Starting phenix.real_space_refine
on Tue Mar 11 20:29:57 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xza_38791/03_2025/8xza_38791.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xza_38791/03_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_38791/03_2025/8xza_38791.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xza_38791/03_2025/8xza_38791.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xza_38791/03_2025/8xza_38791.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xza_38791/03_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-5624/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: 4.80, per 1000 atoms: 0.73
  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: 1.58
  Conformation dependent library (CDL) restraints added in 828.3 milliseconds
  

  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: 0.58
  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: 1.58

  Time building geometry restraints manager: 1.89 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:             2.970
  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:          0.230
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     18.860
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.760
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.020
-------------------------------------------------------------------------------
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  : 0.692 
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: 0.2013
  time to fit residues: 39.7881
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  : 0.751 
-------------------------------------------------------------------------------
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 = 52)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.102000 restraints weight = 21162.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.105144 restraints weight = 11779.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.107241 restraints weight = 7694.183|
|-----------------------------------------------------------------------------|
r_work (final): 0.3878
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7398
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  : 0.785 
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: 0.7300 (mtpt)
REVERT: B  499 THR cc_start: 0.8584 (p) cc_final: 0.8331 (p)
REVERT: A   79 MET cc_start: 0.8819 (tpp) cc_final: 0.8332 (tpp)
REVERT: A  100 LEU cc_start: 0.8724 (mt) cc_final: 0.8459 (mt)
REVERT: A  123 MET cc_start: 0.8242 (mtm) cc_final: 0.8001 (mtm)
REVERT: A  167 TRP cc_start: 0.4144 (m-90) cc_final: 0.3937 (t-100)
REVERT: A  248 MET cc_start: 0.7159 (ptm) cc_final: 0.6878 (ppp)
REVERT: A  455 LEU cc_start: 0.9568 (mt) cc_final: 0.9150 (mt)
REVERT: A  458 TRP cc_start: 0.7271 (m100) cc_final: 0.6807 (m100)
REVERT: A  479 MET cc_start: 0.8976 (ppp) cc_final: 0.8705 (ppp)
REVERT: A  516 THR cc_start: 0.8998 (p) cc_final: 0.8501 (p)
REVERT: A  557 LEU cc_start: 0.8959 (mt) cc_final: 0.8566 (mt)
REVERT: A  567 LEU cc_start: 0.9030 (tp) cc_final: 0.8815 (tp)
  outliers start: 1
  outliers final: 1
  residues processed: 140
  average time/residue: 0.1790
  time to fit residues: 33.8023
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  : 0.706 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 61 optimal weight:    2.9990
   chunk 13 optimal weight:    3.9990
   chunk 48 optimal weight:    0.9990
   chunk 43 optimal weight:    3.9990
   chunk 42 optimal weight:    5.9990
   chunk 14 optimal weight:    0.5980
   chunk 54 optimal weight:    4.9990
   overall best weight:    1.7188

-------------------------------------------------------------------------------
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 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 264 HIS
A 299 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4099 r_free = 0.4099 target = 0.119724 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.095791 restraints weight = 21511.191|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.098754 restraints weight = 12005.361|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.100768 restraints weight = 7908.224|
|-----------------------------------------------------------------------------|
r_work (final): 0.3767
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7564
moved from start:          0.3072

