Starting phenix.real_space_refine
on Tue Feb 11 08:22:03 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8sx3_40825/02_2025/8sx3_40825.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8sx3_40825/02_2025/8sx3_40825.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8sx3_40825/02_2025/8sx3_40825.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8sx3_40825/02_2025/8sx3_40825.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8sx3_40825/02_2025/8sx3_40825.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8sx3_40825/02_2025/8sx3_40825.cif"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.008
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      17      5.16       5
     C    3059      2.51       5
     N     816      2.21       5
     O     924      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 4816
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 913
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 117, 913
          Classifications: {'peptide': 117}
          Link IDs: {'PTRANS': 4, 'TRANS': 112}
    Chain: "B"
      Number of atoms: 821
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 821
          Classifications: {'peptide': 107}
          Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101}
    Chain: "C"
      Number of atoms: 1236
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 154, 1236
          Classifications: {'peptide': 154}
          Link IDs: {'PTRANS': 8, 'TRANS': 145}
    Chain: "H"
      Number of atoms: 1016
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 129, 1016
          Classifications: {'peptide': 129}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 121}
    Chain: "L"
      Number of atoms: 802
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 802
          Classifications: {'peptide': 107}
          Link IDs: {'PTRANS': 4, 'TRANS': 102}
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Time building chain proxies: 4.54, per 1000 atoms: 0.94
  Number of scatterers: 4816
  At special positions: 0
  Unit cell: (55.825, 67.425, 122.525, 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      17     16.00
     O     924      8.00
     N     816      7.00
     C    3059      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  22 " - pdb=" SG  CYS A  97 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B  23 " - pdb=" SG  CYS B  88 " distance=2.05
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  98 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  21 " - pdb=" SG  CYS L  86 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG D   1 " - " NAG D   2 "
    NAG-ASN
      " NAG D   1 " - " ASN C  74 "
  Time building additional restraints: 1.39
  Conformation dependent library (CDL) restraints added in 633.8 milliseconds
  

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1102

  Finding SS restraints...
    Secondary structure from input PDB file:
      15 helices and 11 sheets defined
      18.9% alpha, 38.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.76
  Creating SS restraints...
    Processing helix  chain 'A' and resid 63 through 67
      removed outlier: 5.728A  pdb=" N   SER A  67 " --> pdb=" O   ALA A  64 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 75 through 77
      No H-bonds generated for 'chain 'A' and resid 75 through 77'
    Processing helix  chain 'A' and resid 88 through 92
    Processing helix  chain 'B' and resid 79 through 83
      removed outlier: 3.758A  pdb=" N   PHE B  83 " --> pdb=" O   PRO B  80 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 5 through 21
      Proline residue:  C  16  - end of helix
    Processing helix  chain 'C' and resid 26 through 38
    Processing helix  chain 'C' and resid 97 through 113
    Processing helix  chain 'C' and resid 114 through 122
    Processing helix  chain 'C' and resid 125 through 140
      removed outlier: 3.980A  pdb=" N   ALA C 140 " --> pdb=" O   ARG C 136 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 149 through 151
      No H-bonds generated for 'chain 'C' and resid 149 through 151'
    Processing helix  chain 'H' and resid 53 through 57
    Processing helix  chain 'H' and resid 64 through 67
    Processing helix  chain 'H' and resid 89 through 93
    Processing helix  chain 'L' and resid 25 through 28
    Processing helix  chain 'L' and resid 77 through 81
      removed outlier: 3.509A  pdb=" N   ASP L  81 " --> pdb=" O   ALA L  78 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 7
    Processing sheet with id=AA2, first strand: chain 'A' and resid 11 through 12
      removed outlier: 6.709A  pdb=" N   VAL A  36 " --> pdb=" O   HIS A  52 " (cutoff:3.500A)
      removed outlier: 4.560A  pdb=" N   HIS A  52 " --> pdb=" O   VAL A  36 " (cutoff:3.500A)
      removed outlier: 6.975A  pdb=" N   TRP A  38 " --> pdb=" O   LEU A  50 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   HIS A  52 " --> pdb=" O   PHE A  60 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   PHE A  60 " --> pdb=" O   HIS A  52 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 4 through 7
    Processing sheet with id=AA4, first strand: chain 'B' and resid 11 through 13
      removed outlier: 3.837A  pdb=" N   LEU B  11 " --> pdb=" O   ASN B 103 " (cutoff:3.500A)
      removed outlier: 4.219A  pdb=" N   GLU B 105 " --> pdb=" O   LEU B  11 " (cutoff:3.500A)
      removed outlier: 4.000A  pdb=" N   ALA B  13 " --> pdb=" O   GLU B 105 " (cutoff:3.500A)
      removed outlier: 6.902A  pdb=" N   LEU B  33 " --> pdb=" O   TYR B  49 " (cutoff:3.500A)
      removed outlier: 4.794A  pdb=" N   TYR B  49 " --> pdb=" O   LEU B  33 " (cutoff:3.500A)
      removed outlier: 6.671A  pdb=" N   TRP B  35 " --> pdb=" O   LEU B  47 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 41 through 42
      removed outlier: 7.251A  pdb=" N   GLY C  48 " --> pdb=" O   VAL C  89 " (cutoff:3.500A)
      removed outlier: 8.437A  pdb=" N   PHE C  91 " --> pdb=" O   GLY C  48 " (cutoff:3.500A)
      removed outlier: 6.723A  pdb=" N   ALA C  50 " --> pdb=" O   PHE C  91 " (cutoff:3.500A)
      removed outlier: 7.554A  pdb=" N   LEU C  93 " --> pdb=" O   ALA C  50 " (cutoff:3.500A)
      removed outlier: 9.742A  pdb=" N   LYS C  71 " --> pdb=" O   PRO C  86 " (cutoff:3.500A)
      removed outlier: 5.374A  pdb=" N   ARG C  88 " --> pdb=" O   LEU C  69 " (cutoff:3.500A)
      removed outlier: 8.544A  pdb=" N   ARG C 154 " --> pdb=" O   ILE C  64 " (cutoff:3.500A)
      removed outlier: 6.438A  pdb=" N   VAL C  66 " --> pdb=" O   ARG C 154 " (cutoff:3.500A)
      removed outlier: 7.469A  pdb=" N   LEU C 156 " --> pdb=" O   VAL C  66 " (cutoff:3.500A)
      removed outlier: 6.761A  pdb=" N   ILE C  68 " --> pdb=" O   LEU C 156 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'H' and resid 3 through 7
    Processing sheet with id=AA7, first strand: chain 'H' and resid 11 through 12
      removed outlier: 3.597A  pdb=" N   TRP H  33 " --> pdb=" O   THR H 101 " (cutoff:3.500A)
      removed outlier: 5.844A  pdb=" N   ARG H  38 " --> pdb=" O   TRP H  47 " (cutoff:3.500A)
      removed outlier: 5.294A  pdb=" N   TRP H  47 " --> pdb=" O   ARG H  38 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'H' and resid 11 through 12
      removed outlier: 7.044A  pdb=" N   CYS H  98 " --> pdb=" O   TRP H 121 " (cutoff:3.500A)
      removed outlier: 4.644A  pdb=" N   TRP H 121 " --> pdb=" O   CYS H  98 " (cutoff:3.500A)
      removed outlier: 6.621A  pdb=" N   ARG H 100 " --> pdb=" O   GLN H 119 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'L' and resid 3 through 5
    Processing sheet with id=AB1, first strand: chain 'L' and resid 8 through 12
      removed outlier: 6.296A  pdb=" N   GLN L  35 " --> pdb=" O   LEU L  44 " (cutoff:3.500A)
      removed outlier: 5.279A  pdb=" N   LEU L  44 " --> pdb=" O   GLN L  35 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'L' and resid 8 through 12

