Starting phenix.real_space_refine
on Fri May  9 22:34:50 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9j66_61167/05_2025/9j66_61167.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9j66_61167/05_2025/9j66_61167.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.55
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9j66_61167/05_2025/9j66_61167.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9j66_61167/05_2025/9j66_61167.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9j66_61167/05_2025/9j66_61167.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9j66_61167/05_2025/9j66_61167.cif"
  }
  resolution = 3.55
  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=   0.019
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      19      5.16       5
     C    2580      2.51       5
     N     674      2.21       5
     O     771      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 4044
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 886
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 124, 886
          Classifications: {'peptide': 124}
          Incomplete info: {'truncation_to_alanine': 16}
          Link IDs: {'PTRANS': 4, 'TRANS': 119}
          Unresolved non-hydrogen bonds: 61
          Unresolved non-hydrogen angles: 73
          Unresolved non-hydrogen dihedrals: 51
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1, 'GLU:plan': 3}
          Unresolved non-hydrogen planarities: 30
    Chain: "C"
      Number of atoms: 760
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 760
          Classifications: {'peptide': 107}
          Incomplete info: {'truncation_to_alanine': 15}
          Link IDs: {'PTRANS': 7, 'TRANS': 99}
          Unresolved non-hydrogen bonds: 43
          Unresolved non-hydrogen angles: 51
          Unresolved non-hydrogen dihedrals: 35
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 22
    Chain: "A"
      Number of atoms: 1484
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 193, 1484
          Classifications: {'peptide': 193}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 11}
          Link IDs: {'PTRANS': 11, 'TRANS': 181}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 43
          Unresolved non-hydrogen angles: 53
          Unresolved non-hydrogen dihedrals: 36
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'TYR:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 25
    Chain: "D"
      Number of atoms: 914
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 135, 914
          Classifications: {'peptide': 135}
          Incomplete info: {'truncation_to_alanine': 40}
          Link IDs: {'PTRANS': 7, 'TRANS': 127}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 172
          Unresolved non-hydrogen angles: 217
          Unresolved non-hydrogen dihedrals: 146
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 5, 'ASN:plan1': 5, 'ASP:plan': 6, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 5}
          Unresolved non-hydrogen planarities: 125
  Time building chain proxies: 4.13, per 1000 atoms: 1.02
  Number of scatterers: 4044
  At special positions: 0
  Unit cell: (71.25, 118.75, 89.3, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      19     16.00
     O     771      8.00
     N     674      7.00
     C    2580      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=8, symmetry=0
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  23 " - pdb=" SG  CYS C  88 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 336 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 379 " - pdb=" SG  CYS A 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 391 " - pdb=" SG  CYS A 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 480 " - pdb=" SG  CYS A 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 336 " - pdb=" SG  CYS D 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 379 " - pdb=" SG  CYS D 432 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.98
  Conformation dependent library (CDL) restraints added in 479.6 milliseconds
  

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1028

  Finding SS restraints...
    Secondary structure from input PDB file:
      10 helices and 11 sheets defined
      10.2% alpha, 26.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.52
  Creating SS restraints...
    Processing helix  chain 'A' and resid 337 through 341
    Processing helix  chain 'A' and resid 349 through 353
    Processing helix  chain 'A' and resid 365 through 370
    Processing helix  chain 'A' and resid 383 through 390
      removed outlier: 3.672A  pdb=" N   LEU A 387 " --> pdb=" O   PRO A 384 " (cutoff:3.500A)
      removed outlier: 5.111A  pdb=" N   ASN A 388 " --> pdb=" O   THR A 385 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   LEU A 390 " --> pdb=" O   LEU A 387 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 404 through 408
      removed outlier: 4.398A  pdb=" N   ARG A 408 " --> pdb=" O   GLY A 404 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 404 through 408'
    Processing helix  chain 'A' and resid 417 through 422
    Processing helix  chain 'A' and resid 502 through 505
    Processing helix  chain 'D' and resid 337 through 342
      removed outlier: 3.669A  pdb=" N   PHE D 342 " --> pdb=" O   PHE D 338 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 405 through 410
      removed outlier: 3.573A  pdb=" N   ARG D 408 " --> pdb=" O   ASP D 405 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 416 through 421
    Processing sheet with id=AA1, first strand: chain 'B' and resid 3 through 6
      removed outlier: 5.382A  pdb=" N   SER B  84 " --> pdb=" O   VAL B  18 " (cutoff:3.500A)
      removed outlier: 7.071A  pdb=" N   VAL B  18 " --> pdb=" O   SER B  84 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   SER B  16 " --> pdb=" O   LEU B  86 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 3 through 6
      removed outlier: 3.661A  pdb=" N   ASP B  73 " --> pdb=" O   THR B  78 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 45 through 50
      removed outlier: 7.114A  pdb=" N   TRP B  36 " --> pdb=" O   MET B  48 " (cutoff:3.500A)
      removed outlier: 4.517A  pdb=" N   ARG B  50 " --> pdb=" O   ILE B  34 " (cutoff:3.500A)
      removed outlier: 6.868A  pdb=" N   ILE B  34 " --> pdb=" O   ARG B  50 " (cutoff:3.500A)
      removed outlier: 4.227A  pdb=" N   TYR B 112 " --> pdb=" O   ARG B  98 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 105 through 106
    Processing sheet with id=AA5, first strand: chain 'C' and resid 19 through 24
      removed outlier: 3.855A  pdb=" N   VAL C  19 " --> pdb=" O   ILE C  75 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   ASP C  70 " --> pdb=" O   SER C  67 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   SER C  67 " --> pdb=" O   ASP C  70 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 53 through 54
    Processing sheet with id=AA7, first strand: chain 'C' and resid 85 through 86
    Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358
      removed outlier: 3.607A  pdb=" N   ILE A 402 " --> pdb=" O   TYR A 508 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   TRP A 436 " --> pdb=" O   ARG A 509 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454
    Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474
    Processing sheet with id=AB2, first strand: chain 'D' and resid 395 through 403

