Starting phenix.real_space_refine
on Sun Apr 27 01:26:20 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9j66_61167/04_2025/9j66_61167.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9j66_61167/04_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_61167/04_2025/9j66_61167.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9j66_61167/04_2025/9j66_61167.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9j66_61167/04_2025/9j66_61167.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9j66_61167/04_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-5669/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: 3.96, per 1000 atoms: 0.98
  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: 1.00
  Conformation dependent library (CDL) restraints added in 469.5 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: 0.55
  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: 1.01

  Time building geometry restraints manager: 1.21 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:             4.410
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     15.130
  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:             0.000
  Load rotamer database and sin/cos tables:2.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.760
-------------------------------------------------------------------------------
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  : 0.424 
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: 0.1374
  time to fit residues: 14.6526
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  : 0.387 
-------------------------------------------------------------------------------
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 = 0.3871 r_free = 0.3871 target = 0.160454 restraints weight = 4780.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.164675 restraints weight = 4700.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.166596 restraints weight = 2987.476|
|-----------------------------------------------------------------------------|
r_work (final): 0.3912
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6895
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  : 0.735 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   82 GLU cc_start: 0.7521 (tt0) cc_final: 0.7110 (tp30)
REVERT: C   36 TYR cc_start: 0.8342 (m-10) cc_final: 0.8010 (m-10)
  outliers start: 4
  outliers final: 1
  residues processed: 75
  average time/residue: 0.1466
  time to fit residues: 14.0171
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  : 0.429 
-------------------------------------------------------------------------------
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:    9.9990
   chunk 8 optimal weight:    4.9990
   chunk 11 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9980
   chunk 18 optimal weight:    2.9990
   chunk 47 optimal weight:    0.0970
   chunk 32 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9980
   chunk 53 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   chunk 15 optimal weight:    0.5980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.4118 r_free = 0.4118 target = 0.185130 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.152138 restraints weight = 4918.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.152918 restraints weight = 4320.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.155183 restraints weight = 3742.591|
|-----------------------------------------------------------------------------|
r_work (final): 0.3802
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7105
moved from start:          0.1723

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= 0.188
  Angle     :  0.564   6.695   5681  Z= 0.298
  Chirality :  0.046   0.160    641
  Planarity :  0.005   0.056    735
  Dihedral  :  4.680  62.172    598
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 8.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.12 %
    Favored  : 93.88 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 13.99 %
    Favored  : 83.21 %
  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: -1.91 (0.35), residues: 539
  helix: -3.24 (0.80), residues: 33
  sheet: -1.09 (0.47), residues: 130
  loop : -1.18 (0.31), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP C  35 
 PHE   0.014   0.001   PHE B 110 
 TYR   0.030   0.002   TYR B 109 
 ARG   0.004   0.001   ARG B  50 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03724 (  103)
  hydrogen bonds       : angle       6.75742 (  255)
  SS BOND              : bond        0.00430 (    8)
  SS BOND              : angle       0.75789 (   16)
  covalent geometry    : bond        0.00443 ( 4142)
  covalent geometry    : angle       0.56286 ( 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  : 0.452 
Fit side-chains
   revert: symmetry clash
REVERT: C   36 TYR cc_start: 0.8779 (m-10) cc_final: 0.8191 (m-10)
  outliers start: 11
  outliers final: 9
  residues processed: 69
  average time/residue: 0.1303
  time to fit residues: 11.8964
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  : 0.387 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 25 optimal weight:    0.9980
   chunk 44 optimal weight:    0.9980
   chunk 45 optimal weight:    0.6980
   chunk 31 optimal weight:    1.9990
   chunk 14 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9990
   chunk 43 optimal weight:    4.9990
   chunk 13 optimal weight:    2.9990
   chunk 35 optimal weight:    0.8980
   chunk 39 optimal weight:    0.8980
   overall best weight:    0.8980

-------------------------------------------------------------------------------
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 ** 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 = 0.4078 r_free = 0.4078 target = 0.181498 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.149077 restraints weight = 4964.603|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.149502 restraints weight = 4396.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.151707 restraints weight = 3859.841|
|-----------------------------------------------------------------------------|
r_work (final): 0.3762
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7158
moved from start:          0.2222

