Starting phenix.real_space_refine
on Sat Apr  4 21:59:20 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9jkr_61569/04_2026/9jkr_61569.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9jkr_61569/04_2026/9jkr_61569.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9jkr_61569/04_2026/9jkr_61569.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9jkr_61569/04_2026/9jkr_61569.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9jkr_61569/04_2026/9jkr_61569.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9jkr_61569/04_2026/9jkr_61569.map"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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=  -0.000 sd=   0.021
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      23      5.16       5
     C    2787      2.51       5
     N     741      2.21       5
     O     853      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4404
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 873
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 114, 873
          Classifications: {'peptide': 114}
          Link IDs: {'PTRANS': 5, 'TRANS': 108}
    Chain: "B"
      Number of atoms: 813
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 813
          Classifications: {'peptide': 107}
          Link IDs: {'PTRANS': 6, 'TRANS': 100}
    Chain: "C"
      Number of atoms: 948
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 123, 948
          Classifications: {'peptide': 123}
          Link IDs: {'PTRANS': 5, 'TRANS': 117}
    Chain: "D"
      Number of atoms: 886
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 113, 886
          Classifications: {'peptide': 113}
          Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 106}
    Chain: "I"
      Number of atoms: 884
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 110, 884
          Classifications: {'peptide': 110}
          Link IDs: {'PTRANS': 6, 'TRANS': 103}
  Time building chain proxies: 0.99, per 1000 atoms: 0.22
  Number of scatterers: 4404
  At special positions: 0
  Unit cell: (67.8375, 84.0375, 95.175, 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      23     16.00
     O     853      8.00
     N     741      7.00
     C    2787      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  22 " - pdb=" SG  CYS A  92 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  24 " - pdb=" SG  CYS B  89 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  93 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  23 " - pdb=" SG  CYS D  94 " distance=2.03
    Simple disulfide: pdb=" SG  CYS I  72 " - pdb=" SG  CYS I 114 " distance=2.03
    Simple disulfide: pdb=" SG  CYS I 106 " - pdb=" SG  CYS I 139 " 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: 0.35
  Conformation dependent library (CDL) restraints added in 169.5 milliseconds
  

  1114 Ramachandran restraints generated.
    557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1044

  Finding SS restraints...
    Secondary structure from input PDB file:
      9 helices and 10 sheets defined
      14.3% alpha, 22.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.09
  Creating SS restraints...
    Processing helix  chain 'A' and resid 61 through 64
    Processing helix  chain 'A' and resid 83 through 87
      removed outlier: 4.151A  pdb=" N   THR A  87 " --> pdb=" O   ALA A  84 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 53 through 56
    Processing helix  chain 'C' and resid 84 through 88
    Processing helix  chain 'I' and resid 33 through 45
      removed outlier: 4.352A  pdb=" N   GLN I  37 " --> pdb=" O   VAL I  33 " (cutoff:3.500A)
      removed outlier: 3.988A  pdb=" N   ALA I  39 " --> pdb=" O   ALA I  35 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   ARG I  40 " --> pdb=" O   ILE I  36 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   ARG I  41 " --> pdb=" O   GLN I  37 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 72 through 84
    Processing helix  chain 'I' and resid 86 through 90
      removed outlier: 3.827A  pdb=" N   LYS I  90 " --> pdb=" O   SER I  87 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 91 through 106
      removed outlier: 3.680A  pdb=" N   THR I  96 " --> pdb=" O   LYS I  92 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 120 through 135
    Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 7
      removed outlier: 3.666A  pdb=" N   SER A  23 " --> pdb=" O   GLN A   5 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   GLN A  77 " --> pdb=" O   ASP A  72 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   SER A  70 " --> pdb=" O   TYR A  79 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 57 through 59
      removed outlier: 6.680A  pdb=" N   TRP A  36 " --> pdb=" O   ILE A  48 " (cutoff:3.500A)
      removed outlier: 4.292A  pdb=" N   TYR A  50 " --> pdb=" O   TRP A  34 " (cutoff:3.500A)
      removed outlier: 6.574A  pdb=" N   TRP A  34 " --> pdb=" O   TYR A  50 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   GLN A  39 " --> pdb=" O   VAL A  89 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   ALA A  88 " --> pdb=" O   VAL A 108 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   THR A 106 " --> pdb=" O   TYR A  90 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 5 through 7
      removed outlier: 3.897A  pdb=" N   THR B  75 " --> pdb=" O   ASN B  64 " (cutoff:3.500A)
      removed outlier: 3.991A  pdb=" N   ASN B  64 " --> pdb=" O   THR B  75 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 11 through 13
      removed outlier: 7.206A  pdb=" N   VAL B  12 " --> pdb=" O   GLU B 106 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   GLN B  39 " --> pdb=" O   MET B  86 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 11 through 13
      removed outlier: 7.206A  pdb=" N   VAL B  12 " --> pdb=" O   GLU B 106 " (cutoff:3.500A)
      removed outlier: 3.873A  pdb=" N   GLN B  91 " --> pdb=" O   THR B  98 " (cutoff:3.500A)
      removed outlier: 4.288A  pdb=" N   THR B  98 " --> pdb=" O   GLN B  91 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 4 through 7
      removed outlier: 3.580A  pdb=" N   SER C   7 " --> pdb=" O   SER C  21 " (cutoff:3.500A)
      removed outlier: 4.141A  pdb=" N   SER C  21 " --> pdb=" O   SER C   7 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   VAL C  20 " --> pdb=" O   ILE C  81 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   ILE C  81 " --> pdb=" O   VAL C  20 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 10 through 12
      removed outlier: 3.656A  pdb=" N   TYR C  91 " --> pdb=" O   THR C 115 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   GLN C  39 " --> pdb=" O   VAL C  90 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 50 through 52
    Processing sheet with id=AA9, first strand: chain 'D' and resid 21 through 24
      removed outlier: 3.908A  pdb=" N   GLU D  76 " --> pdb=" O   SER D  73 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   SER D  73 " --> pdb=" O   GLU D  76 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'I' and resid 58 through 61

    120 hydrogen bonds defined for protein.
    288 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: 0.52