    213 hydrogen bonds defined for protein.
    525 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.39

  Time building geometry restraints manager: 1.49 seconds

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

  Histogram of bond lengths:
        1.13 -     1.27: 788
        1.27 -     1.41: 1288
        1.41 -     1.55: 2767
        1.55 -     1.69: 64
        1.69 -     1.82: 26
  Bond restraints: 4933
  Sorted by residual:
  bond pdb=" CG  PRO C 141 "
       pdb=" CD  PRO C 141 "
    ideal  model  delta    sigma   weight residual
    1.503  1.131  0.372 3.40e-02 8.65e+02 1.20e+02
  bond pdb=" N   PRO C 141 "
       pdb=" CD  PRO C 141 "
    ideal  model  delta    sigma   weight residual
    1.473  1.554 -0.081 1.40e-02 5.10e+03 3.36e+01
  bond pdb=" CB  PRO C  82 "
       pdb=" CG  PRO C  82 "
    ideal  model  delta    sigma   weight residual
    1.492  1.658 -0.166 5.00e-02 4.00e+02 1.10e+01
  bond pdb=" CB  PRO C 141 "
       pdb=" CG  PRO C 141 "
    ideal  model  delta    sigma   weight residual
    1.492  1.593 -0.101 5.00e-02 4.00e+02 4.08e+00
  bond pdb=" CB  MET C 124 "
       pdb=" CG  MET C 124 "
    ideal  model  delta    sigma   weight residual
    1.520  1.463  0.057 3.00e-02 1.11e+03 3.60e+00
  ... (remaining 4928 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.46: 6451
        3.46 -     6.92: 217
        6.92 -    10.38: 16
       10.38 -    13.84: 6
       13.84 -    17.30: 3
  Bond angle restraints: 6693
  Sorted by residual:
  angle pdb=" CA  PRO C 141 "
        pdb=" N   PRO C 141 "
        pdb=" CD  PRO C 141 "
      ideal   model   delta    sigma   weight residual
     112.00   94.70   17.30 1.40e+00 5.10e-01 1.53e+02
  angle pdb=" N   PRO C 141 "
        pdb=" CD  PRO C 141 "
        pdb=" CG  PRO C 141 "
      ideal   model   delta    sigma   weight residual
     103.20   86.58   16.62 1.50e+00 4.44e-01 1.23e+02
  angle pdb=" CA  PRO C  82 "
        pdb=" N   PRO C  82 "
        pdb=" CD  PRO C  82 "
      ideal   model   delta    sigma   weight residual
     112.00   99.04   12.96 1.40e+00 5.10e-01 8.57e+01
  angle pdb=" CA  PRO C 141 "
        pdb=" CB  PRO C 141 "
        pdb=" CG  PRO C 141 "
      ideal   model   delta    sigma   weight residual
     104.50   90.52   13.98 1.90e+00 2.77e-01 5.41e+01
  angle pdb=" CA  TYR L  47 "
        pdb=" CB  TYR L  47 "
        pdb=" CG  TYR L  47 "
      ideal   model   delta    sigma   weight residual
     113.90  122.48   -8.58 1.80e+00 3.09e-01 2.27e+01
  ... (remaining 6688 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.91: 2625
       17.91 -    35.81: 217
       35.81 -    53.72: 61
       53.72 -    71.62: 10
       71.62 -    89.53: 3
  Dihedral angle restraints: 2916
    sinusoidal: 1176
      harmonic: 1740
  Sorted by residual:
  dihedral pdb=" CA  PHE H  29 "
           pdb=" C   PHE H  29 "
           pdb=" N   ASP H  30 "
           pdb=" CA  ASP H  30 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -161.42  -18.58     0      5.00e+00 4.00e-02 1.38e+01
  dihedral pdb=" CB  GLU L   6 "
           pdb=" CG  GLU L   6 "
           pdb=" CD  GLU L   6 "
           pdb=" OE1 GLU L   6 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   89.53  -89.53     1      3.00e+01 1.11e-03 1.06e+01
  dihedral pdb=" CA  ASN H  79 "
           pdb=" CB  ASN H  79 "
           pdb=" CG  ASN H  79 "
           pdb=" OD1 ASN H  79 "
      ideal   model   delta sinusoidal    sigma   weight residual
     120.00 -172.97  -67.03     2      2.00e+01 2.50e-03 1.02e+01