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   6752  Z= 0.322
  Angle     :  0.776   9.925   9164  Z= 0.398
  Chirality :  0.050   0.330    968
  Planarity :  0.005   0.046   1168
  Dihedral  :  9.369  98.867   1016
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 20.97
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.85 %
    Favored  : 94.02 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  5.34 %
    Favored  : 94.52 %
  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: -0.33 (0.25), residues: 408
  sheet: -0.21 (0.98), residues: 29
  loop : -1.49 (0.33), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.003   TRP B 353 
 HIS   0.007   0.001   HIS A 264 
 PHE   0.020   0.002   PHE B 347 
 TYR   0.064   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  : 0.699 
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: 0.7738 (mtmt) cc_final: 0.7211 (mtpt)
REVERT: B  499 THR cc_start: 0.8613 (p) cc_final: 0.8350 (p)
REVERT: A  100 LEU cc_start: 0.8706 (mt) cc_final: 0.8443 (mt)
REVERT: A  151 MET cc_start: 0.6419 (tpt) cc_final: 0.5907 (tpp)
REVERT: A  189 MET cc_start: 0.8822 (tmm) cc_final: 0.8382 (tmm)
REVERT: A  248 MET cc_start: 0.7383 (ptm) cc_final: 0.7147 (ppp)
REVERT: A  326 PHE cc_start: 0.6655 (m-80) cc_final: 0.5998 (m-80)
REVERT: A  458 TRP cc_start: 0.7323 (m100) cc_final: 0.6673 (m100)
REVERT: A  479 MET cc_start: 0.9042 (ppp) cc_final: 0.8819 (ppp)
REVERT: A  516 THR cc_start: 0.9036 (p) cc_final: 0.8554 (p)
REVERT: A  557 LEU cc_start: 0.9021 (mt) cc_final: 0.8572 (mt)
REVERT: A  567 LEU cc_start: 0.9047 (tp) cc_final: 0.8804 (tp)
REVERT: A  588 GLU cc_start: 0.8617 (mt-10) cc_final: 0.8068 (mm-30)
  outliers start: 1
  outliers final: 0
  residues processed: 127
  average time/residue: 0.1601
  time to fit residues: 28.1375
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  : 0.696 
-------------------------------------------------------------------------------
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:    3.9990
   chunk 23 optimal weight:    0.7980
   chunk 49 optimal weight:    0.1980
   chunk 61 optimal weight:    0.9990
   chunk 14 optimal weight:    0.5980
   chunk 9 optimal weight:    0.9980
   chunk 47 optimal weight:    1.9990
   chunk 40 optimal weight:    2.9990
   chunk 41 optimal weight:    0.7980
   chunk 37 optimal weight:    4.9990
   chunk 65 optimal weight:    4.9990
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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  24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 551 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4127 r_free = 0.4127 target = 0.122176 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.098675 restraints weight = 21828.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.101740 restraints weight = 11981.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.103838 restraints weight = 7789.537|
|-----------------------------------------------------------------------------|
r_work (final): 0.3818
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7476
moved from start:          0.3434

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6752  Z= 0.218
  Angle     :  0.712   8.913   9164  Z= 0.358
  Chirality :  0.049   0.344    968
  Planarity :  0.005   0.048   1168
  Dihedral  :  8.607  90.389   1016
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 16.53
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.47 %
    Favored  : 94.40 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  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: -1.11 (0.29), residues: 786
  helix: -0.15 (0.25), residues: 404
  sheet: -0.50 (0.92), residues: 29
  loop : -1.38 (0.32), residues: 353

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   0.026   0.002   PHE B 456 
 TYR   0.047   0.002   TYR A 453 
 ARG   0.004   0.001   ARG B 457 

*********************** 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
  124 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 124
  time to evaluate  : 0.753 
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  499 THR cc_start: 0.8476 (p) cc_final: 0.8182 (p)
REVERT: A  151 MET cc_start: 0.6787 (tpt) cc_final: 0.6443 (tpp)
REVERT: A  164 TRP cc_start: 0.6439 (m-90) cc_final: 0.5947 (m-90)
REVERT: A  242 TYR cc_start: 0.6542 (m-80) cc_final: 0.6338 (m-80)
REVERT: A  248 MET cc_start: 0.7419 (ptm) cc_final: 0.7165 (ppp)
REVERT: A  326 PHE cc_start: 0.6671 (m-80) cc_final: 0.6137 (m-80)
REVERT: A  453 TYR cc_start: 0.6038 (m-80) cc_final: 0.5766 (m-80)
REVERT: A  522 PHE cc_start: 0.8828 (m-10) cc_final: 0.8603 (m-10)
REVERT: A  557 LEU cc_start: 0.9038 (mt) cc_final: 0.8679 (mt)
REVERT: A  567 LEU cc_start: 0.9086 (tp) cc_final: 0.8858 (tp)
REVERT: A  588 GLU cc_start: 0.8597 (mt-10) cc_final: 0.8014 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 124
  average time/residue: 0.1678
  time to fit residues: 28.6620
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  : 0.743 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 7 optimal weight:    0.7980
   chunk 41 optimal weight:    0.9990
   chunk 71 optimal weight:    0.0770
   chunk 21 optimal weight:    4.9990
   chunk 46 optimal weight:    5.9990
   chunk 14 optimal weight:    0.9990
   chunk 25 optimal weight:    2.9990
   chunk 26 optimal weight:    0.8980
   chunk 31 optimal weight:    0.6980
   chunk 34 optimal weight:    0.7980
   overall best weight:    0.6538

