 PHE   0.024   0.002   PHE A  28 
 TYR   0.043   0.002   TYR A 453 
 ARG   0.003   0.000   ARG A 459 

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 130
  time to evaluate  : 0.723 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  403 LYS cc_start: 0.7847 (mtmt) cc_final: 0.7601 (mtpt)
REVERT: B  424 LYS cc_start: 0.6957 (ttmt) cc_final: 0.6544 (tptt)
REVERT: B  499 THR cc_start: 0.8487 (p) cc_final: 0.8204 (p)
REVERT: A   62 MET cc_start: 0.8587 (ppp) cc_final: 0.8379 (ppp)
REVERT: A  151 MET cc_start: 0.6445 (tpt) cc_final: 0.6216 (tpp)
REVERT: A  164 TRP cc_start: 0.6539 (m-90) cc_final: 0.5901 (m-90)
REVERT: A  248 MET cc_start: 0.7447 (ptm) cc_final: 0.7195 (ppp)
REVERT: A  304 GLU cc_start: 0.6353 (tp30) cc_final: 0.6119 (tp30)
REVERT: A  308 LYS cc_start: 0.8706 (mmmm) cc_final: 0.8188 (mmtm)
REVERT: A  453 TYR cc_start: 0.5643 (m-80) cc_final: 0.4967 (m-80)
REVERT: A  557 LEU cc_start: 0.9106 (mm) cc_final: 0.8790 (mm)
REVERT: A  567 LEU cc_start: 0.9062 (tp) cc_final: 0.8854 (tp)
REVERT: A  588 GLU cc_start: 0.8646 (mt-10) cc_final: 0.8089 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 130
  average time/residue: 0.1741
  time to fit residues: 30.9943
Evaluate side-chains
  100 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.736 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 38 optimal weight:    0.0770
   chunk 48 optimal weight:    0.9990
   chunk 22 optimal weight:    0.0670
   chunk 53 optimal weight:    0.0980
   chunk 28 optimal weight:    3.9990
   chunk 73 optimal weight:    1.9990
   chunk 26 optimal weight:    4.9990
   chunk 36 optimal weight:    2.9990
   chunk 60 optimal weight:    0.9990
   chunk 45 optimal weight:    0.7980
   chunk 10 optimal weight:    0.7980
   overall best weight:    0.3676

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

Flipped N/Q/H residues before XYZ refinement:
B 409 GLN
B 448 ASN
** A  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 525 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4074 r_free = 0.4074 target = 0.121598 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.097793 restraints weight = 20493.210|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.101074 restraints weight = 11228.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.103274 restraints weight = 7232.665|
|-----------------------------------------------------------------------------|
r_work (final): 0.3749
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7424
moved from start:          0.4289

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   6752  Z= 0.206
  Angle     :  0.712   9.729   9164  Z= 0.362
  Chirality :  0.049   0.405    968
  Planarity :  0.004   0.048   1168
  Dihedral  :  7.883  77.512   1016
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 16.68
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.96 %
    Favored  : 94.91 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  2.16 %
    Favored  : 97.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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: -0.92 (0.29), residues: 786
  helix: -0.07 (0.25), residues: 402
  sheet: -0.42 (0.93), residues: 29
  loop : -1.19 (0.33), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.057   0.002   TRP A 167 
 HIS   0.005   0.001   HIS A 525 
 PHE   0.019   0.002   PHE A 229 
 TYR   0.039   0.002   TYR A  50 
 ARG   0.005   0.001   ARG A 168 

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 133
  time to evaluate  : 0.767 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  424 LYS cc_start: 0.6944 (ttmt) cc_final: 0.6507 (tptt)
REVERT: B  499 THR cc_start: 0.8443 (p) cc_final: 0.8165 (p)
REVERT: A   30 GLU cc_start: 0.8531 (mp0) cc_final: 0.8293 (mp0)
REVERT: A  151 MET cc_start: 0.6497 (tpt) cc_final: 0.6246 (tpp)
REVERT: A  164 TRP cc_start: 0.6889 (m-90) cc_final: 0.6648 (m-90)
REVERT: A  248 MET cc_start: 0.7468 (ptm) cc_final: 0.7226 (ppp)
REVERT: A  308 LYS cc_start: 0.8574 (mmmm) cc_final: 0.8049 (mmtm)
REVERT: A  326 PHE cc_start: 0.6441 (m-80) cc_final: 0.5506 (m-80)
REVERT: A  446 VAL cc_start: 0.8767 (m) cc_final: 0.8445 (p)
REVERT: A  453 TYR cc_start: 0.5441 (m-80) cc_final: 0.4900 (m-80)
REVERT: A  557 LEU cc_start: 0.8867 (mm) cc_final: 0.8499 (mm)
REVERT: A  588 GLU cc_start: 0.8624 (mt-10) cc_final: 0.8062 (mm-30)
  outliers start: 1
  outliers final: 0
  residues processed: 134
  average time/residue: 0.1887
  time to fit residues: 34.1963
Evaluate side-chains
  94 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 0.778 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 5 optimal weight:    0.2980
   chunk 67 optimal weight:    0.9990
   chunk 77 optimal weight:    4.9990
   chunk 73 optimal weight:    1.9990
   chunk 71 optimal weight:    0.9990
   chunk 1 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9980
   chunk 52 optimal weight:    2.9990
   chunk 18 optimal weight:    2.9990
   chunk 50 optimal weight:    0.0170
   chunk 6 optimal weight:    0.9980
   overall best weight:    0.6620