    109 hydrogen bonds defined for protein.
    255 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.00

  Time building geometry restraints manager: 1.15 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1297
        1.34 -     1.46: 1097
        1.46 -     1.58: 1725
        1.58 -     1.70: 1
        1.70 -     1.82: 22
  Bond restraints: 4142
  Sorted by residual:
  bond pdb=" N   ILE D 410 "
       pdb=" CA  ILE D 410 "
    ideal  model  delta    sigma   weight residual
    1.474  1.458  0.016 1.57e-02 4.06e+03 1.04e+00
  bond pdb=" CA  ASP A 364 "
       pdb=" CB  ASP A 364 "
    ideal  model  delta    sigma   weight residual
    1.539  1.581 -0.042 4.88e-02 4.20e+02 7.42e-01
  bond pdb=" CA  VAL C  58 "
       pdb=" CB  VAL C  58 "
    ideal  model  delta    sigma   weight residual
    1.547  1.538  0.009 1.10e-02 8.26e+03 7.23e-01
  bond pdb=" CA  THR A 470 "
       pdb=" CB  THR A 470 "
    ideal  model  delta    sigma   weight residual
    1.528  1.550 -0.022 2.61e-02 1.47e+03 6.81e-01
  bond pdb=" CA  PRO A 479 "
       pdb=" C   PRO A 479 "
    ideal  model  delta    sigma   weight residual
    1.527  1.519  0.008 1.07e-02 8.73e+03 5.69e-01
  ... (remaining 4137 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.98: 5280
        0.98 -     1.96: 310
        1.96 -     2.94: 50
        2.94 -     3.92: 20
        3.92 -     4.90: 5
  Bond angle restraints: 5665
  Sorted by residual:
  angle pdb=" N   ILE D 410 "
        pdb=" CA  ILE D 410 "
        pdb=" C   ILE D 410 "
      ideal   model   delta    sigma   weight residual
     106.21  108.82   -2.61 1.07e+00 8.73e-01 5.93e+00
  angle pdb=" C   SER D 359 "
        pdb=" N   ASN D 360 "
        pdb=" CA  ASN D 360 "
      ideal   model   delta    sigma   weight residual
     122.46  125.88   -3.42 1.41e+00 5.03e-01 5.89e+00
  angle pdb=" CA  TYR B 109 "
        pdb=" CB  TYR B 109 "
        pdb=" CG  TYR B 109 "
      ideal   model   delta    sigma   weight residual
     113.90  118.24   -4.34 1.80e+00 3.09e-01 5.81e+00
  angle pdb=" CA  ILE D 410 "
        pdb=" C   ILE D 410 "
        pdb=" O   ILE D 410 "
      ideal   model   delta    sigma   weight residual
     122.63  120.81    1.82 8.70e-01 1.32e+00 4.36e+00
  angle pdb=" N   ALA C  51 "
        pdb=" CA  ALA C  51 "
        pdb=" CB  ALA C  51 "
      ideal   model   delta    sigma   weight residual
     113.65  110.68    2.97 1.47e+00 4.63e-01 4.08e+00
  ... (remaining 5660 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.58: 2213
       17.58 -    35.15: 153
       35.15 -    52.73: 30
       52.73 -    70.31: 4
       70.31 -    87.88: 4
  Dihedral angle restraints: 2404
    sinusoidal: 796
      harmonic: 1608
  Sorted by residual:
  dihedral pdb=" CB  CYS C  23 "
           pdb=" SG  CYS C  23 "
           pdb=" SG  CYS C  88 "
           pdb=" CB  CYS C  88 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  144.84  -51.84     1      1.00e+01 1.00e-02 3.67e+01
  dihedral pdb=" CB  CYS A 480 "
           pdb=" SG  CYS A 480 "
           pdb=" SG  CYS A 488 "
           pdb=" CB  CYS A 488 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -130.58   44.58     1      1.00e+01 1.00e-02 2.76e+01
  dihedral pdb=" CB  CYS D 379 "
           pdb=" SG  CYS D 379 "
           pdb=" SG  CYS D 432 "
           pdb=" CB  CYS D 432 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -44.66  -41.34     1      1.00e+01 1.00e-02 2.39e+01
  ... (remaining 2401 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 424
       0.035 -    0.070: 139
       0.070 -    0.105: 53
       0.105 -    0.141: 23
       0.141 -    0.176: 2
  Chirality restraints: 641
  Sorted by residual:
  chirality pdb=" CB  THR A 470 "
            pdb=" CA  THR A 470 "
            pdb=" OG1 THR A 470 "
            pdb=" CG2 THR A 470 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.38    0.18 2.00e-01 2.50e+01 7.72e-01
  chirality pdb=" CB  VAL A 524 "
            pdb=" CA  VAL A 524 "
            pdb=" CG1 VAL A 524 "
            pdb=" CG2 VAL A 524 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.47   -0.16 2.00e-01 2.50e+01 6.66e-01
  chirality pdb=" CA  ASN D 360 "
            pdb=" N   ASN D 360 "
            pdb=" C   ASN D 360 "
            pdb=" CB  ASN D 360 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.48e-01
  ... (remaining 638 not shown)