  ... (remaining 2913 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.069: 532
       0.069 -    0.138: 161
       0.138 -    0.207: 28
       0.207 -    0.275: 2
       0.275 -    0.344: 2
  Chirality restraints: 725
  Sorted by residual:
  chirality pdb=" CA  PRO C  82 "
            pdb=" N   PRO C  82 "
            pdb=" C   PRO C  82 "
            pdb=" CB  PRO C  82 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.37    0.34 2.00e-01 2.50e+01 2.96e+00
  chirality pdb=" CA  PRO C 141 "
            pdb=" N   PRO C 141 "
            pdb=" C   PRO C 141 "
            pdb=" CB  PRO C 141 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.38    0.34 2.00e-01 2.50e+01 2.90e+00
  chirality pdb=" CB  ILE A  71 "
            pdb=" CA  ILE A  71 "
            pdb=" CG1 ILE A  71 "
            pdb=" CG2 ILE A  71 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.90   -0.26 2.00e-01 2.50e+01 1.69e+00
  ... (remaining 722 not shown)

  Planarity restraints: 858
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B  35 "    0.042 2.00e-02 2.50e+03   3.03e-02 2.30e+01
        pdb=" CG  TRP B  35 "   -0.083 2.00e-02 2.50e+03
        pdb=" CD1 TRP B  35 "    0.021 2.00e-02 2.50e+03
        pdb=" CD2 TRP B  35 "    0.005 2.00e-02 2.50e+03
        pdb=" NE1 TRP B  35 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP B  35 "    0.006 2.00e-02 2.50e+03
        pdb=" CE3 TRP B  35 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B  35 "    0.005 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B  35 "    0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP B  35 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR H 111 "   -0.081 5.00e-02 4.00e+02   1.20e-01 2.29e+01
        pdb=" N   PRO H 112 "    0.207 5.00e-02 4.00e+02
        pdb=" CA  PRO H 112 "   -0.062 5.00e-02 4.00e+02
        pdb=" CD  PRO H 112 "   -0.064 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA C 140 "    0.087 5.00e-02 4.00e+02   1.17e-01 2.20e+01
        pdb=" N   PRO C 141 "   -0.202 5.00e-02 4.00e+02
        pdb=" CA  PRO C 141 "    0.052 5.00e-02 4.00e+02
        pdb=" CD  PRO C 141 "    0.063 5.00e-02 4.00e+02
  ... (remaining 855 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.70: 156
        2.70 -     3.25: 4474
        3.25 -     3.80: 7562
        3.80 -     4.35: 9516
        4.35 -     4.90: 15908
  Nonbonded interactions: 37616
  Sorted by model distance:
  nonbonded pdb=" O   GLY L  75 "
            pdb=" NE2 GLN L  77 "
     model   vdw
     2.144 3.120
  nonbonded pdb=" OD1 ASP A  91 "
            pdb=" OH  TYR A  95 "
     model   vdw
     2.157 3.040
  nonbonded pdb=" NE2 GLN A  13 "
            pdb=" O   PRO A  14 "
     model   vdw
     2.201 3.120
  nonbonded pdb=" NE2 GLN A  13 "
            pdb=" OE1 GLN A  16 "
     model   vdw
     2.245 3.120
  nonbonded pdb=" OH  TYR A 104 "
            pdb=" NH1 ARG C 131 "
     model   vdw
     2.264 3.120
  ... (remaining 37611 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.050
  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:             0.020
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     17.180
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.860
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.480
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7554
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      :  0.010   0.372   4933  Z= 0.616
  Angle     :  1.446  17.297   6693  Z= 0.795
  Chirality :  0.066   0.344    725
  Planarity :  0.011   0.120    857
  Dihedral  : 14.594  89.530   1802
  Min Nonbonded Distance : 2.144