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   4150  Z= 0.211
  Angle     :  0.589   5.853   5681  Z= 0.312
  Chirality :  0.047   0.161    641
  Planarity :  0.005   0.053    735
  Dihedral  :  5.161  70.859    598
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 9.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.61 %
    Favored  : 92.39 %
  Rotamer:
    Outliers :  3.82 %
    Allowed  : 15.27 %
    Favored  : 80.92 %
  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: -1.97 (0.36), residues: 539
  helix: -3.33 (0.81), residues: 33
  sheet: -1.16 (0.46), residues: 140
  loop : -1.19 (0.32), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP C  35 
 PHE   0.016   0.002   PHE C  94 
 TYR   0.026   0.002   TYR B 109 
 ARG   0.004   0.001   ARG B  50 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03555 (  103)
  hydrogen bonds       : angle       6.83951 (  255)
  SS BOND              : bond        0.00410 (    8)
  SS BOND              : angle       0.96066 (   16)
  covalent geometry    : bond        0.00497 ( 4142)
  covalent geometry    : angle       0.58747 ( 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
  80 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 65
  time to evaluate  : 0.395 
Fit side-chains
   revert: symmetry clash
REVERT: C   36 TYR cc_start: 0.8819 (m-10) cc_final: 0.8194 (m-10)
  outliers start: 15
  outliers final: 12
  residues processed: 72
  average time/residue: 0.1417
  time to fit residues: 13.2024
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  : 0.388 
-------------------------------------------------------------------------------
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  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:    6.9990
   chunk 7 optimal weight:    0.0980
   chunk 25 optimal weight:    0.6980
   chunk 40 optimal weight:    0.5980
   chunk 43 optimal weight:    0.0570
   chunk 32 optimal weight:    0.8980
   chunk 14 optimal weight:    3.9990
   chunk 37 optimal weight:    1.9990
   chunk 10 optimal weight:    2.9990
   chunk 39 optimal weight:    0.5980
   chunk 2 optimal weight:    3.9990
   overall best weight:    0.4098

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

Flipped N/Q/H residues before XYZ refinement:
** B 115 GLN ** 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 = 0.4112 r_free = 0.4112 target = 0.185161 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.152736 restraints weight = 5016.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.153332 restraints weight = 4258.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.155554 restraints weight = 3790.097|
|-----------------------------------------------------------------------------|
r_work (final): 0.3804
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7090
moved from start:          0.2251

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.066   4150  Z= 0.127
  Angle     :  0.529   5.194   5681  Z= 0.280
  Chirality :  0.045   0.149    641
  Planarity :  0.004   0.048    735
  Dihedral  :  4.727  65.218    598
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 8.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.19 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 16.28 %
    Favored  : 80.66 %
  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: -1.79 (0.36), residues: 539
  helix: -3.26 (0.83), residues: 33
  sheet: -0.79 (0.47), residues: 141
  loop : -1.18 (0.31), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B  47 
 PHE   0.013   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        0.03043 (  103)
  hydrogen bonds       : angle       6.26417 (  255)
  SS BOND              : bond        0.00390 (    8)
  SS BOND              : angle       0.84039 (   16)
  covalent geometry    : bond        0.00309 ( 4142)
  covalent geometry    : angle       0.52834 ( 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
  75 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 63
  time to evaluate  : 0.395 
Fit side-chains
   revert: symmetry clash
REVERT: C   36 TYR cc_start: 0.8653 (m-10) cc_final: 0.8147 (m-10)
  outliers start: 12
  outliers final: 10
  residues processed: 69
  average time/residue: 0.1111
  time to fit residues: 10.4706
Evaluate side-chains
  71 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 61
  time to evaluate  : 0.404 
-------------------------------------------------------------------------------
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:    0.4980
   chunk 43 optimal weight:    4.9990
   chunk 22 optimal weight:    0.2980
   chunk 11 optimal weight:    1.9990
   chunk 52 optimal weight:    0.0670
   chunk 18 optimal weight:    3.9990
   chunk 5 optimal weight:    0.5980
   chunk 53 optimal weight:    3.9990
   chunk 15 optimal weight:    0.5980
   chunk 24 optimal weight:    0.8980
   overall best weight:    0.4118

-------------------------------------------------------------------------------
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 = 0.4112 r_free = 0.4112 target = 0.185423 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.153470 restraints weight = 4857.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.154388 restraints weight = 4160.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.156972 restraints weight = 3605.753|
|-----------------------------------------------------------------------------|
r_work (final): 0.3813
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7077
moved from start:          0.2414