  Time building geometry restraints manager: 0.49 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: 1416
        1.34 -     1.46: 1128
        1.46 -     1.58: 1927
        1.58 -     1.70: 0
        1.70 -     1.82: 34
  Bond restraints: 4505
  Sorted by residual:
  bond pdb=" CB  ILE A  95 "
       pdb=" CG2 ILE A  95 "
    ideal  model  delta    sigma   weight residual
    1.521  1.487  0.034 3.30e-02 9.18e+02 1.04e+00
  bond pdb=" C   LYS D 109 "
       pdb=" N   VAL D 110 "
    ideal  model  delta    sigma   weight residual
    1.335  1.321  0.014 1.41e-02 5.03e+03 1.03e+00
  bond pdb=" CG1 ILE D  81 "
       pdb=" CD1 ILE D  81 "
    ideal  model  delta    sigma   weight residual
    1.513  1.474  0.039 3.90e-02 6.57e+02 9.94e-01
  bond pdb=" CG  PRO D   8 "
       pdb=" CD  PRO D   8 "
    ideal  model  delta    sigma   weight residual
    1.512  1.485  0.027 2.70e-02 1.37e+03 9.83e-01
  bond pdb=" CB  VAL I  58 "
       pdb=" CG2 VAL I  58 "
    ideal  model  delta    sigma   weight residual
    1.521  1.489  0.032 3.30e-02 9.18e+02 9.48e-01
  ... (remaining 4500 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.58: 5872
        1.58 -     3.17: 205
        3.17 -     4.75: 23
        4.75 -     6.34: 10
        6.34 -     7.92: 3
  Bond angle restraints: 6113
  Sorted by residual:
  angle pdb=" N   ALA I  51 "
        pdb=" CA  ALA I  51 "
        pdb=" C   ALA I  51 "
      ideal   model   delta    sigma   weight residual
     114.75  108.79    5.96 1.26e+00 6.30e-01 2.23e+01
  angle pdb=" C   TRP D  56 "
        pdb=" N   ALA D  57 "
        pdb=" CA  ALA D  57 "
      ideal   model   delta    sigma   weight residual
     121.54  127.68   -6.14 1.91e+00 2.74e-01 1.03e+01
  angle pdb=" C   LEU C  55 "
        pdb=" N   ASP C  56 "
        pdb=" CA  ASP C  56 "
      ideal   model   delta    sigma   weight residual
     121.54  127.44   -5.90 1.91e+00 2.74e-01 9.55e+00
  angle pdb=" N   TYR B  95 "
        pdb=" CA  TYR B  95 "
        pdb=" C   TYR B  95 "
      ideal   model   delta    sigma   weight residual
     109.81  116.51   -6.70 2.21e+00 2.05e-01 9.18e+00
  angle pdb=" CA  TYR B  95 "
        pdb=" CB  TYR B  95 "
        pdb=" CG  TYR B  95 "
      ideal   model   delta    sigma   weight residual
     113.90  108.56    5.34 1.80e+00 3.09e-01 8.81e+00
  ... (remaining 6108 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.83: 2364
       15.83 -    31.65: 258
       31.65 -    47.47: 59
       47.47 -    63.30: 6
       63.30 -    79.12: 3
  Dihedral angle restraints: 2690
    sinusoidal: 1057
      harmonic: 1633
  Sorted by residual:
  dihedral pdb=" CA  ASP A  26 "
           pdb=" C   ASP A  26 "
           pdb=" N   SER A  27 "
           pdb=" CA  SER A  27 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -136.12  -43.88     0      5.00e+00 4.00e-02 7.70e+01
  dihedral pdb=" CA  CYS I 139 "
           pdb=" C   CYS I 139 "
           pdb=" N   TRP I 140 "
           pdb=" CA  TRP I 140 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.53  -26.47     0      5.00e+00 4.00e-02 2.80e+01
  dihedral pdb=" CA  GLY C  97 "
           pdb=" C   GLY C  97 "
           pdb=" N   ILE C  98 "
           pdb=" CA  ILE C  98 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.59  -26.41     0      5.00e+00 4.00e-02 2.79e+01
  ... (remaining 2687 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 506
       0.045 -    0.090: 125
       0.090 -    0.135: 40
       0.135 -    0.180: 4
       0.180 -    0.225: 1
  Chirality restraints: 676
  Sorted by residual:
  chirality pdb=" CA  TYR B  95 "
            pdb=" N   TYR B  95 "
            pdb=" C   TYR B  95 "
            pdb=" CB  TYR B  95 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.23 2.00e-01 2.50e+01 1.27e+00
  chirality pdb=" CA  ILE D  91 "
            pdb=" N   ILE D  91 "
            pdb=" C   ILE D  91 "
            pdb=" CB  ILE D  91 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.15 2.00e-01 2.50e+01 5.92e-01
  chirality pdb=" CB  THR D  59 "
            pdb=" CA  THR D  59 "
            pdb=" OG1 THR D  59 "
            pdb=" CG2 THR D  59 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.41    0.14 2.00e-01 2.50e+01 5.22e-01
  ... (remaining 673 not shown)

  Planarity restraints: 784
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY I  93 "   -0.025 5.00e-02 4.00e+02   3.74e-02 2.24e+00
        pdb=" N   PRO I  94 "    0.065 5.00e-02 4.00e+02
        pdb=" CA  PRO I  94 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO I  94 "   -0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B  95 "    0.014 2.00e-02 2.50e+03   1.00e-02 2.00e+00
        pdb=" CG  TYR B  95 "   -0.024 2.00e-02 2.50e+03
        pdb=" CD1 TYR B  95 "    0.002 2.00e-02 2.50e+03
        pdb=" CD2 TYR B  95 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE1 TYR B  95 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR B  95 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ  TYR B  95 "    0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR B  95 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL D  64 "    0.023 5.00e-02 4.00e+02   3.50e-02 1.96e+00
        pdb=" N   PRO D  65 "   -0.061 5.00e-02 4.00e+02
        pdb=" CA  PRO D  65 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO D  65 "    0.019 5.00e-02 4.00e+02
  ... (remaining 781 not shown)

  Histogram of nonbonded interaction distances:
        2.07 -     2.63: 58
        2.63 -     3.20: 4055
        3.20 -     3.77: 6291
        3.77 -     4.33: 8757
        4.33 -     4.90: 15074
  Nonbonded interactions: 34235
  Sorted by model distance:
  nonbonded pdb=" O   LEU I  42 "
            pdb=" OG  SER I  46 "
     model   vdw
     2.066 3.040
  nonbonded pdb=" OG  SER D  25 "
            pdb=" O   GLN D  27 "
     model   vdw
     2.141 3.040
  nonbonded pdb=" O   TYR C 107 "
            pdb=" OH  TYR D  42 "
     model   vdw
     2.185 3.040
  nonbonded pdb=" OH  TYR D  42 "
            pdb=" OE1 GLN D  95 "
     model   vdw
     2.194 3.040
  nonbonded pdb=" OE1 GLN B   7 "
            pdb=" OG1 THR B 103 "
     model   vdw
     2.222 3.040
  ... (remaining 34230 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:             1.950
  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:          0.060
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     5.810
  Find NCS groups from input model:        0.030
  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:             0.000
  Load rotamer database and sin/cos tables:1.200
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.100
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7479
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      :  0.006   0.039   4511  Z= 0.240
  Angle     :  0.719   7.919   6125  Z= 0.401
  Chirality :  0.045   0.225    676
  Planarity :  0.004   0.037    784
  Dihedral  : 13.436  79.123   1628
  Min Nonbonded Distance : 2.066

Molprobity Statistics.
  All-atom Clashscore : 11.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.67 %
    Favored  : 88.33 %
  Rotamer:
    Outliers :  0.41 %
    Allowed  :  8.64 %
    Favored  : 90.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.60 (0.32), residues: 557
  helix: -0.14 (0.65), residues: 52
  sheet: -2.49 (0.37), residues: 171
  loop : -2.81 (0.30), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG I  47 
 TYR   0.024   0.002   TYR B  95 
 PHE   0.012   0.002   PHE A  78 
 TRP   0.007   0.001   TRP I 140 
 HIS   0.005   0.001   HIS I 105 

Details of bonding type rmsd
  covalent geometry    : bond        0.00551 ( 4505)
  covalent geometry    : angle       0.71816 ( 6113)
  SS BOND              : bond        0.00352 (    6)
  SS BOND              : angle       1.19727 (   12)
  hydrogen bonds       : bond        0.24959 (  118)
  hydrogen bonds       : angle       9.81757 (  288)

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

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

  1114 Ramachandran restraints generated.
    557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1114 Ramachandran restraints generated.
    557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 227
  time to evaluate  : 0.169 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   29 PHE cc_start: 0.7805 (p90) cc_final: 0.7494 (p90)
REVERT: D    6 GLN cc_start: 0.7622 (mt0) cc_final: 0.7411 (tt0)
REVERT: D   31 TYR cc_start: 0.8303 (t80) cc_final: 0.7934 (t80)
  outliers start: 2
  outliers final: 2
  residues processed: 228
  average time/residue: 0.0796
  time to fit residues: 22.2682
Evaluate side-chains
  153 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 151
  time to evaluate  : 0.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   49 ILE
Chi-restraints excluded: chain D residue   97 TYR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 54 optimal weight:    0.6980
   chunk 24 optimal weight:    2.9990
   chunk 48 optimal weight:    0.7980
   chunk 26 optimal weight:    0.8980
   chunk 2 optimal weight:    0.0000
   chunk 16 optimal weight:    1.9990
   chunk 32 optimal weight:    2.9990
   chunk 31 optimal weight:    0.0030
   chunk 25 optimal weight:    0.8980
   chunk 50 optimal weight:    0.9980
   chunk 53 optimal weight:    0.6980
   overall best weight:    0.4394