  Planarity restraints: 735
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN C  79 "   -0.052 5.00e-02 4.00e+02   7.99e-02 1.02e+01
        pdb=" N   PRO C  80 "    0.138 5.00e-02 4.00e+02
        pdb=" CA  PRO C  80 "   -0.042 5.00e-02 4.00e+02
        pdb=" CD  PRO C  80 "   -0.044 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER C   7 "   -0.025 5.00e-02 4.00e+02   3.84e-02 2.36e+00
        pdb=" N   PRO C   8 "    0.066 5.00e-02 4.00e+02
        pdb=" CA  PRO C   8 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO C   8 "   -0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR D 376 "    0.007 2.00e-02 2.50e+03   1.45e-02 2.11e+00
        pdb=" C   THR D 376 "   -0.025 2.00e-02 2.50e+03
        pdb=" O   THR D 376 "    0.010 2.00e-02 2.50e+03
        pdb=" N   PHE D 377 "    0.008 2.00e-02 2.50e+03
  ... (remaining 732 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 1265
        2.82 -     3.34: 3534
        3.34 -     3.86: 6328
        3.86 -     4.38: 7162
        4.38 -     4.90: 12696
  Nonbonded interactions: 30985
  Sorted by model distance:
  nonbonded pdb=" O   ASP B  90 "
            pdb=" OH  TYR B  94 "
     model   vdw
     2.298 3.040
  nonbonded pdb=" O   ARG B  67 "
            pdb=" OG  SER B  84 "
     model   vdw
     2.338 3.040
  nonbonded pdb=" ND2 ASN A 501 "
            pdb=" O   TYR A 505 "
     model   vdw
     2.372 3.120
  nonbonded pdb=" O   THR B  33 "
            pdb=" OG1 THR B  33 "
     model   vdw
     2.381 3.040
  nonbonded pdb=" N   GLY B  15 "
            pdb=" O   LEU B  86 "
     model   vdw
     2.392 3.120
  ... (remaining 30980 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:             4.320
  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:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     15.270
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.830
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.730
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6997
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   4150  Z= 0.126
  Angle     :  0.553   4.902   5681  Z= 0.308
  Chirality :  0.044   0.176    641
  Planarity :  0.005   0.080    735
  Dihedral  : 12.697  87.884   1352
  Min Nonbonded Distance : 2.298

Molprobity Statistics.
  All-atom Clashscore : 7.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.75 %
    Favored  : 94.25 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.25 %
    Favored  : 99.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.15 (0.35), residues: 539
  helix: -3.38 (0.70), residues: 39
  sheet: -1.32 (0.47), residues: 127
  loop : -1.28 (0.31), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP C  32 
 PHE   0.007   0.001   PHE C  94 
 TYR   0.017   0.001   TYR B 109 
 ARG   0.003   0.000   ARG D 355 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.25605 (  103)
  hydrogen bonds       : angle      11.35749 (  255)
  SS BOND              : bond        0.00265 (    8)
  SS BOND              : angle       0.72383 (   16)
  covalent geometry    : bond        0.00279 ( 4142)
  covalent geometry    : angle       0.55256 ( 5665)

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

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

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 0.488 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   36 TYR cc_start: 0.8491 (m-10) cc_final: 0.8003 (m-10)
REVERT: A  424 LYS cc_start: 0.7974 (tttp) cc_final: 0.7647 (ttpt)
  outliers start: 0
  outliers final: 0
  residues processed: 82
  average time/residue: 0.1265
  time to fit residues: 13.4528
Evaluate side-chains
  68 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 68
  time to evaluate  : 0.508 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 45 optimal weight:    0.7980
   chunk 40 optimal weight:    0.0060
   chunk 22 optimal weight:    0.0570
   chunk 13 optimal weight:    2.9990
   chunk 27 optimal weight:    0.0670
   chunk 21 optimal weight:    0.0170
   chunk 42 optimal weight:    0.0370
   chunk 16 optimal weight:    1.9990
   chunk 25 optimal weight:    0.8980
   chunk 31 optimal weight:    1.9990
   chunk 49 optimal weight:    0.8980
   overall best weight:    0.0368

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

Flipped N/Q/H residues before XYZ refinement:
B  59 ASN
C   6 GLN
C  92 ASN
D 439 ASN
D 506 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4212 r_free = 0.4212 target = 0.194859 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.160751 restraints weight = 4780.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.165079 restraints weight = 4704.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3925 r_free = 0.3925 target = 0.166967 restraints weight = 2976.842|
|-----------------------------------------------------------------------------|
r_work (final): 0.3924
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6889
moved from start:          0.1516