Molprobity Statistics.
  All-atom Clashscore : 2.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 23.26 %
    Favored  : 76.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.92 (0.33), residues: 604
  helix:  0.20 (0.53), residues: 75
  sheet:  1.06 (0.34), residues: 212
  loop :  0.54 (0.35), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.083   0.005   TRP B  35 
 HIS   0.016   0.003   HIS L  29 
 PHE   0.063   0.007   PHE H 107 
 TYR   0.064   0.006   TYR L  85 
 ARG   0.018   0.002   ARG C 131 

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

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

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 154
  time to evaluate  : 0.518 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   87 TYR cc_start: 0.8514 (m-80) cc_final: 0.8310 (m-80)
REVERT: C   29 GLU cc_start: 0.8116 (mp0) cc_final: 0.7851 (mp0)
REVERT: H   47 TRP cc_start: 0.8838 (t60) cc_final: 0.8534 (t60)
REVERT: H   61 ASP cc_start: 0.7857 (m-30) cc_final: 0.7630 (m-30)
REVERT: L   60 PHE cc_start: 0.6118 (p90) cc_final: 0.5839 (p90)
  outliers start: 0
  outliers final: 0
  residues processed: 154
  average time/residue: 0.1929
  time to fit residues: 36.5835
Evaluate side-chains
  119 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 119
  time to evaluate  : 0.556 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 48 optimal weight:   10.0000
   chunk 43 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 15 optimal weight:    3.9990
   chunk 29 optimal weight:    0.6980
   chunk 23 optimal weight:    0.5980
   chunk 45 optimal weight:    0.8980
   chunk 17 optimal weight:    1.9990
   chunk 27 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 52 optimal weight:    0.5980
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
A  13 GLN
A  16 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.111874 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.092768 restraints weight = 10170.029|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.095897 restraints weight = 6257.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.098195 restraints weight = 4396.222|
|-----------------------------------------------------------------------------|
r_work (final): 0.3428
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7744
moved from start:          0.1816

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.069   4933  Z= 0.292
  Angle     :  0.766  11.645   6693  Z= 0.391
  Chirality :  0.047   0.198    725
  Planarity :  0.005   0.063    857
  Dihedral  :  5.283  34.174    712
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 10.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 19.96 %
    Favored  : 76.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.17 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.93 (0.33), residues: 604
  helix:  1.03 (0.60), residues: 77
  sheet:  1.23 (0.33), residues: 221
  loop :  0.13 (0.35), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.040   0.003   TRP B  35 
 HIS   0.006   0.001   HIS L  29 
 PHE   0.016   0.002   PHE H 107 
 TYR   0.017   0.002   TYR L  85 
 ARG   0.006   0.001   ARG C 131 

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

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

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 129
  time to evaluate  : 0.579 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   13 GLN cc_start: 0.7984 (tm-30) cc_final: 0.7685 (tm-30)
REVERT: A   16 GLN cc_start: 0.7975 (mm-40) cc_final: 0.7157 (mm-40)
REVERT: A  102 GLU cc_start: 0.8578 (tm-30) cc_final: 0.8193 (tm-30)
REVERT: B   61 ARG cc_start: 0.7952 (ptt180) cc_final: 0.7685 (ptt180)
REVERT: B   83 PHE cc_start: 0.7666 (m-80) cc_final: 0.7454 (m-80)
REVERT: B   87 TYR cc_start: 0.8414 (m-80) cc_final: 0.8174 (m-80)
REVERT: L   60 PHE cc_start: 0.6569 (p90) cc_final: 0.6335 (p90)
  outliers start: 20
  outliers final: 10
  residues processed: 142
  average time/residue: 0.1772
  time to fit residues: 31.7960
Evaluate side-chains
  117 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 107
  time to evaluate  : 0.595 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  116 THR
Chi-restraints excluded: chain B residue   15 VAL
Chi-restraints excluded: chain B residue   20 THR
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain C residue   58 TYR
Chi-restraints excluded: chain C residue   76 SER
Chi-restraints excluded: chain C residue   97 THR
Chi-restraints excluded: chain H residue   20 LEU
Chi-restraints excluded: chain L residue   20 THR
Chi-restraints excluded: chain L residue   98 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 29 optimal weight:    2.9990
   chunk 51 optimal weight:    0.0030
   chunk 22 optimal weight:    2.9990
   chunk 48 optimal weight:    8.9990
   chunk 43 optimal weight:    3.9990
   chunk 47 optimal weight:    4.9990
   chunk 19 optimal weight:    1.9990
   chunk 35 optimal weight:    0.7980
   chunk 37 optimal weight:    6.9990
   chunk 5 optimal weight:    0.8980
   chunk 9 optimal weight:    0.7980
   overall best weight:    0.8992