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

Flipped N/Q/H residues before XYZ refinement:
B  39 GLN
B  93 ASN
C   3 GLN
C  65 GLN
C 110 HIS
D  44 GLN
** I 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
I 104 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.117980 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.102076 restraints weight = 9171.412|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.105323 restraints weight = 4744.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.107507 restraints weight = 3023.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.108934 restraints weight = 2186.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.110109 restraints weight = 1736.767|
|-----------------------------------------------------------------------------|
r_work (final): 0.3603
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7645
moved from start:          0.3637

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   4511  Z= 0.136
  Angle     :  0.751  13.207   6125  Z= 0.379
  Chirality :  0.045   0.197    676
  Planarity :  0.005   0.042    784
  Dihedral  :  6.064  40.719    617
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 11.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.36 %
    Favored  : 92.64 %
  Rotamer:
    Outliers :  3.50 %
    Allowed  : 20.58 %
    Favored  : 75.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.52 (0.33), residues: 557
  helix:  1.09 (0.74), residues: 52
  sheet: -1.87 (0.36), residues: 187
  loop : -2.06 (0.31), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B  47 
 TYR   0.017   0.002   TYR B  95 
 PHE   0.012   0.002   PHE C  29 
 TRP   0.009   0.001   TRP C 111 
 HIS   0.006   0.001   HIS I 101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 4505)
  covalent geometry    : angle       0.74957 ( 6113)
  SS BOND              : bond        0.00409 (    6)
  SS BOND              : angle       1.25959 (   12)
  hydrogen bonds       : bond        0.03504 (  118)
  hydrogen bonds       : angle       6.28436 (  288)

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

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

  1114 Ramachandran restraints generated.
    557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1114 Ramachandran restraints generated.
    557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 178
  time to evaluate  : 0.176 
Fit side-chains
   revert: symmetry clash
REVERT: A    5 GLN cc_start: 0.8029 (tm-30) cc_final: 0.7613 (tm-30)
REVERT: A   47 TYR cc_start: 0.7655 (t80) cc_final: 0.6559 (t80)
REVERT: A   91 TYR cc_start: 0.8620 (m-80) cc_final: 0.8399 (m-80)
REVERT: D   51 LYS cc_start: 0.8648 (mtmt) cc_final: 0.8266 (mtmm)
REVERT: D   93 TYR cc_start: 0.8726 (m-80) cc_final: 0.8388 (m-10)
REVERT: I   48 ASP cc_start: 0.8548 (t70) cc_final: 0.7528 (t0)
REVERT: I   52 GLU cc_start: 0.8303 (mm-30) cc_final: 0.8004 (tt0)
REVERT: I   77 LEU cc_start: 0.8846 (mm) cc_final: 0.8592 (mm)
REVERT: I   90 LYS cc_start: 0.8767 (mmmt) cc_final: 0.8515 (mmmm)
REVERT: I  126 GLU cc_start: 0.8300 (mt-10) cc_final: 0.8048 (mt-10)
  outliers start: 17
  outliers final: 11
  residues processed: 184
  average time/residue: 0.0637
  time to fit residues: 15.1414
Evaluate side-chains
  161 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 150
  time to evaluate  : 0.167 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 ASN
Chi-restraints excluded: chain A residue   83 THR
Chi-restraints excluded: chain A residue  109 THR
Chi-restraints excluded: chain B residue   49 ILE
Chi-restraints excluded: chain C residue   98 ILE
Chi-restraints excluded: chain C residue  116 THR
Chi-restraints excluded: chain D residue   22 ASN
Chi-restraints excluded: chain D residue   97 TYR
Chi-restraints excluded: chain I residue   43 LEU
Chi-restraints excluded: chain I residue  116 THR
Chi-restraints excluded: chain I residue  120 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 43 optimal weight:    0.9990
   chunk 27 optimal weight:    0.6980
   chunk 24 optimal weight:    4.9990
   chunk 28 optimal weight:    0.9980
   chunk 52 optimal weight:    3.9990
   chunk 47 optimal weight:    5.9990
   chunk 46 optimal weight:    0.9990
   chunk 41 optimal weight:    7.9990
   chunk 13 optimal weight:    0.9990
   chunk 16 optimal weight:    0.0040
   chunk 4 optimal weight:    1.9990
   overall best weight:    0.7396

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

Flipped N/Q/H residues before XYZ refinement:
B   7 GLN
C  65 GLN
D  37 ASN
I  37 GLN
** I 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.117210 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.101273 restraints weight = 9168.202|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.104476 restraints weight = 4738.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.106697 restraints weight = 3034.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.108238 restraints weight = 2186.304|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.109330 restraints weight = 1707.346|
|-----------------------------------------------------------------------------|
r_work (final): 0.3589
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7763
moved from start:          0.4664

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   4511  Z= 0.131
  Angle     :  0.683  14.946   6125  Z= 0.345
  Chirality :  0.044   0.195    676
  Planarity :  0.005   0.044    784
  Dihedral  :  5.836  46.214    617
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 8.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.82 %
    Favored  : 93.18 %
  Rotamer:
    Outliers :  5.56 %
    Allowed  : 22.43 %
    Favored  : 72.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.16 (0.33), residues: 557
  helix:  0.99 (0.74), residues: 57
  sheet: -1.58 (0.36), residues: 190
  loop : -1.82 (0.31), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG D  34 
 TYR   0.017   0.002   TYR C  60 
 PHE   0.010   0.002   PHE C  29 
 TRP   0.010   0.001   TRP C 111 
 HIS   0.005   0.001   HIS I 105 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 4505)
  covalent geometry    : angle       0.68106 ( 6113)
  SS BOND              : bond        0.00242 (    6)
  SS BOND              : angle       1.21574 (   12)
  hydrogen bonds       : bond        0.03143 (  118)
  hydrogen bonds       : angle       5.56525 (  288)

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

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

  1114 Ramachandran restraints generated.
    557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1114 Ramachandran restraints generated.
    557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 170
  time to evaluate  : 0.177 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 GLN cc_start: 0.8032 (tm-30) cc_final: 0.7789 (tm-30)
REVERT: A   47 TYR cc_start: 0.7777 (t80) cc_final: 0.7145 (t80)
REVERT: A   86 ASP cc_start: 0.7606 (m-30) cc_final: 0.7377 (m-30)
REVERT: A   91 TYR cc_start: 0.8545 (m-80) cc_final: 0.8229 (m-80)
REVERT: B   31 ASN cc_start: 0.8159 (m-40) cc_final: 0.7196 (t0)
REVERT: C   52 MET cc_start: 0.8301 (OUTLIER) cc_final: 0.7929 (mtp)
REVERT: D    3 VAL cc_start: 0.9402 (t) cc_final: 0.9194 (m)
REVERT: D    6 GLN cc_start: 0.8535 (mt0) cc_final: 0.7695 (tt0)
REVERT: I   48 ASP cc_start: 0.8509 (t70) cc_final: 0.8019 (t0)
REVERT: I   77 LEU cc_start: 0.8915 (mm) cc_final: 0.8632 (mm)
  outliers start: 27
  outliers final: 20
  residues processed: 179
  average time/residue: 0.0596
  time to fit residues: 14.0837
Evaluate side-chains
  166 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 145
  time to evaluate  : 0.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 ASN
Chi-restraints excluded: chain A residue   83 THR
Chi-restraints excluded: chain A residue   89 VAL
Chi-restraints excluded: chain A residue  106 THR
Chi-restraints excluded: chain A residue  109 THR
Chi-restraints excluded: chain B residue   49 ILE
Chi-restraints excluded: chain B residue   98 THR
Chi-restraints excluded: chain C residue   52 MET
Chi-restraints excluded: chain C residue  106 GLU
Chi-restraints excluded: chain C residue  107 TYR
Chi-restraints excluded: chain C residue  116 THR
Chi-restraints excluded: chain D residue   10 SER
Chi-restraints excluded: chain D residue   52 LEU
Chi-restraints excluded: chain D residue   81 ILE
Chi-restraints excluded: chain D residue   97 TYR
Chi-restraints excluded: chain I residue   43 LEU
Chi-restraints excluded: chain I residue   58 VAL
Chi-restraints excluded: chain I residue   87 SER
Chi-restraints excluded: chain I residue   98 MET
Chi-restraints excluded: chain I residue  116 THR
Chi-restraints excluded: chain I residue  120 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 48 optimal weight:    0.9980
   chunk 37 optimal weight:    0.8980
   chunk 47 optimal weight:    0.9980
   chunk 34 optimal weight:    8.9990
   chunk 25 optimal weight:    4.9990
   chunk 16 optimal weight:    7.9990
   chunk 8 optimal weight:    7.9990
   chunk 41 optimal weight:    6.9990
   chunk 36 optimal weight:    1.9990
   chunk 5 optimal weight:    4.9990
   chunk 19 optimal weight:    1.9990
   overall best weight:    1.3784