-------------------------------------------------------------------------------
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**
B 492 GLN
** A  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 598 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.120012 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.097234 restraints weight = 20331.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.100439 restraints weight = 10977.999|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.102602 restraints weight = 6978.930|
|-----------------------------------------------------------------------------|
r_work (final): 0.3725
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7429
moved from start:          0.3775

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6752  Z= 0.209
  Angle     :  0.720   9.500   9164  Z= 0.359
  Chirality :  0.050   0.450    968
  Planarity :  0.005   0.087   1168
  Dihedral  :  8.225  82.631   1016
  Min Nonbonded Distance : 2.383

Molprobity Statistics.
  All-atom Clashscore : 17.62
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.73 %
    Favored  : 94.15 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  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: -0.88 (0.29), residues: 786
  helix:  0.04 (0.26), residues: 396
  sheet: -0.55 (0.93), residues: 29
  loop : -1.24 (0.33), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.003   TRP B 353 
 HIS   0.005   0.001   HIS A 525 
 PHE   0.018   0.002   PHE A 229 
 TYR   0.043   0.002   TYR A 453 
 ARG   0.005   0.000   ARG A 305 

*********************** 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
  129 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 129
  time to evaluate  : 0.720 
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: 0.7743 (mtmt) cc_final: 0.7478 (mtpt)
REVERT: B  499 THR cc_start: 0.8561 (p) cc_final: 0.8290 (p)
REVERT: A   30 GLU cc_start: 0.8708 (mp0) cc_final: 0.8355 (mp0)
REVERT: A  164 TRP cc_start: 0.6508 (m-90) cc_final: 0.5881 (m-90)
REVERT: A  242 TYR cc_start: 0.5986 (m-80) cc_final: 0.5692 (m-80)
REVERT: A  248 MET cc_start: 0.7434 (ptm) cc_final: 0.7179 (ppp)
REVERT: A  302 ASP cc_start: 0.8226 (t0) cc_final: 0.7862 (t70)
REVERT: A  326 PHE cc_start: 0.6487 (m-80) cc_final: 0.6182 (m-80)
REVERT: A  453 TYR cc_start: 0.5623 (m-80) cc_final: 0.5143 (m-80)
REVERT: A  557 LEU cc_start: 0.9082 (mt) cc_final: 0.8691 (mt)
REVERT: A  588 GLU cc_start: 0.8612 (mt-10) cc_final: 0.8047 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 129
  average time/residue: 0.1758
  time to fit residues: 30.8248
Evaluate side-chains
  104 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.726 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 48 optimal weight:    0.6980
   chunk 22 optimal weight:    0.3980
   chunk 53 optimal weight:    0.9990
   chunk 28 optimal weight:    3.9990
   chunk 73 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 36 optimal weight:    3.9990
   chunk 60 optimal weight:    3.9990
   chunk 45 optimal weight:    5.9990
   chunk 10 optimal weight:    0.8980
   overall best weight:    0.9984

-------------------------------------------------------------------------------
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 193 ASN
** A 400 HIS ** 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 = 0.4120 r_free = 0.4120 target = 0.121611 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.097657 restraints weight = 21663.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.100761 restraints weight = 11902.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.102847 restraints weight = 7683.160|
|-----------------------------------------------------------------------------|
r_work (final): 0.3796
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7512
moved from start:          0.4145