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.109507 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.090055 restraints weight = 10161.849|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.093180 restraints weight = 6314.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.095453 restraints weight = 4463.414|
|-----------------------------------------------------------------------------|
r_work (final): 0.3392
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7809
moved from start:          0.2487

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   4933  Z= 0.255
  Angle     :  0.726  10.940   6693  Z= 0.365
  Chirality :  0.045   0.180    725
  Planarity :  0.005   0.060    857
  Dihedral  :  5.002  31.205    712
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 12.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 21.32 %
    Favored  : 74.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.17 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.86 (0.33), residues: 604
  helix:  0.55 (0.58), residues: 77
  sheet:  1.31 (0.33), residues: 211
  loop :  0.14 (0.35), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP B  35 
 HIS   0.005   0.002   HIS L  29 
 PHE   0.018   0.002   PHE C  91 
 TYR   0.018   0.002   TYR L  85 
 ARG   0.007   0.001   ARG C  37 

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

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

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 121
  time to evaluate  : 0.578 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   56 ASP cc_start: 0.8587 (p0) cc_final: 0.7906 (p0)
REVERT: A  102 GLU cc_start: 0.8574 (tm-30) cc_final: 0.8237 (tm-30)
REVERT: B   36 TYR cc_start: 0.7885 (m-80) cc_final: 0.7162 (m-80)
REVERT: B   61 ARG cc_start: 0.7905 (ptt180) cc_final: 0.7649 (ptt180)
REVERT: B   83 PHE cc_start: 0.7808 (m-80) cc_final: 0.7490 (m-80)
REVERT: C   22 MET cc_start: 0.8634 (mmp) cc_final: 0.8409 (mmp)
REVERT: H   84 GLU cc_start: 0.8944 (mm-30) cc_final: 0.8624 (mm-30)
  outliers start: 20
  outliers final: 13
  residues processed: 128
  average time/residue: 0.1593
  time to fit residues: 26.3242
Evaluate side-chains
  123 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 110
  time to evaluate  : 0.579 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 PHE
Chi-restraints excluded: chain A residue   66 LYS
Chi-restraints excluded: chain B residue   15 VAL
Chi-restraints excluded: chain B residue   20 THR
Chi-restraints excluded: chain B residue   54 LEU
Chi-restraints excluded: chain B residue   97 THR
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain C residue   58 TYR
Chi-restraints excluded: chain C residue   76 SER
Chi-restraints excluded: chain C residue   97 THR
Chi-restraints excluded: chain H residue   20 LEU
Chi-restraints excluded: chain L residue   97 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 37 optimal weight:    5.9990
   chunk 4 optimal weight:    1.9990
   chunk 46 optimal weight:    2.9990
   chunk 56 optimal weight:    0.8980
   chunk 39 optimal weight:    2.9990
   chunk 52 optimal weight:    2.9990
   chunk 48 optimal weight:    6.9990
   chunk 8 optimal weight:    1.9990
   chunk 13 optimal weight:    2.9990
   chunk 10 optimal weight:    0.5980
   chunk 29 optimal weight:    0.9980
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
B  30 HIS
** H  76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  35 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.104923 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.085220 restraints weight = 10589.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.088184 restraints weight = 6785.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.090287 restraints weight = 4951.684|
|-----------------------------------------------------------------------------|
r_work (final): 0.3310
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7931
moved from start:          0.3181

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   4933  Z= 0.315
  Angle     :  0.699  10.698   6693  Z= 0.356
  Chirality :  0.046   0.180    725
  Planarity :  0.004   0.041    857
  Dihedral  :  5.168  30.113    712
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 13.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.81 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 21.51 %
    Favored  : 74.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.17 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.67 (0.33), residues: 604
  helix:  0.93 (0.58), residues: 77
  sheet:  1.03 (0.33), residues: 220
  loop : -0.05 (0.35), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B  35 
 HIS   0.007   0.002   HIS L  29 
 PHE   0.021   0.003   PHE A  81 
 TYR   0.017   0.002   TYR L  85 
 ARG   0.005   0.001   ARG H 100 