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

Flipped N/Q/H residues before XYZ refinement:
B  56 GLN
B  78 ASN
C  65 GLN
** C  77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 110 HIS
D  37 ASN
I  82 GLN
** I 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.112706 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.096818 restraints weight = 9183.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.099835 restraints weight = 4874.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.101872 restraints weight = 3158.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.103284 restraints weight = 2319.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.104282 restraints weight = 1850.727|
|-----------------------------------------------------------------------------|
r_work (final): 0.3510
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7952
moved from start:          0.5838

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   4511  Z= 0.184
  Angle     :  0.715   9.376   6125  Z= 0.368
  Chirality :  0.044   0.176    676
  Planarity :  0.005   0.041    784
  Dihedral  :  6.267  52.652    617
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 11.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.80 %
    Favored  : 91.20 %
  Rotamer:
    Outliers :  7.00 %
    Allowed  : 23.87 %
    Favored  : 69.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.05 (0.33), residues: 557
  helix:  0.97 (0.70), residues: 61
  sheet: -1.42 (0.37), residues: 184
  loop : -1.83 (0.31), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 104 
 TYR   0.020   0.002   TYR B  95 
 PHE   0.021   0.002   PHE A  78 
 TRP   0.012   0.001   TRP C 111 
 HIS   0.005   0.001   HIS I 105 

Details of bonding type rmsd
  covalent geometry    : bond        0.00429 ( 4505)
  covalent geometry    : angle       0.71355 ( 6113)
  SS BOND              : bond        0.00640 (    6)
  SS BOND              : angle       1.23090 (   12)
  hydrogen bonds       : bond        0.03231 (  118)
  hydrogen bonds       : angle       5.56648 (  288)

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

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

  1114 Ramachandran restraints generated.
    557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1114 Ramachandran restraints generated.
    557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 163
  time to evaluate  : 0.186 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 GLN cc_start: 0.8146 (tm-30) cc_final: 0.7712 (tm-30)
REVERT: A   47 TYR cc_start: 0.8308 (t80) cc_final: 0.7611 (t80)
REVERT: A   69 MET cc_start: 0.8209 (mtt) cc_final: 0.7919 (mtt)
REVERT: A   86 ASP cc_start: 0.7898 (m-30) cc_final: 0.7676 (m-30)
REVERT: A   91 TYR cc_start: 0.8496 (m-80) cc_final: 0.8196 (m-80)
REVERT: B   31 ASN cc_start: 0.8386 (m-40) cc_final: 0.7653 (t0)
REVERT: C   52 MET cc_start: 0.8571 (OUTLIER) cc_final: 0.8196 (mtp)
REVERT: C   60 TYR cc_start: 0.8185 (m-80) cc_final: 0.7896 (m-80)
REVERT: D    3 VAL cc_start: 0.9406 (t) cc_final: 0.9162 (m)
REVERT: D   37 ASN cc_start: 0.7948 (OUTLIER) cc_final: 0.7450 (t160)
REVERT: I   48 ASP cc_start: 0.8642 (t70) cc_final: 0.8304 (t0)
REVERT: I  111 GLU cc_start: 0.7249 (tm-30) cc_final: 0.6976 (tm-30)
  outliers start: 34
  outliers final: 28
  residues processed: 175
  average time/residue: 0.0593
  time to fit residues: 13.6224
Evaluate side-chains
  175 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 145
  time to evaluate  : 0.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 VAL
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain A residue   75 ASN
Chi-restraints excluded: chain A residue   83 THR
Chi-restraints excluded: chain A residue   87 THR
Chi-restraints excluded: chain A residue  106 THR
Chi-restraints excluded: chain A residue  109 THR
Chi-restraints excluded: chain B residue   49 ILE
Chi-restraints excluded: chain B residue   79 VAL
Chi-restraints excluded: chain B residue   98 THR
Chi-restraints excluded: chain C residue    5 VAL
Chi-restraints excluded: chain C residue   11 VAL
Chi-restraints excluded: chain C residue   52 MET
Chi-restraints excluded: chain C residue   74 LYS
Chi-restraints excluded: chain C residue   83 LEU
Chi-restraints excluded: chain C residue  107 TYR
Chi-restraints excluded: chain C residue  116 THR
Chi-restraints excluded: chain D residue   10 SER
Chi-restraints excluded: chain D residue   13 VAL
Chi-restraints excluded: chain D residue   20 THR
Chi-restraints excluded: chain D residue   37 ASN
Chi-restraints excluded: chain D residue   52 LEU
Chi-restraints excluded: chain D residue   81 ILE
Chi-restraints excluded: chain D residue   97 TYR
Chi-restraints excluded: chain I residue   43 LEU
Chi-restraints excluded: chain I residue   58 VAL
Chi-restraints excluded: chain I residue   87 SER
Chi-restraints excluded: chain I residue  116 THR
Chi-restraints excluded: chain I residue  118 ILE
Chi-restraints excluded: chain I residue  120 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 7 optimal weight:    5.9990
   chunk 6 optimal weight:    5.9990
   chunk 35 optimal weight:    5.9990
   chunk 29 optimal weight:    5.9990
   chunk 8 optimal weight:    3.9990
   chunk 9 optimal weight:    0.8980
   chunk 27 optimal weight:    0.2980
   chunk 46 optimal weight:    1.9990
   chunk 17 optimal weight:    9.9990
   chunk 45 optimal weight:    5.9990
   chunk 52 optimal weight:    0.9980
   overall best weight:    1.6384

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

Flipped N/Q/H residues before XYZ refinement:
C  65 GLN
** C  77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  95 GLN
** I 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.108110 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.092269 restraints weight = 9247.660|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.095288 restraints weight = 4778.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.097359 restraints weight = 3047.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.098721 restraints weight = 2210.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.099788 restraints weight = 1757.289|
|-----------------------------------------------------------------------------|
r_work (final): 0.3430
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7953
moved from start:          0.6337

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033   4511  Z= 0.200
  Angle     :  0.719  10.509   6125  Z= 0.368
  Chirality :  0.045   0.174    676
  Planarity :  0.005   0.039    784
  Dihedral  :  6.255  54.028    617
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 12.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.90 %
    Favored  : 92.10 %
  Rotamer:
    Outliers :  6.79 %
    Allowed  : 25.31 %
    Favored  : 67.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.71 (0.34), residues: 557
  helix:  1.12 (0.70), residues: 61
  sheet: -1.00 (0.39), residues: 174
  loop : -1.70 (0.32), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG I  47 
 TYR   0.014   0.002   TYR C 107 
 PHE   0.023   0.002   PHE A  78 
 TRP   0.014   0.001   TRP C 111 
 HIS   0.006   0.001   HIS I 105 

Details of bonding type rmsd
  covalent geometry    : bond        0.00466 ( 4505)
  covalent geometry    : angle       0.71664 ( 6113)
  SS BOND              : bond        0.00393 (    6)
  SS BOND              : angle       1.39695 (   12)
  hydrogen bonds       : bond        0.03110 (  118)
  hydrogen bonds       : angle       5.55161 (  288)