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062   4150  Z= 0.125
  Angle     :  0.525   5.398   5681  Z= 0.276
  Chirality :  0.045   0.146    641
  Planarity :  0.004   0.047    735
  Dihedral  :  4.645  65.151    598
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 8.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.94 %
    Favored  : 94.06 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 17.56 %
    Favored  : 78.88 %
  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 (0.35), residues: 539
  helix: -3.26 (0.82), residues: 33
  sheet: -0.81 (0.46), residues: 136
  loop : -1.13 (0.31), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP B  47 
 PHE   0.012   0.001   PHE C  94 
 TYR   0.020   0.001   TYR B 109 
 ARG   0.003   0.000   ARG A 457 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02971 (  103)
  hydrogen bonds       : angle       6.12627 (  255)
  SS BOND              : bond        0.00361 (    8)
  SS BOND              : angle       0.79634 (   16)
  covalent geometry    : bond        0.00303 ( 4142)
  covalent geometry    : angle       0.52431 ( 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: 14
    poor density    : 66
  time to evaluate  : 0.430 
Fit side-chains
   revert: symmetry clash
REVERT: C   36 TYR cc_start: 0.8663 (m-10) cc_final: 0.8133 (m-10)
REVERT: C  105 ASP cc_start: 0.5242 (m-30) cc_final: 0.4566 (m-30)
  outliers start: 14
  outliers final: 13
  residues processed: 71
  average time/residue: 0.1220
  time to fit residues: 11.9284
Evaluate side-chains
  76 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 63
  time to evaluate  : 0.440 
-------------------------------------------------------------------------------
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  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:    0.6980
   chunk 37 optimal weight:    0.9990
   chunk 21 optimal weight:    0.5980
   chunk 30 optimal weight:    0.6980
   chunk 33 optimal weight:    3.9990
   chunk 31 optimal weight:    0.5980
   chunk 14 optimal weight:    2.9990
   chunk 29 optimal weight:    0.1980
   chunk 38 optimal weight:    0.8980
   chunk 5 optimal weight:    0.6980
   overall best weight:    0.5580

-------------------------------------------------------------------------------
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 = 0.4088 r_free = 0.4088 target = 0.183172 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.151332 restraints weight = 4978.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.151991 restraints weight = 4170.600|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.154147 restraints weight = 3742.041|
|-----------------------------------------------------------------------------|
r_work (final): 0.3792
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7119
moved from start:          0.2521

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063   4150  Z= 0.149
  Angle     :  0.541   5.582   5681  Z= 0.285
  Chirality :  0.045   0.150    641
  Planarity :  0.004   0.048    735
  Dihedral  :  4.832  69.714    598
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 9.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.12 %
    Favored  : 93.88 %
  Rotamer:
    Outliers :  4.07 %
    Allowed  : 18.83 %
    Favored  : 77.10 %
  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: -1.78 (0.35), residues: 539
  helix: -3.27 (0.83), residues: 33
  sheet: -0.83 (0.47), residues: 136
  loop : -1.14 (0.31), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP B  47 
 PHE   0.012   0.001   PHE C  94 
 TYR   0.021   0.001   TYR B 109 
 ARG   0.003   0.000   ARG A 457 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03099 (  103)
  hydrogen bonds       : angle       6.23697 (  255)
  SS BOND              : bond        0.00388 (    8)
  SS BOND              : angle       0.81311 (   16)
  covalent geometry    : bond        0.00359 ( 4142)
  covalent geometry    : angle       0.53969 ( 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
  78 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 62
  time to evaluate  : 0.459 
Fit side-chains
   revert: symmetry clash
REVERT: C   36 TYR cc_start: 0.8719 (m-10) cc_final: 0.8183 (m-10)
REVERT: C  105 ASP cc_start: 0.5374 (m-30) cc_final: 0.4701 (m-30)
  outliers start: 16
  outliers final: 14
  residues processed: 68
  average time/residue: 0.1159
  time to fit residues: 10.8000
Evaluate side-chains
  76 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 62
  time to evaluate  : 0.439 
-------------------------------------------------------------------------------
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  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:    0.9980
   chunk 15 optimal weight:    0.2980
   chunk 12 optimal weight:    2.9990
   chunk 14 optimal weight:    1.9990
   chunk 46 optimal weight:    2.9990
   chunk 35 optimal weight:    0.0060
   chunk 19 optimal weight:    0.8980
   chunk 31 optimal weight:    1.9990
   chunk 48 optimal weight:    2.9990
   chunk 20 optimal weight:    0.7980
   overall best weight:    0.5996