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

Flipped N/Q/H residues before XYZ refinement:
** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 523 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4148 r_free = 0.4148 target = 0.123428 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.100070 restraints weight = 21341.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.103131 restraints weight = 11589.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.105192 restraints weight = 7532.206|
|-----------------------------------------------------------------------------|
r_work (final): 0.3830
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7462
moved from start:          0.4594

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   6752  Z= 0.205
  Angle     :  0.721  10.699   9164  Z= 0.361
  Chirality :  0.050   0.472    968
  Planarity :  0.004   0.047   1168
  Dihedral  :  7.608  57.734   1016
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 16.45
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.09 %
    Favored  : 94.78 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  2.16 %
    Favored  : 97.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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: -0.92 (0.29), residues: 786
  helix: -0.10 (0.25), residues: 415
  sheet: -0.40 (0.96), residues: 29
  loop : -1.17 (0.34), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.002   TRP B 353 
 HIS   0.006   0.001   HIS A 525 
 PHE   0.023   0.002   PHE A 229 
 TYR   0.050   0.002   TYR A  50 
 ARG   0.003   0.000   ARG A 459 

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 123
  time to evaluate  : 1.005 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  424 LYS cc_start: 0.7134 (ttmt) cc_final: 0.6606 (tptt)
REVERT: B  499 THR cc_start: 0.8473 (p) cc_final: 0.8190 (p)
REVERT: A   30 GLU cc_start: 0.8594 (mp0) cc_final: 0.8298 (mp0)
REVERT: A  151 MET cc_start: 0.6382 (tpt) cc_final: 0.6163 (tpp)
REVERT: A  248 MET cc_start: 0.7538 (ptm) cc_final: 0.7313 (ppp)
REVERT: A  302 ASP cc_start: 0.8136 (t70) cc_final: 0.7886 (t70)
REVERT: A  308 LYS cc_start: 0.8700 (mmmm) cc_final: 0.8163 (mmtm)
REVERT: A  326 PHE cc_start: 0.6278 (m-80) cc_final: 0.6009 (m-80)
REVERT: A  446 VAL cc_start: 0.8856 (m) cc_final: 0.8620 (p)
REVERT: A  453 TYR cc_start: 0.4904 (m-80) cc_final: 0.4315 (m-80)
REVERT: A  588 GLU cc_start: 0.8689 (mt-10) cc_final: 0.8120 (mm-30)
  outliers start: 1
  outliers final: 0
  residues processed: 124
  average time/residue: 0.1750
  time to fit residues: 29.9153
Evaluate side-chains
  103 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.742 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 10 optimal weight:    0.2980
   chunk 65 optimal weight:    4.9990
   chunk 8 optimal weight:    0.8980
   chunk 60 optimal weight:    4.9990
   chunk 55 optimal weight:    2.9990
   chunk 24 optimal weight:    0.8980
   chunk 20 optimal weight:    3.9990
   chunk 23 optimal weight:    0.7980
   chunk 28 optimal weight:    2.9990
   chunk 70 optimal weight:    4.9990
   chunk 57 optimal weight:    1.9990
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  58 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 = 0.4029 r_free = 0.4029 target = 0.118666 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.095754 restraints weight = 20191.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.098816 restraints weight = 11165.264|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.100863 restraints weight = 7197.603|
|-----------------------------------------------------------------------------|
r_work (final): 0.3703
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7497
moved from start:          0.4851

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   6752  Z= 0.237
  Angle     :  0.753  10.419   9164  Z= 0.380
  Chirality :  0.051   0.416    968
  Planarity :  0.004   0.046   1168
  Dihedral  :  7.037  55.330   1016
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 18.79
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.22 %
    Favored  : 94.66 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.30 %
    Favored  : 98.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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: -0.96 (0.29), residues: 786
  helix: -0.16 (0.25), residues: 413
  sheet: -0.34 (1.01), residues: 30
  loop : -1.16 (0.34), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.074   0.003   TRP A 167 
 HIS   0.006   0.001   HIS A 525 
 PHE   0.027   0.002   PHE A 229 
 TYR   0.042   0.002   TYR A 453 
 ARG   0.003   0.001   ARG A 305 