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

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

  1114 Ramachandran restraints generated.
    557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1114 Ramachandran restraints generated.
    557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 150
  time to evaluate  : 0.182 
Fit side-chains
   revert: symmetry clash
REVERT: A    5 GLN cc_start: 0.8258 (tm-30) cc_final: 0.7817 (tm-30)
REVERT: A   76 ASN cc_start: 0.7956 (m-40) cc_final: 0.7633 (m-40)
REVERT: A   77 GLN cc_start: 0.8295 (mt0) cc_final: 0.7170 (pt0)
REVERT: A   91 TYR cc_start: 0.8528 (m-80) cc_final: 0.8095 (m-80)
REVERT: B   31 ASN cc_start: 0.8519 (m-40) cc_final: 0.7747 (t0)
REVERT: B   86 MET cc_start: 0.7040 (mtp) cc_final: 0.6626 (ttt)
REVERT: C   52 MET cc_start: 0.8756 (OUTLIER) cc_final: 0.8155 (mtp)
REVERT: C   60 TYR cc_start: 0.8341 (m-80) cc_final: 0.8043 (m-80)
REVERT: D    3 VAL cc_start: 0.9396 (t) cc_final: 0.9155 (m)
REVERT: D    5 THR cc_start: 0.9079 (m) cc_final: 0.8876 (p)
REVERT: I   90 LYS cc_start: 0.8982 (mmmt) cc_final: 0.8754 (mmmm)
REVERT: I  103 LYS cc_start: 0.8898 (mtmm) cc_final: 0.8349 (mtmm)
REVERT: I  111 GLU cc_start: 0.7401 (tm-30) cc_final: 0.6964 (tm-30)
  outliers start: 33
  outliers final: 30
  residues processed: 161
  average time/residue: 0.0561
  time to fit residues: 11.7428
Evaluate side-chains
  177 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 146
  time to evaluate  : 0.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 ASN
Chi-restraints excluded: chain A residue   83 THR
Chi-restraints excluded: chain A residue   87 THR
Chi-restraints excluded: chain A residue   89 VAL
Chi-restraints excluded: chain A residue  106 THR
Chi-restraints excluded: chain A residue  108 VAL
Chi-restraints excluded: chain A residue  109 THR
Chi-restraints excluded: chain B residue   49 ILE
Chi-restraints excluded: chain B residue   52 VAL
Chi-restraints excluded: chain B residue   98 THR
Chi-restraints excluded: chain C residue    5 VAL
Chi-restraints excluded: chain C residue   11 VAL
Chi-restraints excluded: chain C residue   52 MET
Chi-restraints excluded: chain C residue   73 ASP
Chi-restraints excluded: chain C residue   74 LYS
Chi-restraints excluded: chain C residue  107 TYR
Chi-restraints excluded: chain C residue  116 THR
Chi-restraints excluded: chain D residue   10 SER
Chi-restraints excluded: chain D residue   13 VAL
Chi-restraints excluded: chain D residue   20 THR
Chi-restraints excluded: chain D residue   52 LEU
Chi-restraints excluded: chain D residue   81 ILE
Chi-restraints excluded: chain D residue   97 TYR
Chi-restraints excluded: chain I residue   43 LEU
Chi-restraints excluded: chain I residue   58 VAL
Chi-restraints excluded: chain I residue   77 LEU
Chi-restraints excluded: chain I residue   87 SER
Chi-restraints excluded: chain I residue  112 THR
Chi-restraints excluded: chain I residue  116 THR
Chi-restraints excluded: chain I residue  118 ILE
Chi-restraints excluded: chain I residue  120 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 4 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9980
   chunk 5 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9980
   chunk 35 optimal weight:    3.9990
   chunk 6 optimal weight:    3.9990
   chunk 44 optimal weight:    6.9990
   chunk 14 optimal weight:    0.7980
   chunk 22 optimal weight:    0.5980
   chunk 33 optimal weight:    0.9990
   chunk 18 optimal weight:    3.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
B   7 GLN
B  56 GLN
B  78 ASN
C  77 ASN
D  37 ASN
D  95 GLN
** I 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.110506 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.094609 restraints weight = 9259.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.097671 restraints weight = 4755.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.099802 restraints weight = 3012.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.101287 restraints weight = 2168.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.102327 restraints weight = 1701.481|
|-----------------------------------------------------------------------------|
r_work (final): 0.3470
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7907
moved from start:          0.6694

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4511  Z= 0.140
  Angle     :  0.670   9.041   6125  Z= 0.343
  Chirality :  0.042   0.172    676
  Planarity :  0.004   0.042    784
  Dihedral  :  6.017  57.840    617
  Min Nonbonded Distance : 2.288

Molprobity Statistics.
  All-atom Clashscore : 10.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.72 %
    Favored  : 92.28 %
  Rotamer:
    Outliers :  7.20 %
    Allowed  : 25.31 %
    Favored  : 67.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.40 (0.35), residues: 557
  helix:  1.24 (0.70), residues: 61
  sheet: -0.63 (0.40), residues: 173
  loop : -1.57 (0.32), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D  34 
 TYR   0.012   0.001   TYR A  50 
 PHE   0.021   0.002   PHE A  78 
 TRP   0.012   0.001   TRP C 111 
 HIS   0.004   0.001   HIS I 105 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 4505)
  covalent geometry    : angle       0.66922 ( 6113)
  SS BOND              : bond        0.00458 (    6)
  SS BOND              : angle       1.13476 (   12)
  hydrogen bonds       : bond        0.02815 (  118)
  hydrogen bonds       : angle       5.36628 (  288)

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

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

  1114 Ramachandran restraints generated.
    557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1114 Ramachandran restraints generated.
    557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 156
  time to evaluate  : 0.131 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 GLN cc_start: 0.8204 (tm-30) cc_final: 0.7706 (tm-30)
REVERT: A   47 TYR cc_start: 0.8405 (t80) cc_final: 0.7534 (t80)
REVERT: A   91 TYR cc_start: 0.8407 (m-80) cc_final: 0.8021 (m-80)
REVERT: B   31 ASN cc_start: 0.8504 (m-40) cc_final: 0.7735 (t0)
REVERT: B   86 MET cc_start: 0.6892 (mtp) cc_final: 0.6531 (ttt)
REVERT: C   52 MET cc_start: 0.8731 (OUTLIER) cc_final: 0.8116 (mtp)
REVERT: D    3 VAL cc_start: 0.9391 (t) cc_final: 0.9151 (m)
REVERT: D   24 LYS cc_start: 0.8872 (tttt) cc_final: 0.8525 (tttm)
REVERT: I   82 GLN cc_start: 0.8869 (tp40) cc_final: 0.8271 (tp-100)
REVERT: I  103 LYS cc_start: 0.8886 (mtmm) cc_final: 0.8317 (mtmm)
REVERT: I  111 GLU cc_start: 0.7311 (tm-30) cc_final: 0.6915 (tm-30)
  outliers start: 35
  outliers final: 27
  residues processed: 170
  average time/residue: 0.0589
  time to fit residues: 13.1094
Evaluate side-chains
  172 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 144
  time to evaluate  : 0.112 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 ASN
Chi-restraints excluded: chain A residue   83 THR
Chi-restraints excluded: chain A residue   89 VAL
Chi-restraints excluded: chain A residue  106 THR
Chi-restraints excluded: chain A residue  108 VAL
Chi-restraints excluded: chain A residue  109 THR
Chi-restraints excluded: chain B residue   49 ILE
Chi-restraints excluded: chain B residue   52 VAL
Chi-restraints excluded: chain B residue   98 THR
Chi-restraints excluded: chain C residue    4 LEU
Chi-restraints excluded: chain C residue   11 VAL
Chi-restraints excluded: chain C residue   52 MET
Chi-restraints excluded: chain C residue   73 ASP
Chi-restraints excluded: chain C residue   74 LYS
Chi-restraints excluded: chain C residue  107 TYR
Chi-restraints excluded: chain C residue  116 THR
Chi-restraints excluded: chain D residue   13 VAL
Chi-restraints excluded: chain D residue   20 THR
Chi-restraints excluded: chain D residue   52 LEU
Chi-restraints excluded: chain D residue   81 ILE
Chi-restraints excluded: chain D residue   97 TYR
Chi-restraints excluded: chain I residue   43 LEU
Chi-restraints excluded: chain I residue   77 LEU
Chi-restraints excluded: chain I residue  109 THR
Chi-restraints excluded: chain I residue  112 THR
Chi-restraints excluded: chain I residue  116 THR
Chi-restraints excluded: chain I residue  118 ILE
Chi-restraints excluded: chain I residue  120 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 10 optimal weight:    4.9990
   chunk 25 optimal weight:    5.9990
   chunk 24 optimal weight:    2.9990
   chunk 12 optimal weight:    3.9990
   chunk 52 optimal weight:    5.9990
   chunk 29 optimal weight:    6.9990
   chunk 21 optimal weight:    8.9990
   chunk 38 optimal weight:    2.9990
   chunk 44 optimal weight:    6.9990
   chunk 13 optimal weight:    1.9990
   chunk 54 optimal weight:    0.4980
   overall best weight:    2.4988