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   6752  Z= 0.236
  Angle     :  0.718   9.570   9164  Z= 0.362
  Chirality :  0.049   0.395    968
  Planarity :  0.004   0.046   1168
  Dihedral  :  7.847  70.640   1016
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 17.23
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.47 %
    Favored  : 94.40 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  2.31 %
    Favored  : 97.55 %
  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: -1.03 (0.29), residues: 786
  helix: -0.14 (0.25), residues: 404
  sheet: -0.42 (0.96), residues: 29
  loop : -1.27 (0.33), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.055   0.003   TRP A 167 
 HIS   0.005   0.001   HIS A 525 
 PHE   0.025   0.002   PHE A 229 
 TYR   0.044   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
  137 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 136
  time to evaluate  : 0.775 
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  403 LYS cc_start: 0.7877 (mtmt) cc_final: 0.7586 (mtpt)
REVERT: B  499 THR cc_start: 0.8458 (p) cc_final: 0.8184 (p)
REVERT: A  164 TRP cc_start: 0.7161 (m-90) cc_final: 0.6569 (m-90)
REVERT: A  248 MET cc_start: 0.7509 (ptm) cc_final: 0.7253 (ppp)
REVERT: A  382 MET cc_start: 0.8464 (mtm) cc_final: 0.8048 (mtm)
REVERT: A  440 LYS cc_start: 0.8241 (tmtt) cc_final: 0.7988 (ttpt)
REVERT: A  453 TYR cc_start: 0.5380 (m-80) cc_final: 0.4801 (m-80)
REVERT: A  455 LEU cc_start: 0.9393 (mt) cc_final: 0.9034 (mt)
REVERT: A  557 LEU cc_start: 0.9061 (mt) cc_final: 0.8697 (mt)
REVERT: A  588 GLU cc_start: 0.8689 (mt-10) cc_final: 0.8113 (mm-30)
  outliers start: 1
  outliers final: 0
  residues processed: 137
  average time/residue: 0.1758
  time to fit residues: 32.7440
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  : 0.728 
-------------------------------------------------------------------------------
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:    0.0370
   chunk 67 optimal weight:    2.9990
   chunk 77 optimal weight:    3.9990
   chunk 73 optimal weight:    0.6980
   chunk 71 optimal weight:    0.0970
   chunk 1 optimal weight:    0.5980
   chunk 29 optimal weight:    0.6980
   chunk 52 optimal weight:    0.5980
   chunk 18 optimal weight:    1.9990
   chunk 50 optimal weight:    0.9980
   chunk 6 optimal weight:    0.6980
   overall best weight:    0.4056

-------------------------------------------------------------------------------
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 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.120745 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.097720 restraints weight = 20229.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.100937 restraints weight = 11097.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.103086 restraints weight = 7097.120|
|-----------------------------------------------------------------------------|
r_work (final): 0.3741
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7429
moved from start:          0.4438

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   6752  Z= 0.202
  Angle     :  0.723   9.997   9164  Z= 0.361
  Chirality :  0.051   0.500    968
  Planarity :  0.004   0.045   1168
  Dihedral  :  7.344  55.056   1016
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 15.05
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.73 %
    Favored  : 94.15 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  2.31 %
    Favored  : 97.55 %
  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: -0.89 (0.29), residues: 786
  helix: -0.04 (0.25), residues: 401
  sheet: -0.40 (0.95), residues: 29
  loop : -1.17 (0.33), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.002   TRP B 353 
 HIS   0.006   0.001   HIS A 525 
 PHE   0.020   0.002   PHE A 229 
 TYR   0.053   0.002   TYR A  50 
 ARG   0.005   0.000   ARG A 305 