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 126
  time to evaluate  : 0.747 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  499 THR cc_start: 0.8510 (p) cc_final: 0.8236 (p)
REVERT: A  151 MET cc_start: 0.6444 (tpt) cc_final: 0.6179 (tpp)
REVERT: A  164 TRP cc_start: 0.6955 (m-90) cc_final: 0.6702 (m-90)
REVERT: A  189 MET cc_start: 0.8829 (tmm) cc_final: 0.8141 (tmm)
REVERT: A  248 MET cc_start: 0.7654 (ptm) cc_final: 0.7421 (ppp)
REVERT: A  308 LYS cc_start: 0.8729 (mmmm) cc_final: 0.8094 (mmtm)
REVERT: A  446 VAL cc_start: 0.8828 (m) cc_final: 0.8573 (p)
REVERT: A  451 PHE cc_start: 0.9092 (t80) cc_final: 0.8865 (t80)
REVERT: A  453 TYR cc_start: 0.5039 (m-80) cc_final: 0.4267 (m-80)
REVERT: A  455 LEU cc_start: 0.9441 (mt) cc_final: 0.9216 (mt)
REVERT: A  588 GLU cc_start: 0.8756 (mt-10) cc_final: 0.8150 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 126
  average time/residue: 0.1753
  time to fit residues: 30.2428
Evaluate side-chains
  100 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.793 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 21 optimal weight:    4.9990
   chunk 28 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   chunk 36 optimal weight:    9.9990
   chunk 1 optimal weight:    0.3980
   chunk 68 optimal weight:    3.9990
   chunk 59 optimal weight:    2.9990
   chunk 2 optimal weight:    0.7980
   chunk 60 optimal weight:    2.9990
   chunk 15 optimal weight:    5.9990
   chunk 61 optimal weight:    2.9990
   overall best weight:    1.6386

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

Flipped N/Q/H residues before XYZ refinement:
** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 477 ASN
** A  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 193 ASN
A 400 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.115671 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.092924 restraints weight = 20125.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.096007 restraints weight = 11010.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.097990 restraints weight = 6997.098|
|-----------------------------------------------------------------------------|
r_work (final): 0.3640
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7587
moved from start:          0.5196

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.059   6752  Z= 0.313
  Angle     :  0.820  10.194   9164  Z= 0.418
  Chirality :  0.053   0.397    968
  Planarity :  0.005   0.046   1168
  Dihedral  :  7.031  55.473   1016
  Min Nonbonded Distance : 2.160

Molprobity Statistics.
  All-atom Clashscore : 22.30
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  6.11 %
    Favored  : 93.77 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  1.15 %
    Favored  : 98.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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: -1.20 (0.29), residues: 786
  helix: -0.30 (0.24), residues: 406
  sheet: -1.06 (0.86), residues: 40
  loop : -1.27 (0.34), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.068   0.003   TRP A 167 
 HIS   0.006   0.001   HIS A 525 
 PHE   0.040   0.003   PHE B 347 
 TYR   0.062   0.003   TYR A  50 
 ARG   0.003   0.000   ARG A  95 

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 129
  time to evaluate  : 0.805 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  499 THR cc_start: 0.8486 (p) cc_final: 0.8245 (p)
REVERT: A   30 GLU cc_start: 0.8817 (mp0) cc_final: 0.8386 (mp0)
REVERT: A  151 MET cc_start: 0.6494 (tpt) cc_final: 0.6157 (tpp)
REVERT: A  164 TRP cc_start: 0.6921 (m-90) cc_final: 0.6247 (m-90)
REVERT: A  248 MET cc_start: 0.7700 (ptm) cc_final: 0.7447 (ppp)
REVERT: A  304 GLU cc_start: 0.6688 (tp30) cc_final: 0.6272 (tp30)
REVERT: A  308 LYS cc_start: 0.8752 (mmmm) cc_final: 0.8439 (mmmt)
REVERT: A  451 PHE cc_start: 0.9127 (t80) cc_final: 0.8871 (t80)
REVERT: A  453 TYR cc_start: 0.5221 (m-80) cc_final: 0.4357 (m-80)
REVERT: A  455 LEU cc_start: 0.9441 (mt) cc_final: 0.9210 (mt)
REVERT: A  588 GLU cc_start: 0.8904 (mt-10) cc_final: 0.8291 (mm-30)
  outliers start: 1
  outliers final: 0
  residues processed: 130
  average time/residue: 0.1938
  time to fit residues: 33.5168
Evaluate side-chains
  99 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.745 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 48 optimal weight:    0.4980
   chunk 39 optimal weight:    1.9990
   chunk 12 optimal weight:    3.9990
   chunk 22 optimal weight:    0.5980
   chunk 62 optimal weight:    1.9990
   chunk 66 optimal weight:    0.8980
   chunk 20 optimal weight:    1.9990
   chunk 75 optimal weight:    3.9990
   chunk 28 optimal weight:    0.7980
   chunk 13 optimal weight:    0.0970
   chunk 9 optimal weight:    0.8980
   overall best weight:    0.5778