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

Flipped N/Q/H residues before XYZ refinement:
B   7 GLN
B  78 ASN
C  59 GLN
C  65 GLN
D  37 ASN
D  44 GLN
** I 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.103626 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.088297 restraints weight = 9475.457|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.091185 restraints weight = 4888.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.093132 restraints weight = 3117.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.094483 restraints weight = 2272.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.095469 restraints weight = 1805.398|
|-----------------------------------------------------------------------------|
r_work (final): 0.3363
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8034
moved from start:          0.7071

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.046   4511  Z= 0.284
  Angle     :  0.799   7.656   6125  Z= 0.416
  Chirality :  0.046   0.191    676
  Planarity :  0.005   0.039    784
  Dihedral  :  6.605  57.991    617
  Min Nonbonded Distance : 2.232

Molprobity Statistics.
  All-atom Clashscore : 13.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.05 %
    Favored  : 89.95 %
  Rotamer:
    Outliers :  7.61 %
    Allowed  : 26.95 %
    Favored  : 65.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.62 (0.34), residues: 557
  helix:  0.81 (0.66), residues: 61
  sheet: -0.71 (0.40), residues: 173
  loop : -1.70 (0.31), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG I  47 
 TYR   0.017   0.002   TYR C 107 
 PHE   0.022   0.003   PHE A  78 
 TRP   0.014   0.001   TRP C 111 
 HIS   0.004   0.001   HIS I 105 

Details of bonding type rmsd
  covalent geometry    : bond        0.00661 ( 4505)
  covalent geometry    : angle       0.79737 ( 6113)
  SS BOND              : bond        0.00343 (    6)
  SS BOND              : angle       1.47153 (   12)
  hydrogen bonds       : bond        0.03603 (  118)
  hydrogen bonds       : angle       5.73517 (  288)

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

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

  1114 Ramachandran restraints generated.
    557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1114 Ramachandran restraints generated.
    557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 151
  time to evaluate  : 0.151 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 GLN cc_start: 0.8235 (tm-30) cc_final: 0.7715 (tm-30)
REVERT: A   91 TYR cc_start: 0.8453 (m-80) cc_final: 0.8072 (m-80)
REVERT: B   31 ASN cc_start: 0.8650 (m-40) cc_final: 0.7857 (t0)
REVERT: B   86 MET cc_start: 0.7205 (mtp) cc_final: 0.6939 (ttt)
REVERT: C   60 TYR cc_start: 0.8280 (m-80) cc_final: 0.8017 (m-80)
REVERT: D    3 VAL cc_start: 0.9467 (t) cc_final: 0.9217 (m)
REVERT: D   24 LYS cc_start: 0.8941 (tttt) cc_final: 0.8547 (tttm)
REVERT: D   34 ARG cc_start: 0.8310 (mmm160) cc_final: 0.7947 (mmt90)
REVERT: D   37 ASN cc_start: 0.8160 (OUTLIER) cc_final: 0.7215 (t160)
REVERT: I   82 GLN cc_start: 0.9030 (tp40) cc_final: 0.8391 (tp-100)
REVERT: I  111 GLU cc_start: 0.7318 (tm-30) cc_final: 0.6896 (tm-30)
  outliers start: 37
  outliers final: 30
  residues processed: 167
  average time/residue: 0.0648
  time to fit residues: 13.9516
Evaluate side-chains
  177 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 146
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 ASN
Chi-restraints excluded: chain A residue   83 THR
Chi-restraints excluded: chain A residue   89 VAL
Chi-restraints excluded: chain A residue   95 ILE
Chi-restraints excluded: chain A residue  106 THR
Chi-restraints excluded: chain A residue  108 VAL
Chi-restraints excluded: chain A residue  109 THR
Chi-restraints excluded: chain B residue   49 ILE
Chi-restraints excluded: chain B residue   52 VAL
Chi-restraints excluded: chain C residue    4 LEU
Chi-restraints excluded: chain C residue   11 VAL
Chi-restraints excluded: chain C residue   29 PHE
Chi-restraints excluded: chain C residue   59 GLN
Chi-restraints excluded: chain C residue   73 ASP
Chi-restraints excluded: chain C residue   74 LYS
Chi-restraints excluded: chain C residue  107 TYR
Chi-restraints excluded: chain C residue  116 THR
Chi-restraints excluded: chain D residue   10 SER
Chi-restraints excluded: chain D residue   13 VAL
Chi-restraints excluded: chain D residue   20 THR
Chi-restraints excluded: chain D residue   37 ASN
Chi-restraints excluded: chain D residue   52 LEU
Chi-restraints excluded: chain D residue   81 ILE
Chi-restraints excluded: chain D residue   97 TYR
Chi-restraints excluded: chain I residue   43 LEU
Chi-restraints excluded: chain I residue   77 LEU
Chi-restraints excluded: chain I residue  109 THR
Chi-restraints excluded: chain I residue  112 THR
Chi-restraints excluded: chain I residue  116 THR
Chi-restraints excluded: chain I residue  118 ILE
Chi-restraints excluded: chain I residue  120 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 52 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9990
   chunk 28 optimal weight:    4.9990
   chunk 18 optimal weight:    3.9990
   chunk 1 optimal weight:    0.9980
   chunk 19 optimal weight:    0.7980
   chunk 44 optimal weight:    6.9990
   chunk 47 optimal weight:    0.9990
   chunk 48 optimal weight:    0.8980
   chunk 22 optimal weight:    0.8980
   chunk 41 optimal weight:    2.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
B   7 GLN
** C   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  59 GLN
D  37 ASN
** I  32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.108627 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.092867 restraints weight = 9262.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.095868 restraints weight = 4775.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.097945 restraints weight = 3036.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.099382 restraints weight = 2198.577|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.100380 restraints weight = 1733.155|
|-----------------------------------------------------------------------------|
r_work (final): 0.3440
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7959
moved from start:          0.7278

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   4511  Z= 0.150
  Angle     :  0.734   8.453   6125  Z= 0.373
  Chirality :  0.044   0.165    676
  Planarity :  0.004   0.041    784
  Dihedral  :  6.331  59.639    617
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 10.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.82 %
    Favored  : 93.18 %
  Rotamer:
    Outliers :  4.94 %
    Allowed  : 28.81 %
    Favored  : 66.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.31 (0.35), residues: 557
  helix:  1.17 (0.68), residues: 61
  sheet: -0.47 (0.41), residues: 167
  loop : -1.53 (0.32), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 104 
 TYR   0.018   0.002   TYR C  60 
 PHE   0.020   0.002   PHE A  78 
 TRP   0.011   0.001   TRP C 111 
 HIS   0.004   0.001   HIS I 105 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 ( 4505)
  covalent geometry    : angle       0.72592 ( 6113)
  SS BOND              : bond        0.00493 (    6)
  SS BOND              : angle       2.52375 (   12)
  hydrogen bonds       : bond        0.02858 (  118)
  hydrogen bonds       : angle       5.46750 (  288)