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

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

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 110
  time to evaluate  : 0.524 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   56 ASP cc_start: 0.8700 (p0) cc_final: 0.7888 (p0)
REVERT: A  102 GLU cc_start: 0.8553 (tm-30) cc_final: 0.8277 (tm-30)
REVERT: B   36 TYR cc_start: 0.8033 (m-80) cc_final: 0.7104 (m-10)
REVERT: B   83 PHE cc_start: 0.7792 (m-80) cc_final: 0.7435 (m-80)
REVERT: B   87 TYR cc_start: 0.8336 (m-80) cc_final: 0.7846 (m-80)
  outliers start: 20
  outliers final: 15
  residues processed: 121
  average time/residue: 0.1569
  time to fit residues: 24.5323
Evaluate side-chains
  119 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 104
  time to evaluate  : 0.583 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 PHE
Chi-restraints excluded: chain B residue   15 VAL
Chi-restraints excluded: chain B residue   20 THR
Chi-restraints excluded: chain B residue   54 LEU
Chi-restraints excluded: chain B residue   97 THR
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain C residue   58 TYR
Chi-restraints excluded: chain C residue   76 SER
Chi-restraints excluded: chain C residue   89 VAL
Chi-restraints excluded: chain C residue   97 THR
Chi-restraints excluded: chain H residue   20 LEU
Chi-restraints excluded: chain L residue   35 GLN
Chi-restraints excluded: chain L residue   97 SER
Chi-restraints excluded: chain L residue   98 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 30 optimal weight:    0.8980
   chunk 56 optimal weight:    0.6980
   chunk 15 optimal weight:    1.9990
   chunk 18 optimal weight:    0.7980
   chunk 48 optimal weight:    0.9980
   chunk 39 optimal weight:    0.8980
   chunk 44 optimal weight:    4.9990
   chunk 28 optimal weight:    3.9990
   chunk 6 optimal weight:    2.9990
   chunk 12 optimal weight:    0.8980
   chunk 17 optimal weight:    6.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
B  76 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.105229 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.085827 restraints weight = 10675.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.088928 restraints weight = 6711.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.091235 restraints weight = 4785.371|
|-----------------------------------------------------------------------------|
r_work (final): 0.3321
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7896
moved from start:          0.3384

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   4933  Z= 0.244
  Angle     :  0.691  10.566   6693  Z= 0.344
  Chirality :  0.044   0.170    725
  Planarity :  0.004   0.037    857
  Dihedral  :  5.025  31.530    712
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 14.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 22.67 %
    Favored  : 73.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.17 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.64 (0.34), residues: 604
  helix:  0.94 (0.59), residues: 77
  sheet:  1.01 (0.33), residues: 225
  loop : -0.10 (0.36), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B  35 
 HIS   0.004   0.001   HIS L  29 
 PHE   0.014   0.002   PHE C  91 
 TYR   0.018   0.002   TYR L  85 
 ARG   0.003   0.000   ARG L  22 

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

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

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 111
  time to evaluate  : 0.541 
Fit side-chains
   revert: symmetry clash
REVERT: A   13 GLN cc_start: 0.7916 (tm-30) cc_final: 0.7324 (tm-30)
REVERT: A   56 ASP cc_start: 0.8656 (p0) cc_final: 0.7803 (p0)
REVERT: B   36 TYR cc_start: 0.8062 (m-80) cc_final: 0.7077 (m-10)
REVERT: B   83 PHE cc_start: 0.7841 (m-80) cc_final: 0.7357 (m-80)
  outliers start: 19
  outliers final: 14
  residues processed: 122
  average time/residue: 0.1542
  time to fit residues: 24.2414
Evaluate side-chains
  117 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 103
  time to evaluate  : 0.637 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   15 VAL
Chi-restraints excluded: chain B residue   54 LEU
Chi-restraints excluded: chain B residue   97 THR
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain C residue   58 TYR
Chi-restraints excluded: chain C residue   76 SER
Chi-restraints excluded: chain C residue   85 VAL
Chi-restraints excluded: chain C residue   97 THR
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   20 LEU
Chi-restraints excluded: chain H residue  117 TYR
Chi-restraints excluded: chain L residue   97 SER
Chi-restraints excluded: chain L residue   98 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 5 optimal weight:    0.8980
   chunk 34 optimal weight:    0.9990
   chunk 13 optimal weight:    0.8980
   chunk 33 optimal weight:    1.9990
   chunk 14 optimal weight:    0.8980
   chunk 0 optimal weight:    6.9990
   chunk 39 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9990
   chunk 51 optimal weight:    0.9980
   chunk 54 optimal weight:    4.9990
   chunk 40 optimal weight:    0.8980
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
L  35 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.104738 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.085186 restraints weight = 10663.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.088255 restraints weight = 6766.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.090476 restraints weight = 4865.748|
|-----------------------------------------------------------------------------|
r_work (final): 0.3303
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7906
moved from start:          0.3585

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   4933  Z= 0.256
  Angle     :  0.681  10.476   6693  Z= 0.343
  Chirality :  0.044   0.170    725
  Planarity :  0.004   0.037    857
  Dihedral  :  5.004  30.247    712
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 13.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  4.07 %
    Allowed  : 23.26 %
    Favored  : 72.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.17 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.62 (0.34), residues: 604
  helix:  0.98 (0.60), residues: 77
  sheet:  1.04 (0.33), residues: 225
  loop : -0.16 (0.36), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.048   0.002   TRP B  35 
 HIS   0.005   0.001   HIS L  29 
 PHE   0.014   0.002   PHE C  91 
 TYR   0.017   0.002   TYR L  85 
 ARG   0.004   0.001   ARG C 131 