-------------------------------------------------------------------------------
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 = 0.4083 r_free = 0.4083 target = 0.182799 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.151601 restraints weight = 4872.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.152499 restraints weight = 4145.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.154839 restraints weight = 3598.595|
|-----------------------------------------------------------------------------|
r_work (final): 0.3796
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7106
moved from start:          0.2679

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   4150  Z= 0.155
  Angle     :  0.546   5.621   5681  Z= 0.288
  Chirality :  0.045   0.154    641
  Planarity :  0.004   0.047    735
  Dihedral  :  4.878  69.135    598
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 8.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.68 %
    Favored  : 93.32 %
  Rotamer:
    Outliers :  4.58 %
    Allowed  : 18.07 %
    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: -1.80 (0.35), residues: 539
  helix: -3.32 (0.81), residues: 33
  sheet: -0.74 (0.48), residues: 134
  loop : -1.20 (0.31), residues: 372

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   0.018   0.001   TYR B 109 
 ARG   0.003   0.000   ARG A 457 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03063 (  103)
  hydrogen bonds       : angle       6.27990 (  255)
  SS BOND              : bond        0.00389 (    8)
  SS BOND              : angle       0.85177 (   16)
  covalent geometry    : bond        0.00366 ( 4142)
  covalent geometry    : angle       0.54469 ( 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: 18
    poor density    : 62
  time to evaluate  : 0.437 
Fit side-chains
   revert: symmetry clash
REVERT: C   36 TYR cc_start: 0.8721 (m-10) cc_final: 0.8080 (m-10)
  outliers start: 18
  outliers final: 16
  residues processed: 70
  average time/residue: 0.1151
  time to fit residues: 11.0682
Evaluate side-chains
  78 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 62
  time to evaluate  : 0.433 
-------------------------------------------------------------------------------
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 29 optimal weight:    0.4980
   chunk 14 optimal weight:    2.9990
   chunk 42 optimal weight:    5.9990
   chunk 53 optimal weight:    0.8980
   chunk 10 optimal weight:    2.9990
   chunk 51 optimal weight:    0.0000
   chunk 39 optimal weight:    0.6980
   chunk 19 optimal weight:    2.9990
   chunk 28 optimal weight:    0.8980
   chunk 4 optimal weight:    0.0000
   chunk 21 optimal weight:    0.5980
   overall best weight:    0.3588

-------------------------------------------------------------------------------
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 360 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4105 r_free = 0.4105 target = 0.185134 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.151905 restraints weight = 4930.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.155807 restraints weight = 4487.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.157830 restraints weight = 2963.452|
|-----------------------------------------------------------------------------|
r_work (final): 0.3827
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7066
moved from start:          0.2696

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   4150  Z= 0.122
  Angle     :  0.534   4.853   5681  Z= 0.281
  Chirality :  0.044   0.146    641
  Planarity :  0.004   0.047    735
  Dihedral  :  4.692  66.611    598
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 8.21
  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: -1.69 (0.36), residues: 539
  helix: -3.32 (0.81), residues: 33
  sheet: -0.77 (0.47), residues: 142
  loop : -1.07 (0.32), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B  47 
 PHE   0.009   0.001   PHE C  94 
 TYR   0.019   0.001   TYR B 109 
 ARG   0.002   0.000   ARG B  67 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02871 (  103)
  hydrogen bonds       : angle       6.02089 (  255)
  SS BOND              : bond        0.00400 (    8)
  SS BOND              : angle       1.07833 (   16)
  covalent geometry    : bond        0.00293 ( 4142)
  covalent geometry    : angle       0.53164 ( 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
  78 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 62
  time to evaluate  : 0.401 
Fit side-chains
   revert: symmetry clash
REVERT: C   36 TYR cc_start: 0.8635 (m-10) cc_final: 0.8052 (m-10)
  outliers start: 16
  outliers final: 14
  residues processed: 67
  average time/residue: 0.1125
  time to fit residues: 10.3318
Evaluate side-chains
  76 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 62
  time to evaluate  : 0.398 
-------------------------------------------------------------------------------
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  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  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:    0.0770
   chunk 34 optimal weight:    1.9990
   chunk 29 optimal weight:    0.5980
   chunk 16 optimal weight:    0.4980
   chunk 14 optimal weight:    2.9990
   chunk 47 optimal weight:    0.4980
   chunk 6 optimal weight:    0.7980
   chunk 7 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9980
   chunk 0 optimal weight:    2.9990
   chunk 27 optimal weight:    0.8980
   overall best weight:    0.4938