*********************** 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
  134 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 133
  time to evaluate  : 0.795 
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: 0.6845 (ttmt) cc_final: 0.6440 (tptt)
REVERT: B  499 THR cc_start: 0.8438 (p) cc_final: 0.8160 (p)
REVERT: A   30 GLU cc_start: 0.8686 (mp0) cc_final: 0.8299 (mp0)
REVERT: A  248 MET cc_start: 0.7507 (ptm) cc_final: 0.7241 (ppp)
REVERT: A  357 ILE cc_start: 0.8895 (mp) cc_final: 0.8593 (mp)
REVERT: A  382 MET cc_start: 0.8529 (mtm) cc_final: 0.8145 (mtm)
REVERT: A  405 GLU cc_start: 0.7707 (pp20) cc_final: 0.7424 (tp30)
REVERT: A  446 VAL cc_start: 0.8807 (m) cc_final: 0.8562 (p)
REVERT: A  453 TYR cc_start: 0.4895 (m-80) cc_final: 0.4469 (m-80)
REVERT: A  557 LEU cc_start: 0.9069 (mt) cc_final: 0.8637 (mt)
REVERT: A  588 GLU cc_start: 0.8659 (mt-10) cc_final: 0.8093 (mm-30)
  outliers start: 1
  outliers final: 0
  residues processed: 134
  average time/residue: 0.1809
  time to fit residues: 32.5445
Evaluate side-chains
  101 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 0.727 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 60 optimal weight:    5.9990
   chunk 55 optimal weight:    3.9990
   chunk 24 optimal weight:    4.9990
   chunk 20 optimal weight:    0.9980
   chunk 23 optimal weight:    0.5980
   chunk 28 optimal weight:    1.9990
   chunk 70 optimal weight:    1.9990
   chunk 57 optimal weight:    2.9990
   overall best weight:    1.5186

-------------------------------------------------------------------------------
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 400 HIS ** 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 = 0.4075 r_free = 0.4075 target = 0.118663 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.094867 restraints weight = 21405.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.097875 restraints weight = 11711.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.099910 restraints weight = 7609.284|
|-----------------------------------------------------------------------------|
r_work (final): 0.3752
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7587
moved from start:          0.4865

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.057   6752  Z= 0.296
  Angle     :  0.779  12.371   9164  Z= 0.393
  Chirality :  0.052   0.409    968
  Planarity :  0.005   0.057   1168
  Dihedral  :  7.325  54.380   1016
  Min Nonbonded Distance : 2.377

Molprobity Statistics.
  All-atom Clashscore : 19.26
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.22 %
    Favored  : 94.66 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  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: -1.02 (0.30), residues: 786
  helix: -0.21 (0.25), residues: 412
  sheet: -0.78 (0.88), residues: 40
  loop : -1.13 (0.35), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.065   0.003   TRP A 167 
 HIS   0.007   0.001   HIS A 525 
 PHE   0.032   0.002   PHE A 229 
 TYR   0.050   0.002   TYR A 453 
 ARG   0.014   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
  130 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 130
  time to evaluate  : 0.752 
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: symmetry clash
REVERT: B  499 THR cc_start: 0.8417 (p) cc_final: 0.8190 (p)
REVERT: A   30 GLU cc_start: 0.8680 (mp0) cc_final: 0.8325 (mp0)
REVERT: A  151 MET cc_start: 0.6401 (tpt) cc_final: 0.5950 (tpp)
REVERT: A  223 LYS cc_start: 0.8869 (mttp) cc_final: 0.8522 (mtmm)
REVERT: A  248 MET cc_start: 0.7595 (ptm) cc_final: 0.7327 (ppp)
REVERT: A  304 GLU cc_start: 0.7068 (tp30) cc_final: 0.6579 (tp30)
REVERT: A  453 TYR cc_start: 0.5080 (m-80) cc_final: 0.4396 (m-80)
REVERT: A  557 LEU cc_start: 0.9077 (mt) cc_final: 0.8706 (mt)
REVERT: A  588 GLU cc_start: 0.8844 (mt-10) cc_final: 0.8252 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 130
  average time/residue: 0.1746
  time to fit residues: 31.0295
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  : 0.746 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 11 optimal weight:    0.9980
   chunk 36 optimal weight:    5.9990
   chunk 1 optimal weight:    0.9980
   chunk 68 optimal weight:    2.9990
   chunk 59 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9980
   chunk 60 optimal weight:    6.9990
   chunk 15 optimal weight:    7.9990
   chunk 61 optimal weight:    1.9990
   overall best weight:    1.3984