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

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

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 107
  time to evaluate  : 0.542 
Fit side-chains
   revert: symmetry clash
REVERT: A   56 ASP cc_start: 0.8691 (p0) cc_final: 0.7823 (p0)
REVERT: A   66 LYS cc_start: 0.7414 (pttm) cc_final: 0.7005 (tppt)
REVERT: A  102 GLU cc_start: 0.8590 (tp30) cc_final: 0.8325 (tm-30)
REVERT: B   83 PHE cc_start: 0.7924 (m-80) cc_final: 0.7591 (m-80)
REVERT: B   87 TYR cc_start: 0.8348 (m-80) cc_final: 0.7921 (m-80)
  outliers start: 21
  outliers final: 20
  residues processed: 120
  average time/residue: 0.1468
  time to fit residues: 23.0016
Evaluate side-chains
  122 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 102
  time to evaluate  : 0.579 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   15 VAL
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   54 LEU
Chi-restraints excluded: chain B residue   97 THR
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain C residue   58 TYR
Chi-restraints excluded: chain C residue   76 SER
Chi-restraints excluded: chain C residue   80 GLN
Chi-restraints excluded: chain C residue   85 VAL
Chi-restraints excluded: chain C residue   97 THR
Chi-restraints excluded: chain C residue  105 LEU
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   20 LEU
Chi-restraints excluded: chain H residue  117 TYR
Chi-restraints excluded: chain L residue   35 GLN
Chi-restraints excluded: chain L residue   86 CYS
Chi-restraints excluded: chain L residue   97 SER
Chi-restraints excluded: chain L residue   98 VAL
Chi-restraints excluded: chain L residue  108 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 57 optimal weight:    0.9980
   chunk 49 optimal weight:    9.9990
   chunk 56 optimal weight:    0.9980
   chunk 7 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9980
   chunk 37 optimal weight:    2.9990
   chunk 52 optimal weight:    0.5980
   chunk 41 optimal weight:    1.9990
   chunk 23 optimal weight:    4.9990
   chunk 55 optimal weight:    0.8980
   chunk 8 optimal weight:    1.9990
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
C 155 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.104636 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.084722 restraints weight = 10574.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.087835 restraints weight = 6715.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.090121 restraints weight = 4830.918|
|-----------------------------------------------------------------------------|
r_work (final): 0.3293
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7920
moved from start:          0.3695

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   4933  Z= 0.255
  Angle     :  0.701  11.666   6693  Z= 0.347
  Chirality :  0.044   0.169    725
  Planarity :  0.004   0.036    857
  Dihedral  :  4.999  28.991    712
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 14.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  5.04 %
    Allowed  : 23.45 %
    Favored  : 71.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.53 (0.33), residues: 604
  helix:  0.70 (0.58), residues: 77
  sheet:  1.01 (0.33), residues: 225
  loop : -0.19 (0.36), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP B  35 
 HIS   0.004   0.001   HIS L  29 
 PHE   0.014   0.002   PHE H 107 
 TYR   0.021   0.002   TYR L  85 
 ARG   0.003   0.000   ARG H 100 

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

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

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 108
  time to evaluate  : 0.579 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   56 ASP cc_start: 0.8691 (p0) cc_final: 0.7796 (p0)
REVERT: A   66 LYS cc_start: 0.7390 (pttm) cc_final: 0.6977 (tppt)
REVERT: B   83 PHE cc_start: 0.7778 (m-80) cc_final: 0.7216 (m-80)
  outliers start: 26
  outliers final: 21
  residues processed: 125
  average time/residue: 0.1515
  time to fit residues: 24.7947
Evaluate side-chains
  121 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 100
  time to evaluate  : 0.582 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 SER
Chi-restraints excluded: chain B residue   15 VAL
Chi-restraints excluded: chain B residue   20 THR
Chi-restraints excluded: chain B residue   54 LEU
Chi-restraints excluded: chain B residue   97 THR
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain C residue   58 TYR
Chi-restraints excluded: chain C residue   76 SER
Chi-restraints excluded: chain C residue   80 GLN
Chi-restraints excluded: chain C residue   85 VAL
Chi-restraints excluded: chain C residue   89 VAL
Chi-restraints excluded: chain C residue   97 THR
Chi-restraints excluded: chain C residue  105 LEU
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   20 LEU
Chi-restraints excluded: chain H residue  117 TYR
Chi-restraints excluded: chain L residue   35 GLN
Chi-restraints excluded: chain L residue   86 CYS
Chi-restraints excluded: chain L residue   97 SER
Chi-restraints excluded: chain L residue   98 VAL
Chi-restraints excluded: chain L residue  108 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 11 optimal weight:    2.9990
   chunk 38 optimal weight:    3.9990
   chunk 16 optimal weight:    1.9990
   chunk 43 optimal weight:    4.9990
   chunk 8 optimal weight:    0.9980
   chunk 53 optimal weight:    0.5980
   chunk 42 optimal weight:    0.0010
   chunk 57 optimal weight:    3.9990
   chunk 23 optimal weight:    0.9980
   chunk 50 optimal weight:    2.9990
   chunk 0 optimal weight:    6.9990
   overall best weight:    0.9188

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

Flipped N/Q/H residues before XYZ refinement:
** H  76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.104291 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.084257 restraints weight = 10697.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.087393 restraints weight = 6780.282|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.089676 restraints weight = 4883.746|
|-----------------------------------------------------------------------------|
r_work (final): 0.3292
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7928
moved from start:          0.3891