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

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

  1114 Ramachandran restraints generated.
    557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1114 Ramachandran restraints generated.
    557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 160
  time to evaluate  : 0.173 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 GLN cc_start: 0.8186 (tm-30) cc_final: 0.7606 (tm-30)
REVERT: A   77 GLN cc_start: 0.8408 (mt0) cc_final: 0.7434 (pt0)
REVERT: A   91 TYR cc_start: 0.8430 (m-80) cc_final: 0.8021 (m-80)
REVERT: B   31 ASN cc_start: 0.8566 (m-40) cc_final: 0.7787 (t0)
REVERT: B   86 MET cc_start: 0.6916 (mtp) cc_final: 0.6640 (ttt)
REVERT: C   60 TYR cc_start: 0.8291 (m-80) cc_final: 0.7992 (m-80)
REVERT: D    3 VAL cc_start: 0.9356 (t) cc_final: 0.9134 (m)
REVERT: D   24 LYS cc_start: 0.8931 (tttt) cc_final: 0.8529 (tttm)
REVERT: D   34 ARG cc_start: 0.8253 (mmm160) cc_final: 0.7915 (mmt90)
REVERT: D   37 ASN cc_start: 0.8232 (OUTLIER) cc_final: 0.7311 (t160)
REVERT: D   51 LYS cc_start: 0.8580 (mtmt) cc_final: 0.8200 (mtmm)
REVERT: I   82 GLN cc_start: 0.8973 (tp40) cc_final: 0.8315 (tp-100)
REVERT: I  103 LYS cc_start: 0.8950 (mtmm) cc_final: 0.8364 (mtmm)
REVERT: I  111 GLU cc_start: 0.7234 (tm-30) cc_final: 0.6989 (tm-30)
  outliers start: 24
  outliers final: 23
  residues processed: 167
  average time/residue: 0.0588
  time to fit residues: 12.9279
Evaluate side-chains
  178 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 154
  time to evaluate  : 0.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 THR
Chi-restraints excluded: chain A residue   89 VAL
Chi-restraints excluded: chain A residue  108 VAL
Chi-restraints excluded: chain A residue  109 THR
Chi-restraints excluded: chain B residue    6 THR
Chi-restraints excluded: chain B residue   49 ILE
Chi-restraints excluded: chain B residue   52 VAL
Chi-restraints excluded: chain C residue   11 VAL
Chi-restraints excluded: chain C residue   29 PHE
Chi-restraints excluded: chain C residue   59 GLN
Chi-restraints excluded: chain C residue   73 ASP
Chi-restraints excluded: chain C residue   74 LYS
Chi-restraints excluded: chain C residue  107 TYR
Chi-restraints excluded: chain C residue  116 THR
Chi-restraints excluded: chain D residue   37 ASN
Chi-restraints excluded: chain D residue   52 LEU
Chi-restraints excluded: chain D residue   81 ILE
Chi-restraints excluded: chain D residue   97 TYR
Chi-restraints excluded: chain I residue   43 LEU
Chi-restraints excluded: chain I residue   77 LEU
Chi-restraints excluded: chain I residue  109 THR
Chi-restraints excluded: chain I residue  112 THR
Chi-restraints excluded: chain I residue  116 THR
Chi-restraints excluded: chain I residue  120 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 21 optimal weight:    8.9990
   chunk 18 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9990
   chunk 12 optimal weight:    0.6980
   chunk 48 optimal weight:    1.9990
   chunk 27 optimal weight:    3.9990
   chunk 1 optimal weight:    0.7980
   chunk 39 optimal weight:    0.8980
   chunk 13 optimal weight:    2.9990
   chunk 16 optimal weight:    2.9990
   chunk 53 optimal weight:    2.9990
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
** A  76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B   7 GLN
** C   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  59 GLN
D  37 ASN
** I  32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.108271 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.092451 restraints weight = 9294.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.095431 restraints weight = 4799.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.097490 restraints weight = 3074.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.098896 restraints weight = 2233.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.099817 restraints weight = 1769.005|
|-----------------------------------------------------------------------------|
r_work (final): 0.3431
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7969
moved from start:          0.7462

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   4511  Z= 0.163
  Angle     :  0.745   9.870   6125  Z= 0.379
  Chirality :  0.044   0.167    676
  Planarity :  0.004   0.043    784
  Dihedral  :  6.198  58.655    617
  Min Nonbonded Distance : 2.347

Molprobity Statistics.
  All-atom Clashscore : 10.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.44 %
    Favored  : 91.56 %
  Rotamer:
    Outliers :  6.17 %
    Allowed  : 28.19 %
    Favored  : 65.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.22 (0.35), residues: 557
  helix:  1.30 (0.68), residues: 61
  sheet: -0.45 (0.41), residues: 167
  loop : -1.46 (0.32), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 104 
 TYR   0.016   0.002   TYR C  60 
 PHE   0.021   0.002   PHE A  78 
 TRP   0.012   0.001   TRP C 111 
 HIS   0.004   0.001   HIS I 105 

Details of bonding type rmsd
  covalent geometry    : bond        0.00384 ( 4505)
  covalent geometry    : angle       0.73688 ( 6113)
  SS BOND              : bond        0.00543 (    6)
  SS BOND              : angle       2.59815 (   12)
  hydrogen bonds       : bond        0.02880 (  118)
  hydrogen bonds       : angle       5.33801 (  288)

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

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

  1114 Ramachandran restraints generated.
    557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1114 Ramachandran restraints generated.
    557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 154
  time to evaluate  : 0.180 
Fit side-chains
   revert: symmetry clash
REVERT: A    5 GLN cc_start: 0.8149 (tm-30) cc_final: 0.7625 (tm-30)
REVERT: A   91 TYR cc_start: 0.8421 (m-80) cc_final: 0.7986 (m-80)
REVERT: B   31 ASN cc_start: 0.8574 (m-40) cc_final: 0.7796 (t0)
REVERT: B   86 MET cc_start: 0.6930 (mtp) cc_final: 0.6637 (ttt)
REVERT: D    3 VAL cc_start: 0.9409 (t) cc_final: 0.9164 (m)
REVERT: D   24 LYS cc_start: 0.8961 (tttt) cc_final: 0.8521 (tttm)
REVERT: D   51 LYS cc_start: 0.8563 (mtmt) cc_final: 0.8174 (mtmm)
REVERT: I   82 GLN cc_start: 0.8967 (tp40) cc_final: 0.8301 (tp-100)
REVERT: I  103 LYS cc_start: 0.8932 (mtmm) cc_final: 0.8368 (mtmm)
REVERT: I  111 GLU cc_start: 0.7152 (tm-30) cc_final: 0.6910 (tm-30)
  outliers start: 30
  outliers final: 28
  residues processed: 162
  average time/residue: 0.0581
  time to fit residues: 12.4835
Evaluate side-chains
  177 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 149
  time to evaluate  : 0.187 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 ASN
Chi-restraints excluded: chain A residue   83 THR
Chi-restraints excluded: chain A residue   89 VAL
Chi-restraints excluded: chain A residue  108 VAL
Chi-restraints excluded: chain A residue  109 THR
Chi-restraints excluded: chain B residue    6 THR
Chi-restraints excluded: chain B residue   49 ILE
Chi-restraints excluded: chain B residue   52 VAL
Chi-restraints excluded: chain C residue   11 VAL
Chi-restraints excluded: chain C residue   29 PHE
Chi-restraints excluded: chain C residue   59 GLN
Chi-restraints excluded: chain C residue   73 ASP
Chi-restraints excluded: chain C residue   74 LYS
Chi-restraints excluded: chain C residue  107 TYR
Chi-restraints excluded: chain C residue  116 THR
Chi-restraints excluded: chain D residue    5 THR
Chi-restraints excluded: chain D residue   10 SER
Chi-restraints excluded: chain D residue   13 VAL
Chi-restraints excluded: chain D residue   20 THR
Chi-restraints excluded: chain D residue   52 LEU
Chi-restraints excluded: chain D residue   81 ILE
Chi-restraints excluded: chain D residue   97 TYR
Chi-restraints excluded: chain I residue   43 LEU
Chi-restraints excluded: chain I residue   77 LEU
Chi-restraints excluded: chain I residue  109 THR
Chi-restraints excluded: chain I residue  112 THR
Chi-restraints excluded: chain I residue  116 THR
Chi-restraints excluded: chain I residue  120 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 6 optimal weight:    1.9990
   chunk 19 optimal weight:    2.9990
   chunk 17 optimal weight:    4.9990
   chunk 48 optimal weight:    1.9990
   chunk 49 optimal weight:    2.9990
   chunk 13 optimal weight:    4.9990
   chunk 46 optimal weight:    3.9990
   chunk 39 optimal weight:    0.4980
   chunk 45 optimal weight:    5.9990
   chunk 12 optimal weight:    5.9990
   chunk 37 optimal weight:    0.6980
   overall best weight:    1.6386