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.063   4150  Z= 0.097
  Angle     :  0.519   5.602   5681  Z= 0.273
  Chirality :  0.045   0.135    641
  Planarity :  0.005   0.060    735
  Dihedral  :  3.945  42.161    598
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 6.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.38 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  : 11.45 %
    Favored  : 87.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.93 (0.35), residues: 539
  helix: -3.31 (0.70), residues: 40
  sheet: -1.25 (0.45), residues: 136
  loop : -1.04 (0.32), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B  36 
 PHE   0.009   0.001   PHE C  94 
 TYR   0.038   0.001   TYR B 109 
 ARG   0.005   0.000   ARG A 457 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03676 (  103)
  hydrogen bonds       : angle       6.81455 (  255)
  SS BOND              : bond        0.00436 (    8)
  SS BOND              : angle       0.86214 (   16)
  covalent geometry    : bond        0.00226 ( 4142)
  covalent geometry    : angle       0.51753 ( 5665)

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

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

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 73
  time to evaluate  : 0.420 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   82 GLU cc_start: 0.7510 (tt0) cc_final: 0.7109 (tp30)
REVERT: C   36 TYR cc_start: 0.8342 (m-10) cc_final: 0.8012 (m-10)
  outliers start: 4
  outliers final: 1
  residues processed: 75
  average time/residue: 0.1428
  time to fit residues: 13.7133
Evaluate side-chains
  66 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 65
  time to evaluate  : 0.392 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  438 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 14 optimal weight:    4.9990
   chunk 8 optimal weight:    4.9990
   chunk 11 optimal weight:    2.9990
   chunk 7 optimal weight:    0.8980
   chunk 18 optimal weight:    3.9990
   chunk 47 optimal weight:    0.0370
   chunk 32 optimal weight:    0.9990
   chunk 5 optimal weight:    0.6980
   chunk 53 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 15 optimal weight:    0.5980
   overall best weight:    0.6460

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

Flipped N/Q/H residues before XYZ refinement:
B  59 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4132 r_free = 0.4132 target = 0.186520 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.152683 restraints weight = 4913.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.155792 restraints weight = 4482.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.158457 restraints weight = 3121.837|
|-----------------------------------------------------------------------------|
r_work (final): 0.3835
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7065
moved from start:          0.1696

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058   4150  Z= 0.166
  Angle     :  0.548   6.432   5681  Z= 0.290
  Chirality :  0.045   0.157    641
  Planarity :  0.005   0.056    735
  Dihedral  :  4.544  59.477    598
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 8.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.12 %
    Favored  : 93.88 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 13.49 %
    Favored  : 83.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.87 (0.36), residues: 539
  helix: -3.21 (0.81), residues: 33
  sheet: -1.16 (0.46), residues: 136
  loop : -1.10 (0.32), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP C  35 
 PHE   0.014   0.001   PHE B 110 
 TYR   0.029   0.001   TYR B 109 
 ARG   0.004   0.000   ARG B  50 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03642 (  103)
  hydrogen bonds       : angle       6.65845 (  255)
  SS BOND              : bond        0.00400 (    8)
  SS BOND              : angle       0.80343 (   16)
  covalent geometry    : bond        0.00392 ( 4142)
  covalent geometry    : angle       0.54725 ( 5665)

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

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

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 66
  time to evaluate  : 0.442 
Fit side-chains
   revert: symmetry clash
REVERT: C   36 TYR cc_start: 0.8723 (m-10) cc_final: 0.8121 (m-10)
  outliers start: 11
  outliers final: 9
  residues processed: 69
  average time/residue: 0.1319
  time to fit residues: 12.0203
Evaluate side-chains
  72 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 63
  time to evaluate  : 0.457 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    2 VAL
Chi-restraints excluded: chain C residue    5 THR
Chi-restraints excluded: chain C residue    9 SER
Chi-restraints excluded: chain C residue   97 THR
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  438 SER
Chi-restraints excluded: chain A residue  461 LEU
Chi-restraints excluded: chain A residue  500 THR
Chi-restraints excluded: chain A residue  516 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 53 optimal weight:    2.9990
   chunk 25 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9990
   chunk 45 optimal weight:    0.6980
   chunk 31 optimal weight:    0.8980
   chunk 14 optimal weight:    0.5980
   chunk 30 optimal weight:    0.0470
   chunk 43 optimal weight:    5.9990
   chunk 13 optimal weight:    1.9990
   chunk 35 optimal weight:    0.7980
   chunk 39 optimal weight:    0.9980
   overall best weight:    0.6078

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

Flipped N/Q/H residues before XYZ refinement:
B  59 ASN
C  92 ASN
D 439 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4117 r_free = 0.4117 target = 0.185263 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.152637 restraints weight = 4906.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.152960 restraints weight = 4306.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.155664 restraints weight = 3740.618|
|-----------------------------------------------------------------------------|
r_work (final): 0.3804
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7087
moved from start:          0.2036

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   4150  Z= 0.156
  Angle     :  0.538   5.425   5681  Z= 0.284
  Chirality :  0.045   0.152    641
  Planarity :  0.004   0.052    735
  Dihedral  :  4.720  65.408    598
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 8.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.12 %
    Favored  : 93.88 %
  Rotamer:
    Outliers :  3.82 %
    Allowed  : 14.76 %
    Favored  : 81.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.77 (0.36), residues: 539
  helix: -3.31 (0.80), residues: 33
  sheet: -0.84 (0.46), residues: 146
  loop : -1.12 (0.32), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP B  47 
 PHE   0.013   0.001   PHE C  94 
 TYR   0.025   0.001   TYR B 109 
 ARG   0.003   0.000   ARG B  50 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03276 (  103)
  hydrogen bonds       : angle       6.43876 (  255)
  SS BOND              : bond        0.00380 (    8)
  SS BOND              : angle       0.85698 (   16)
  covalent geometry    : bond        0.00373 ( 4142)
  covalent geometry    : angle       0.53730 ( 5665)