-------------------------------------------------------------------------------
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 400 HIS ** 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 = 0.3984 r_free = 0.3984 target = 0.115669 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.092586 restraints weight = 20298.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.095616 restraints weight = 11095.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.097582 restraints weight = 7113.007|
|-----------------------------------------------------------------------------|
r_work (final): 0.3641
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7568
moved from start:          0.5135

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.074   6752  Z= 0.296
  Angle     :  0.793  13.650   9164  Z= 0.400
  Chirality :  0.053   0.423    968
  Planarity :  0.005   0.047   1168
  Dihedral  :  7.064  55.879   1016
  Min Nonbonded Distance : 2.213

Molprobity Statistics.
  All-atom Clashscore : 20.19
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.85 %
    Favored  : 94.02 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.87 %
    Favored  : 99.13 %
  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: -1.10 (0.30), residues: 786
  helix: -0.23 (0.25), residues: 404
  sheet: -0.92 (0.85), residues: 40
  loop : -1.22 (0.35), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.066   0.003   TRP A 167 
 HIS   0.004   0.001   HIS A 377 
 PHE   0.030   0.002   PHE A 229 
 TYR   0.061   0.003   TYR A  50 
 ARG   0.014   0.001   ARG A 305 

*********************** 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
  122 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 122
  time to evaluate  : 0.772 
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  392 PHE cc_start: 0.7162 (m-80) cc_final: 0.6886 (m-80)
REVERT: B  499 THR cc_start: 0.8417 (p) cc_final: 0.8140 (p)
REVERT: B  514 PHE cc_start: 0.5715 (m-10) cc_final: 0.5500 (m-10)
REVERT: A  151 MET cc_start: 0.6427 (tpt) cc_final: 0.6059 (tpp)
REVERT: A  164 TRP cc_start: 0.6828 (m-90) cc_final: 0.6100 (m-90)
REVERT: A  248 MET cc_start: 0.7668 (ptm) cc_final: 0.7405 (ppp)
REVERT: A  304 GLU cc_start: 0.7090 (tp30) cc_final: 0.6555 (tp30)
REVERT: A  405 GLU cc_start: 0.7659 (pp20) cc_final: 0.7427 (tp30)
REVERT: A  453 TYR cc_start: 0.5069 (m-80) cc_final: 0.4279 (m-80)
REVERT: A  455 LEU cc_start: 0.9299 (mt) cc_final: 0.9040 (mt)
REVERT: A  557 LEU cc_start: 0.9092 (mt) cc_final: 0.8723 (mt)
REVERT: A  588 GLU cc_start: 0.8901 (mt-10) cc_final: 0.8307 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 122
  average time/residue: 0.1780
  time to fit residues: 29.8611
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  : 0.915 
-------------------------------------------------------------------------------
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:    0.0670
   chunk 39 optimal weight:    3.9990
   chunk 12 optimal weight:    2.9990
   chunk 22 optimal weight:    0.7980
   chunk 62 optimal weight:    0.7980
   chunk 66 optimal weight:    0.9980
   chunk 20 optimal weight:    0.6980
   chunk 75 optimal weight:    1.9990
   chunk 28 optimal weight:    0.6980
   chunk 13 optimal weight:    0.7980
   chunk 9 optimal weight:    0.0980
   overall best weight:    0.4718

-------------------------------------------------------------------------------
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**

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 = 0.118812 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.095714 restraints weight = 20386.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.098857 restraints weight = 11190.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.100844 restraints weight = 7147.280|
|-----------------------------------------------------------------------------|
r_work (final): 0.3703
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7487
moved from start:          0.5288

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061   6752  Z= 0.213
  Angle     :  0.749   8.738   9164  Z= 0.381
  Chirality :  0.051   0.405    968
  Planarity :  0.004   0.047   1168
  Dihedral  :  6.510  56.453   1016
  Min Nonbonded Distance : 2.206