-------------------------------------------------------------------------------
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 = 0.4093 r_free = 0.4093 target = 0.183889 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.150347 restraints weight = 4937.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.154602 restraints weight = 4538.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.157016 restraints weight = 2974.974|
|-----------------------------------------------------------------------------|
r_work (final): 0.3817
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7081
moved from start:          0.2733

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   4150  Z= 0.138
  Angle     :  0.548   5.127   5681  Z= 0.288
  Chirality :  0.045   0.148    641
  Planarity :  0.004   0.047    735
  Dihedral  :  4.771  68.641    598
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 8.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.31 %
    Favored  : 93.69 %
  Rotamer:
    Outliers :  3.82 %
    Allowed  : 18.58 %
    Favored  : 77.61 %
  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: -1.75 (0.36), residues: 539
  helix: -3.37 (0.72), residues: 39
  sheet: -0.76 (0.47), residues: 142
  loop : -1.07 (0.32), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B  47 
 PHE   0.010   0.001   PHE C  94 
 TYR   0.018   0.001   TYR B 109 
 ARG   0.003   0.000   ARG B  67 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02983 (  103)
  hydrogen bonds       : angle       6.09352 (  255)
  SS BOND              : bond        0.00446 (    8)
  SS BOND              : angle       1.05112 (   16)
  covalent geometry    : bond        0.00327 ( 4142)
  covalent geometry    : angle       0.54607 ( 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
  77 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 62
  time to evaluate  : 0.437 
Fit side-chains
   revert: symmetry clash
REVERT: C   36 TYR cc_start: 0.8685 (m-10) cc_final: 0.8062 (m-10)
  outliers start: 15
  outliers final: 14
  residues processed: 67
  average time/residue: 0.1223
  time to fit residues: 11.2886
Evaluate side-chains
  76 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 62
  time to evaluate  : 0.409 
-------------------------------------------------------------------------------
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  500 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 34 optimal weight:    0.8980
   chunk 37 optimal weight:    0.4980
   chunk 14 optimal weight:    3.9990
   chunk 16 optimal weight:    0.9990
   chunk 50 optimal weight:    0.1980
   chunk 51 optimal weight:    5.9990
   chunk 43 optimal weight:    5.9990
   chunk 31 optimal weight:    0.0770
   chunk 47 optimal weight:    0.8980
   chunk 20 optimal weight:    0.6980
   chunk 13 optimal weight:    0.7980
   overall best weight:    0.4538

-------------------------------------------------------------------------------
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**
C  92 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.184034 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.151396 restraints weight = 4913.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.154956 restraints weight = 4499.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.156904 restraints weight = 3003.338|
|-----------------------------------------------------------------------------|
r_work (final): 0.3817
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7070
moved from start:          0.2786

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   4150  Z= 0.133
  Angle     :  0.543   4.942   5681  Z= 0.285
  Chirality :  0.045   0.145    641
  Planarity :  0.004   0.047    735
  Dihedral  :  4.742  68.245    598
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 8.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.94 %
    Favored  : 94.06 %
  Rotamer:
    Outliers :  3.82 %
    Allowed  : 19.08 %
    Favored  : 77.10 %
  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: -3.37 (0.72), residues: 39
  sheet: -0.70 (0.47), residues: 142
  loop : -1.04 (0.32), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B  47 
 PHE   0.008   0.001   PHE A 515 
 TYR   0.018   0.001   TYR B 109 
 ARG   0.003   0.000   ARG B  50 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02924 (  103)
  hydrogen bonds       : angle       6.03066 (  255)
  SS BOND              : bond        0.00403 (    8)
  SS BOND              : angle       1.01915 (   16)
  covalent geometry    : bond        0.00320 ( 4142)
  covalent geometry    : angle       0.54141 ( 5665)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2147.35 seconds
wall clock time: 38 minutes 2.04 seconds (2282.04 seconds total)