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

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

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 64
  time to evaluate  : 0.410 
Fit side-chains
   revert: symmetry clash
REVERT: C   36 TYR cc_start: 0.8704 (m-10) cc_final: 0.8093 (m-10)
  outliers start: 15
  outliers final: 12
  residues processed: 71
  average time/residue: 0.1218
  time to fit residues: 11.5079
Evaluate side-chains
  76 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 64
  time to evaluate  : 0.408 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    2 VAL
Chi-restraints excluded: chain C residue    5 THR
Chi-restraints excluded: chain C residue    9 SER
Chi-restraints excluded: chain C residue   73 LEU
Chi-restraints excluded: chain C residue   92 ASN
Chi-restraints excluded: chain C residue   97 THR
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  420 ASP
Chi-restraints excluded: chain A residue  438 SER
Chi-restraints excluded: chain A residue  461 LEU
Chi-restraints excluded: chain A residue  500 THR
Chi-restraints excluded: chain A residue  516 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 52 optimal weight:   10.0000
   chunk 7 optimal weight:    0.9990
   chunk 25 optimal weight:    0.0870
   chunk 40 optimal weight:    1.9990
   chunk 43 optimal weight:    5.9990
   chunk 32 optimal weight:    0.6980
   chunk 14 optimal weight:    0.7980
   chunk 37 optimal weight:    1.9990
   chunk 10 optimal weight:    0.0170
   chunk 39 optimal weight:    0.5980
   chunk 2 optimal weight:    0.0980
   overall best weight:    0.2996

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

Flipped N/Q/H residues before XYZ refinement:
B  59 ASN

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 = 0.186678 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.154940 restraints weight = 4968.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.156580 restraints weight = 4178.951|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.159164 restraints weight = 3350.185|
|-----------------------------------------------------------------------------|
r_work (final): 0.3846
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7024
moved from start:          0.2131

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.071   4150  Z= 0.111
  Angle     :  0.508   5.353   5681  Z= 0.267
  Chirality :  0.044   0.146    641
  Planarity :  0.004   0.050    735
  Dihedral  :  4.486  62.247    598
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 8.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.38 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 15.78 %
    Favored  : 81.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.69 (0.36), residues: 539
  helix: -3.32 (0.77), residues: 33
  sheet: -0.62 (0.47), residues: 141
  loop : -1.13 (0.31), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  47 
 PHE   0.011   0.001   PHE C  94 
 TYR   0.023   0.001   TYR B 109 
 ARG   0.005   0.000   ARG A 457 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02915 (  103)
  hydrogen bonds       : angle       6.10207 (  255)
  SS BOND              : bond        0.00304 (    8)
  SS BOND              : angle       0.78759 (   16)
  covalent geometry    : bond        0.00274 ( 4142)
  covalent geometry    : angle       0.50650 ( 5665)

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

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

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 65
  time to evaluate  : 0.468 
Fit side-chains
   revert: symmetry clash
REVERT: C   36 TYR cc_start: 0.8608 (m-10) cc_final: 0.8102 (m-10)
  outliers start: 11
  outliers final: 10
  residues processed: 71
  average time/residue: 0.1169
  time to fit residues: 11.2988
Evaluate side-chains
  75 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 65
  time to evaluate  : 0.442 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    2 VAL
Chi-restraints excluded: chain C residue    5 THR
Chi-restraints excluded: chain C residue    9 SER
Chi-restraints excluded: chain C residue   54 LEU
Chi-restraints excluded: chain C residue   73 LEU
Chi-restraints excluded: chain C residue   97 THR
Chi-restraints excluded: chain A residue  420 ASP
Chi-restraints excluded: chain A residue  438 SER
Chi-restraints excluded: chain A residue  461 LEU
Chi-restraints excluded: chain A residue  516 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 25 optimal weight:    0.9990
   chunk 51 optimal weight:    3.9990
   chunk 43 optimal weight:    4.9990
   chunk 22 optimal weight:    0.0570
   chunk 11 optimal weight:    1.9990
   chunk 52 optimal weight:    7.9990
   chunk 18 optimal weight:    4.9990
   chunk 5 optimal weight:    0.9980
   chunk 53 optimal weight:    0.3980
   chunk 15 optimal weight:    0.9990
   chunk 24 optimal weight:    0.7980
   overall best weight:    0.6500

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

Flipped N/Q/H residues before XYZ refinement:
B  59 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.183513 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.151346 restraints weight = 4865.457|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.152176 restraints weight = 4240.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.154396 restraints weight = 3684.106|
|-----------------------------------------------------------------------------|
r_work (final): 0.3789
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7119
moved from start:          0.2358