Molprobity Statistics.
  All-atom Clashscore : 17.85
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.85 %
    Favored  : 94.02 %
  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: -0.98 (0.30), residues: 786
  helix: -0.10 (0.26), residues: 393
  sheet: -0.67 (0.86), residues: 39
  loop : -1.20 (0.33), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.063   0.002   TRP A 167 
 HIS   0.003   0.001   HIS A 264 
 PHE   0.021   0.002   PHE A 229 
 TYR   0.053   0.002   TYR A  50 
 ARG   0.007   0.001   ARG A 305 

********************** 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
  126 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 126
  time to evaluate  : 0.758 
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  499 THR cc_start: 0.8287 (p) cc_final: 0.7959 (p)
REVERT: A   30 GLU cc_start: 0.8823 (mp0) cc_final: 0.8395 (mp0)
REVERT: A  151 MET cc_start: 0.6439 (tpt) cc_final: 0.6065 (tpp)
REVERT: A  164 TRP cc_start: 0.6843 (m-90) cc_final: 0.6106 (m-90)
REVERT: A  189 MET cc_start: 0.8726 (tmm) cc_final: 0.8094 (tmm)
REVERT: A  248 MET cc_start: 0.7532 (ptm) cc_final: 0.7295 (ppp)
REVERT: A  304 GLU cc_start: 0.6713 (tp30) cc_final: 0.6225 (tp30)
REVERT: A  305 ARG cc_start: 0.8024 (ptt-90) cc_final: 0.7776 (ptt-90)
REVERT: A  375 MET cc_start: 0.8930 (mmm) cc_final: 0.8714 (mmm)
REVERT: A  440 LYS cc_start: 0.8159 (tmtt) cc_final: 0.7843 (mmtm)
REVERT: A  453 TYR cc_start: 0.5105 (m-80) cc_final: 0.4760 (m-80)
REVERT: A  557 LEU cc_start: 0.9072 (mt) cc_final: 0.8738 (mt)
REVERT: A  588 GLU cc_start: 0.8862 (mt-10) cc_final: 0.8298 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 126
  average time/residue: 0.1659
  time to fit residues: 28.7883
Evaluate side-chains
  105 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 0.747 
-------------------------------------------------------------------------------
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:    0.0570
   chunk 14 optimal weight:    0.0970
   chunk 49 optimal weight:    0.8980
   chunk 75 optimal weight:    0.9980
   chunk 19 optimal weight:    1.9990
   chunk 61 optimal weight:    5.9990
   chunk 70 optimal weight:    0.0670
   chunk 37 optimal weight:    4.9990
   chunk 73 optimal weight:    0.9990
   chunk 65 optimal weight:    1.9990
   chunk 77 optimal weight:    5.9990
   overall best weight:    0.4234

-------------------------------------------------------------------------------
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 121 ASN
** A 400 HIS ** 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 = 0.119743 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.096304 restraints weight = 20224.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.099580 restraints weight = 11140.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.101806 restraints weight = 7025.135|
|-----------------------------------------------------------------------------|
r_work (final): 0.3722
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7459
moved from start:          0.5458

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   6752  Z= 0.202
  Angle     :  0.735  11.795   9164  Z= 0.371
  Chirality :  0.050   0.390    968
  Planarity :  0.004   0.047   1168
  Dihedral  :  6.267  56.576   1016
  Min Nonbonded Distance : 2.227

Molprobity Statistics.
  All-atom Clashscore : 16.53
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.60 %
    Favored  : 94.27 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.43 %
    Favored  : 99.57 %
  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: -0.88 (0.30), residues: 786
  helix: -0.06 (0.26), residues: 394
  sheet: -0.86 (0.85), residues: 40
  loop : -1.07 (0.34), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.060   0.002   TRP A 167 
 HIS   0.003   0.001   HIS A  34 
 PHE   0.020   0.002   PHE A 229 
 TYR   0.047   0.002   TYR A  50 
 ARG   0.008   0.001   ARG A 305 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2460.41 seconds
wall clock time: 43 minutes 36.00 seconds (2616.00 seconds total)