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

Flipped N/Q/H residues before XYZ refinement:
** A  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 193 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4020 r_free = 0.4020 target = 0.117874 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.094845 restraints weight = 20139.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.097916 restraints weight = 10930.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.100061 restraints weight = 6983.046|
|-----------------------------------------------------------------------------|
r_work (final): 0.3689
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7500
moved from start:          0.5273

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061   6752  Z= 0.228
  Angle     :  0.760   8.655   9164  Z= 0.387
  Chirality :  0.051   0.416    968
  Planarity :  0.004   0.047   1168
  Dihedral  :  6.649  56.662   1016
  Min Nonbonded Distance : 2.223

Molprobity Statistics.
  All-atom Clashscore : 19.41
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.73 %
    Favored  : 94.15 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.29 %
    Favored  : 99.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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: -1.01 (0.30), residues: 786
  helix: -0.08 (0.26), residues: 394
  sheet: -0.96 (0.86), residues: 40
  loop : -1.23 (0.34), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.071   0.003   TRP A 167 
 HIS   0.005   0.001   HIS A 525 
 PHE   0.038   0.002   PHE A 326 
 TYR   0.047   0.003   TYR A  50 
 ARG   0.003   0.000   ARG A 203 

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 129
  time to evaluate  : 0.776 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  499 THR cc_start: 0.8341 (p) cc_final: 0.8066 (p)
REVERT: A   30 GLU cc_start: 0.8707 (mp0) cc_final: 0.8214 (mp0)
REVERT: A  151 MET cc_start: 0.6395 (tpt) cc_final: 0.6104 (tpp)
REVERT: A  164 TRP cc_start: 0.6902 (m-90) cc_final: 0.6225 (m-90)
REVERT: A  248 MET cc_start: 0.7664 (ptm) cc_final: 0.7441 (ppp)
REVERT: A  304 GLU cc_start: 0.6673 (tp30) cc_final: 0.6369 (tp30)
REVERT: A  308 LYS cc_start: 0.8711 (mmmm) cc_final: 0.8317 (mmtm)
REVERT: A  322 MET cc_start: 0.6913 (mmm) cc_final: 0.6525 (mmm)
REVERT: A  453 TYR cc_start: 0.4771 (m-80) cc_final: 0.4426 (m-80)
REVERT: A  517 ARG cc_start: 0.8541 (ttp80) cc_final: 0.8305 (ttm170)
REVERT: A  588 GLU cc_start: 0.8861 (mt-10) cc_final: 0.8243 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 129
  average time/residue: 0.1936
  time to fit residues: 33.3502
Evaluate side-chains
  99 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.761 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 42 optimal weight:    0.0270
   chunk 14 optimal weight:    0.0170
   chunk 49 optimal weight:    0.4980
   chunk 75 optimal weight:    0.8980
   chunk 19 optimal weight:    0.6980
   chunk 61 optimal weight:    4.9990
   chunk 70 optimal weight:    3.9990
   chunk 37 optimal weight:    4.9990
   chunk 73 optimal weight:    0.9980
   chunk 65 optimal weight:    0.7980
   chunk 77 optimal weight:    7.9990
   overall best weight:    0.4076

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

Flipped N/Q/H residues before XYZ refinement:
** A  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 121 ASN
** A 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 598 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 = 0.4047 r_free = 0.4047 target = 0.119938 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.097793 restraints weight = 20012.660|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.101131 restraints weight = 10615.176|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.103327 restraints weight = 6561.881|
|-----------------------------------------------------------------------------|
r_work (final): 0.3735
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7429
moved from start:          0.5485

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6752  Z= 0.204
  Angle     :  0.730   8.719   9164  Z= 0.371
  Chirality :  0.051   0.382    968
  Planarity :  0.004   0.047   1168
  Dihedral  :  6.352  56.342   1016
  Min Nonbonded Distance : 2.250

Molprobity Statistics.
  All-atom Clashscore : 17.54
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.22 %
    Favored  : 94.66 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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: -0.94 (0.30), residues: 786
  helix: -0.09 (0.26), residues: 394
  sheet: -0.61 (0.86), residues: 39
  loop : -1.15 (0.34), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.068   0.003   TRP A 167 
 HIS   0.002   0.001   HIS A 377 
 PHE   0.024   0.002   PHE A 229 
 TYR   0.046   0.002   TYR A  50 
 ARG   0.003   0.000   ARG A 305 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2469.11 seconds
wall clock time: 46 minutes 5.37 seconds (2765.37 seconds total)