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   4150  Z= 0.164
  Angle     :  0.545   5.837   5681  Z= 0.288
  Chirality :  0.045   0.154    641
  Planarity :  0.004   0.049    735
  Dihedral  :  4.833  68.178    598
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 8.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.68 %
    Favored  : 93.32 %
  Rotamer:
    Outliers :  3.82 %
    Allowed  : 17.05 %
    Favored  : 79.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.76 (0.36), residues: 539
  helix: -3.41 (0.76), residues: 33
  sheet: -0.65 (0.47), residues: 141
  loop : -1.20 (0.31), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP B  47 
 PHE   0.013   0.001   PHE C  94 
 TYR   0.022   0.001   TYR B 109 
 ARG   0.003   0.000   ARG A 457 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03186 (  103)
  hydrogen bonds       : angle       6.37109 (  255)
  SS BOND              : bond        0.00386 (    8)
  SS BOND              : angle       0.84141 (   16)
  covalent geometry    : bond        0.00390 ( 4142)
  covalent geometry    : angle       0.54421 ( 5665)

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

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

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 65
  time to evaluate  : 0.464 
Fit side-chains
   revert: symmetry clash
REVERT: C   36 TYR cc_start: 0.8769 (m-10) cc_final: 0.8163 (m-10)
  outliers start: 15
  outliers final: 13
  residues processed: 71
  average time/residue: 0.1350
  time to fit residues: 12.7311
Evaluate side-chains
  78 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 65
  time to evaluate  : 0.451 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    2 VAL
Chi-restraints excluded: chain C residue    5 THR
Chi-restraints excluded: chain C residue    9 SER
Chi-restraints excluded: chain C residue   73 LEU
Chi-restraints excluded: chain C residue   97 THR
Chi-restraints excluded: chain A residue  376 THR
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain A residue  420 ASP
Chi-restraints excluded: chain A residue  438 SER
Chi-restraints excluded: chain A residue  461 LEU
Chi-restraints excluded: chain A residue  500 THR
Chi-restraints excluded: chain A residue  516 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 8 optimal weight:    4.9990
   chunk 44 optimal weight:    0.0770
   chunk 37 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9990
   chunk 30 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 31 optimal weight:    0.6980
   chunk 14 optimal weight:    3.9990
   chunk 29 optimal weight:    0.1980
   chunk 38 optimal weight:    0.9990
   chunk 5 optimal weight:    0.6980
   overall best weight:    0.5338

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

Flipped N/Q/H residues before XYZ refinement:
B  59 ASN
** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 439 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4100 r_free = 0.4100 target = 0.184174 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.152144 restraints weight = 4954.082|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.152516 restraints weight = 4265.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.155332 restraints weight = 3705.586|
|-----------------------------------------------------------------------------|
r_work (final): 0.3796
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7089
moved from start:          0.2470

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061   4150  Z= 0.143
  Angle     :  0.533   5.414   5681  Z= 0.281
  Chirality :  0.045   0.151    641
  Planarity :  0.004   0.047    735
  Dihedral  :  4.772  68.926    598
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 9.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.75 %
    Favored  : 94.25 %
  Rotamer:
    Outliers :  4.07 %
    Allowed  : 18.58 %
    Favored  : 77.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.77 (0.35), residues: 539
  helix: -3.41 (0.77), residues: 33
  sheet: -0.79 (0.46), residues: 136
  loop : -1.14 (0.31), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP B  47 
 PHE   0.013   0.001   PHE C  94 
 TYR   0.020   0.001   TYR B 109 
 ARG   0.004   0.001   ARG B  67 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03022 (  103)
  hydrogen bonds       : angle       6.18640 (  255)
  SS BOND              : bond        0.00390 (    8)
  SS BOND              : angle       0.83519 (   16)
  covalent geometry    : bond        0.00346 ( 4142)
  covalent geometry    : angle       0.53152 ( 5665)

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

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

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 65
  time to evaluate  : 0.431 
Fit side-chains
   revert: symmetry clash
REVERT: C   36 TYR cc_start: 0.8695 (m-10) cc_final: 0.8091 (m-10)
REVERT: C  105 ASP cc_start: 0.5316 (m-30) cc_final: 0.4646 (m-30)
  outliers start: 16
  outliers final: 14
  residues processed: 70
  average time/residue: 0.1159
  time to fit residues: 11.0559
Evaluate side-chains
  79 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 65
  time to evaluate  : 0.436 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    2 VAL
Chi-restraints excluded: chain C residue    5 THR
Chi-restraints excluded: chain C residue    9 SER
Chi-restraints excluded: chain C residue   54 LEU
Chi-restraints excluded: chain C residue   73 LEU
Chi-restraints excluded: chain C residue   97 THR
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain A residue  420 ASP
Chi-restraints excluded: chain A residue  438 SER
Chi-restraints excluded: chain A residue  461 LEU
Chi-restraints excluded: chain A residue  470 THR
Chi-restraints excluded: chain A residue  500 THR
Chi-restraints excluded: chain A residue  516 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 8 optimal weight:    4.9990
   chunk 6 optimal weight:    0.7980
   chunk 15 optimal weight:    0.9980
   chunk 12 optimal weight:    2.9990
   chunk 14 optimal weight:    1.9990
   chunk 46 optimal weight:    0.0270
   chunk 35 optimal weight:    0.7980
   chunk 19 optimal weight:    0.4980
   chunk 31 optimal weight:    0.7980
   chunk 48 optimal weight:    2.9990
   chunk 20 optimal weight:    0.2980
   overall best weight:    0.4838