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

Flipped N/Q/H residues before XYZ refinement:
B   7 GLN
** C   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  37 ASN
** I 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.106350 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.090622 restraints weight = 9312.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.093513 restraints weight = 4840.650|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.095530 restraints weight = 3112.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.096942 restraints weight = 2270.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 19)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.097757 restraints weight = 1797.033|
|-----------------------------------------------------------------------------|
r_work (final): 0.3400
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8010
moved from start:          0.7597

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   4511  Z= 0.208
  Angle     :  0.771   8.431   6125  Z= 0.397
  Chirality :  0.045   0.177    676
  Planarity :  0.005   0.042    784
  Dihedral  :  6.343  57.729    617
  Min Nonbonded Distance : 2.400

Molprobity Statistics.
  All-atom Clashscore : 12.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.80 %
    Favored  : 91.20 %
  Rotamer:
    Outliers :  6.58 %
    Allowed  : 28.40 %
    Favored  : 65.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.20 (0.35), residues: 557
  helix:  1.20 (0.68), residues: 61
  sheet: -0.36 (0.42), residues: 167
  loop : -1.47 (0.32), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG D  34 
 TYR   0.014   0.002   TYR D  55 
 PHE   0.019   0.002   PHE A  78 
 TRP   0.011   0.001   TRP C 111 
 HIS   0.004   0.001   HIS I 105 

Details of bonding type rmsd
  covalent geometry    : bond        0.00490 ( 4505)
  covalent geometry    : angle       0.76313 ( 6113)
  SS BOND              : bond        0.00547 (    6)
  SS BOND              : angle       2.59385 (   12)
  hydrogen bonds       : bond        0.03141 (  118)
  hydrogen bonds       : angle       5.39220 (  288)

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

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

  1114 Ramachandran restraints generated.
    557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1114 Ramachandran restraints generated.
    557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 150
  time to evaluate  : 0.147 
Fit side-chains
   revert: symmetry clash
REVERT: A    5 GLN cc_start: 0.8148 (tm-30) cc_final: 0.7612 (tm-30)
REVERT: A   77 GLN cc_start: 0.8307 (OUTLIER) cc_final: 0.7252 (pt0)
REVERT: A   91 TYR cc_start: 0.8441 (m-80) cc_final: 0.7959 (m-80)
REVERT: B   31 ASN cc_start: 0.8596 (m-40) cc_final: 0.7823 (t0)
REVERT: B   86 MET cc_start: 0.7028 (mtp) cc_final: 0.6766 (ttt)
REVERT: D    3 VAL cc_start: 0.9406 (t) cc_final: 0.9160 (m)
REVERT: D   24 LYS cc_start: 0.8946 (tttt) cc_final: 0.8520 (tttm)
REVERT: D   37 ASN cc_start: 0.8212 (OUTLIER) cc_final: 0.7237 (t160)
REVERT: I   82 GLN cc_start: 0.8994 (tp40) cc_final: 0.8319 (tp-100)
REVERT: I  103 LYS cc_start: 0.8954 (mtmm) cc_final: 0.8397 (mtmm)
REVERT: I  111 GLU cc_start: 0.7332 (tm-30) cc_final: 0.7082 (tm-30)
  outliers start: 32
  outliers final: 28
  residues processed: 163
  average time/residue: 0.0544
  time to fit residues: 11.7924
Evaluate side-chains
  178 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 148
  time to evaluate  : 0.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 ASN
Chi-restraints excluded: chain A residue   77 GLN
Chi-restraints excluded: chain A residue   83 THR
Chi-restraints excluded: chain A residue   89 VAL
Chi-restraints excluded: chain A residue  106 THR
Chi-restraints excluded: chain A residue  108 VAL
Chi-restraints excluded: chain A residue  109 THR
Chi-restraints excluded: chain B residue    6 THR
Chi-restraints excluded: chain B residue   49 ILE
Chi-restraints excluded: chain B residue   52 VAL
Chi-restraints excluded: chain B residue   70 THR
Chi-restraints excluded: chain C residue   11 VAL
Chi-restraints excluded: chain C residue   73 ASP
Chi-restraints excluded: chain C residue   74 LYS
Chi-restraints excluded: chain C residue  107 TYR
Chi-restraints excluded: chain C residue  116 THR
Chi-restraints excluded: chain D residue    5 THR
Chi-restraints excluded: chain D residue   10 SER
Chi-restraints excluded: chain D residue   13 VAL
Chi-restraints excluded: chain D residue   20 THR
Chi-restraints excluded: chain D residue   37 ASN
Chi-restraints excluded: chain D residue   52 LEU
Chi-restraints excluded: chain D residue   81 ILE
Chi-restraints excluded: chain D residue   97 TYR
Chi-restraints excluded: chain I residue   43 LEU
Chi-restraints excluded: chain I residue   77 LEU
Chi-restraints excluded: chain I residue  109 THR
Chi-restraints excluded: chain I residue  112 THR
Chi-restraints excluded: chain I residue  116 THR
Chi-restraints excluded: chain I residue  120 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 50 optimal weight:    0.9990
   chunk 44 optimal weight:    6.9990
   chunk 2 optimal weight:    0.1980
   chunk 20 optimal weight:    1.9990
   chunk 16 optimal weight:    0.3980
   chunk 51 optimal weight:    0.8980
   chunk 27 optimal weight:    1.9990
   chunk 32 optimal weight:    5.9990
   chunk 36 optimal weight:    5.9990
   chunk 6 optimal weight:    3.9990
   chunk 4 optimal weight:    0.4980
   overall best weight:    0.5982

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

Flipped N/Q/H residues before XYZ refinement:
B   7 GLN
** C   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  59 GLN
** I  32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.109783 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.093963 restraints weight = 9205.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.096910 restraints weight = 4842.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.098978 restraints weight = 3129.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.100434 restraints weight = 2285.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.101366 restraints weight = 1806.203|
|-----------------------------------------------------------------------------|
r_work (final): 0.3459
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7968
moved from start:          0.7656

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4511  Z= 0.146
  Angle     :  0.756  10.654   6125  Z= 0.384
  Chirality :  0.044   0.161    676
  Planarity :  0.004   0.044    784
  Dihedral  :  6.223  55.914    617
  Min Nonbonded Distance : 2.360

Molprobity Statistics.
  All-atom Clashscore : 11.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.80 %
    Favored  : 91.20 %
  Rotamer:
    Outliers :  5.76 %
    Allowed  : 30.04 %
    Favored  : 64.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.06 (0.35), residues: 557
  helix:  1.33 (0.69), residues: 61
  sheet: -0.27 (0.41), residues: 173
  loop : -1.38 (0.33), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG D  34 
 TYR   0.016   0.002   TYR D  55 
 PHE   0.019   0.002   PHE A  78 
 TRP   0.008   0.001   TRP C 111 
 HIS   0.006   0.002   HIS I 105 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 4505)
  covalent geometry    : angle       0.74868 ( 6113)
  SS BOND              : bond        0.00495 (    6)
  SS BOND              : angle       2.53186 (   12)
  hydrogen bonds       : bond        0.02877 (  118)
  hydrogen bonds       : angle       5.24431 (  288)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 967.09 seconds
wall clock time: 17 minutes 23.37 seconds (1043.37 seconds total)