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

Flipped N/Q/H residues before XYZ refinement:
B  59 ASN
** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4098 r_free = 0.4098 target = 0.184198 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.151621 restraints weight = 4841.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.155046 restraints weight = 4323.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.158066 restraints weight = 2938.290|
|-----------------------------------------------------------------------------|
r_work (final): 0.3825
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7059
moved from start:          0.2587

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   4150  Z= 0.134
  Angle     :  0.524   5.204   5681  Z= 0.276
  Chirality :  0.045   0.152    641
  Planarity :  0.004   0.048    735
  Dihedral  :  4.712  67.844    598
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 8.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.49 %
    Favored  : 93.51 %
  Rotamer:
    Outliers :  4.07 %
    Allowed  : 19.08 %
    Favored  : 76.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.77 (0.35), residues: 539
  helix: -3.44 (0.75), residues: 33
  sheet: -0.77 (0.47), residues: 136
  loop : -1.14 (0.31), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B  47 
 PHE   0.011   0.001   PHE C  94 
 TYR   0.019   0.001   TYR B 109 
 ARG   0.004   0.000   ARG B  67 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02973 (  103)
  hydrogen bonds       : angle       6.09032 (  255)
  SS BOND              : bond        0.00390 (    8)
  SS BOND              : angle       0.82149 (   16)
  covalent geometry    : bond        0.00321 ( 4142)
  covalent geometry    : angle       0.52341 ( 5665)

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

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

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 64
  time to evaluate  : 0.438 
Fit side-chains
   revert: symmetry clash
REVERT: C   36 TYR cc_start: 0.8689 (m-10) cc_final: 0.8051 (m-10)
REVERT: C  105 ASP cc_start: 0.5546 (m-30) cc_final: 0.4905 (m-30)
  outliers start: 16
  outliers final: 15
  residues processed: 71
  average time/residue: 0.1163
  time to fit residues: 11.2221
Evaluate side-chains
  78 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 63
  time to evaluate  : 0.444 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    2 VAL
Chi-restraints excluded: chain C residue    5 THR
Chi-restraints excluded: chain C residue    9 SER
Chi-restraints excluded: chain C residue   54 LEU
Chi-restraints excluded: chain C residue   73 LEU
Chi-restraints excluded: chain C residue   97 THR
Chi-restraints excluded: chain A residue  376 THR
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain A residue  420 ASP
Chi-restraints excluded: chain A residue  438 SER
Chi-restraints excluded: chain A residue  461 LEU
Chi-restraints excluded: chain A residue  470 THR
Chi-restraints excluded: chain A residue  500 THR
Chi-restraints excluded: chain A residue  516 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 29 optimal weight:    0.6980
   chunk 14 optimal weight:    2.9990
   chunk 42 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9980
   chunk 10 optimal weight:    0.6980
   chunk 51 optimal weight:    3.9990
   chunk 39 optimal weight:    0.0980
   chunk 19 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9980
   chunk 4 optimal weight:    0.9980
   chunk 21 optimal weight:    0.8980
   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  59 ASN
** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 439 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4074 r_free = 0.4074 target = 0.182034 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.150423 restraints weight = 4966.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.151112 restraints weight = 4329.968|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.153877 restraints weight = 3683.894|
|-----------------------------------------------------------------------------|
r_work (final): 0.3787
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7134
moved from start:          0.2690

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   4150  Z= 0.171
  Angle     :  0.559   5.421   5681  Z= 0.295
  Chirality :  0.045   0.156    641
  Planarity :  0.004   0.047    735
  Dihedral  :  4.999  71.694    598
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 9.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.31 %
    Favored  : 93.69 %
  Rotamer:
    Outliers :  4.58 %
    Allowed  : 18.83 %
    Favored  : 76.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.88 (0.36), residues: 539
  helix: -3.64 (0.63), residues: 39
  sheet: -0.84 (0.47), residues: 136
  loop : -1.15 (0.32), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B  47 
 PHE   0.013   0.001   PHE C  94 
 TYR   0.020   0.001   TYR B 109 
 ARG   0.004   0.001   ARG B  67 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03123 (  103)
  hydrogen bonds       : angle       6.35765 (  255)
  SS BOND              : bond        0.00422 (    8)
  SS BOND              : angle       0.90192 (   16)
  covalent geometry    : bond        0.00405 ( 4142)
  covalent geometry    : angle       0.55761 ( 5665)

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

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

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 62
  time to evaluate  : 0.473 
Fit side-chains
   revert: symmetry clash
REVERT: C   36 TYR cc_start: 0.8789 (m-10) cc_final: 0.8148 (m-10)
  outliers start: 18
  outliers final: 15
  residues processed: 69
  average time/residue: 0.1196
  time to fit residues: 11.2778
Evaluate side-chains
  77 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 62
  time to evaluate  : 0.461 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    2 VAL
Chi-restraints excluded: chain C residue    5 THR
Chi-restraints excluded: chain C residue    9 SER
Chi-restraints excluded: chain C residue   73 LEU
Chi-restraints excluded: chain C residue   97 THR
Chi-restraints excluded: chain A residue  376 THR
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain A residue  391 CYS
Chi-restraints excluded: chain A residue  420 ASP
Chi-restraints excluded: chain A residue  438 SER
Chi-restraints excluded: chain A residue  461 LEU
Chi-restraints excluded: chain A residue  470 THR
Chi-restraints excluded: chain A residue  500 THR
Chi-restraints excluded: chain A residue  516 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 17 optimal weight:    0.9980
   chunk 34 optimal weight:    1.9990
   chunk 29 optimal weight:    0.0030
   chunk 16 optimal weight:    0.9990
   chunk 14 optimal weight:    2.9990
   chunk 47 optimal weight:    0.9980
   chunk 6 optimal weight:    1.9990
   chunk 7 optimal weight:    0.0060
   chunk 26 optimal weight:    0.6980
   chunk 0 optimal weight:    2.9990
   chunk 27 optimal weight:    0.6980
   overall best weight:    0.4806

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

Flipped N/Q/H residues before XYZ refinement:
B  59 ASN
** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 439 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.183976 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.151486 restraints weight = 4924.766|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.155399 restraints weight = 4353.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.157225 restraints weight = 2870.991|
|-----------------------------------------------------------------------------|
r_work (final): 0.3802
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7066
moved from start:          0.2739

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   4150  Z= 0.136
  Angle     :  0.539   5.052   5681  Z= 0.285
  Chirality :  0.045   0.149    641
  Planarity :  0.004   0.047    735
  Dihedral  :  4.787  68.623    598
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 8.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.49 %
    Favored  : 93.51 %
  Rotamer:
    Outliers :  4.33 %
    Allowed  : 19.08 %
    Favored  : 76.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.72 (0.36), residues: 539
  helix: -3.47 (0.75), residues: 33
  sheet: -0.83 (0.47), residues: 142
  loop : -1.05 (0.32), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B  47 
 PHE   0.011   0.001   PHE C  94 
 TYR   0.018   0.001   TYR B 109 
 ARG   0.004   0.000   ARG B  67 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02948 (  103)
  hydrogen bonds       : angle       6.11129 (  255)
  SS BOND              : bond        0.00436 (    8)
  SS BOND              : angle       0.87643 (   16)
  covalent geometry    : bond        0.00324 ( 4142)
  covalent geometry    : angle       0.53811 ( 5665)

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

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

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 64
  time to evaluate  : 0.474 
Fit side-chains
   revert: symmetry clash
REVERT: C   36 TYR cc_start: 0.8671 (m-10) cc_final: 0.8079 (m-10)
  outliers start: 17
  outliers final: 16
  residues processed: 69
  average time/residue: 0.1163
  time to fit residues: 10.9905
Evaluate side-chains
  79 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 63
  time to evaluate  : 0.444 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    2 VAL
Chi-restraints excluded: chain C residue    5 THR
Chi-restraints excluded: chain C residue    9 SER
Chi-restraints excluded: chain C residue   54 LEU
Chi-restraints excluded: chain C residue   73 LEU
Chi-restraints excluded: chain C residue   97 THR
Chi-restraints excluded: chain A residue  376 THR
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain A residue  391 CYS
Chi-restraints excluded: chain A residue  420 ASP
Chi-restraints excluded: chain A residue  438 SER
Chi-restraints excluded: chain A residue  461 LEU
Chi-restraints excluded: chain A residue  470 THR
Chi-restraints excluded: chain A residue  500 THR
Chi-restraints excluded: chain A residue  516 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 34 optimal weight:    0.9980
   chunk 37 optimal weight:    0.0050
   chunk 14 optimal weight:    2.9990
   chunk 16 optimal weight:    0.0170
   chunk 50 optimal weight:    0.9990
   chunk 51 optimal weight:    4.9990
   chunk 43 optimal weight:    4.9990
   chunk 31 optimal weight:    0.5980
   chunk 47 optimal weight:    0.7980
   chunk 20 optimal weight:    0.0980
   chunk 13 optimal weight:    0.0470
   overall best weight:    0.1530

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

Flipped N/Q/H residues before XYZ refinement:
B  59 ASN
** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4144 r_free = 0.4144 target = 0.189163 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.156692 restraints weight = 4869.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.160385 restraints weight = 4515.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.162870 restraints weight = 2962.010|
|-----------------------------------------------------------------------------|
r_work (final): 0.3881
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6969
moved from start:          0.2848

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.052   4150  Z= 0.095
  Angle     :  0.503   4.620   5681  Z= 0.264
  Chirality :  0.044   0.138    641
  Planarity :  0.004   0.046    735
  Dihedral  :  4.259  59.383    598
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 6.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.38 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 20.10 %
    Favored  : 76.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.62 (0.36), residues: 539
  helix: -3.35 (0.70), residues: 39
  sheet: -0.62 (0.49), residues: 132
  loop : -1.00 (0.31), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  47 
 PHE   0.007   0.001   PHE C  71 
 TYR   0.016   0.001   TYR B 109 
 ARG   0.003   0.000   ARG B  67 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02721 (  103)
  hydrogen bonds       : angle       5.57837 (  255)
  SS BOND              : bond        0.00418 (    8)
  SS BOND              : angle       0.79573 (   16)
  covalent geometry    : bond        0.00229 ( 4142)
  covalent geometry    : angle       0.50186 ( 5665)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1794.32 seconds
wall clock time: 32 minutes 13.99 seconds (1933.99 seconds total)