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   4933  Z= 0.256
  Angle     :  0.708  10.570   6693  Z= 0.352
  Chirality :  0.044   0.171    725
  Planarity :  0.004   0.036    857
  Dihedral  :  5.009  27.874    712
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 15.38
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  3.15 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  4.65 %
    Allowed  : 24.61 %
    Favored  : 70.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.56 (0.34), residues: 604
  helix:  0.67 (0.58), residues: 77
  sheet:  1.06 (0.33), residues: 225
  loop : -0.19 (0.36), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP B  35 
 HIS   0.004   0.001   HIS L  29 
 PHE   0.015   0.002   PHE H 107 
 TYR   0.018   0.002   TYR L  85 
 ARG   0.003   0.000   ARG H 100 

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

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

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 108
  time to evaluate  : 0.541 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   56 ASP cc_start: 0.8692 (p0) cc_final: 0.7777 (p0)
REVERT: A   66 LYS cc_start: 0.7348 (pttm) cc_final: 0.6919 (tppt)
REVERT: A   79 GLN cc_start: 0.7433 (mm-40) cc_final: 0.7189 (mm110)
REVERT: A  104 TYR cc_start: 0.8318 (m-80) cc_final: 0.8007 (m-80)
REVERT: B   36 TYR cc_start: 0.8334 (m-80) cc_final: 0.8063 (m-10)
REVERT: B   83 PHE cc_start: 0.7848 (m-80) cc_final: 0.7232 (m-80)
  outliers start: 24
  outliers final: 23
  residues processed: 126
  average time/residue: 0.1534
  time to fit residues: 25.0202
Evaluate side-chains
  123 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 100
  time to evaluate  : 0.581 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 SER
Chi-restraints excluded: chain B residue   15 VAL
Chi-restraints excluded: chain B residue   20 THR
Chi-restraints excluded: chain B residue   54 LEU
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain C residue   58 TYR
Chi-restraints excluded: chain C residue   76 SER
Chi-restraints excluded: chain C residue   80 GLN
Chi-restraints excluded: chain C residue   85 VAL
Chi-restraints excluded: chain C residue   89 VAL
Chi-restraints excluded: chain C residue   93 LEU
Chi-restraints excluded: chain C residue   97 THR
Chi-restraints excluded: chain C residue  102 VAL
Chi-restraints excluded: chain C residue  105 LEU
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   20 LEU
Chi-restraints excluded: chain H residue  117 TYR
Chi-restraints excluded: chain L residue   44 LEU
Chi-restraints excluded: chain L residue   86 CYS
Chi-restraints excluded: chain L residue   97 SER
Chi-restraints excluded: chain L residue   98 VAL
Chi-restraints excluded: chain L residue  108 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 29 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9980
   chunk 40 optimal weight:    0.7980
   chunk 20 optimal weight:    0.9990
   chunk 35 optimal weight:    0.8980
   chunk 23 optimal weight:    0.7980
   chunk 50 optimal weight:    3.9990
   chunk 17 optimal weight:    5.9990
   chunk 57 optimal weight:    3.9990
   chunk 51 optimal weight:    0.9990
   chunk 49 optimal weight:    9.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
** H  76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.104432 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.084322 restraints weight = 10383.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.087360 restraints weight = 6599.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.089599 restraints weight = 4750.505|
|-----------------------------------------------------------------------------|
r_work (final): 0.3289
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7922
moved from start:          0.3973

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   4933  Z= 0.265
  Angle     :  0.725  11.172   6693  Z= 0.358
  Chirality :  0.044   0.168    725
  Planarity :  0.004   0.036    857
  Dihedral  :  5.017  27.757    712
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 16.33
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  3.48 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 25.78 %
    Favored  : 70.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.48 (0.34), residues: 604
  helix:  0.61 (0.58), residues: 77
  sheet:  1.12 (0.34), residues: 219
  loop : -0.30 (0.36), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP B  35 
 HIS   0.004   0.001   HIS L  29 
 PHE   0.018   0.002   PHE A  81 
 TYR   0.026   0.002   TYR B  87 
 ARG   0.003   0.000   ARG C 131 

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

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

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 103
  time to evaluate  : 0.579 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   56 ASP cc_start: 0.8692 (p0) cc_final: 0.7770 (p0)
REVERT: A   66 LYS cc_start: 0.7296 (pttm) cc_final: 0.6852 (tppt)
REVERT: A  104 TYR cc_start: 0.8306 (m-80) cc_final: 0.8030 (m-80)
REVERT: B   62 PHE cc_start: 0.8186 (m-80) cc_final: 0.7882 (m-10)
REVERT: B   83 PHE cc_start: 0.7893 (m-80) cc_final: 0.7261 (m-80)
  outliers start: 20
  outliers final: 20
  residues processed: 119
  average time/residue: 0.1611
  time to fit residues: 24.6434
Evaluate side-chains
  117 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 97
  time to evaluate  : 0.606 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   15 VAL
Chi-restraints excluded: chain B residue   54 LEU
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain C residue   58 TYR
Chi-restraints excluded: chain C residue   76 SER
Chi-restraints excluded: chain C residue   80 GLN
Chi-restraints excluded: chain C residue   85 VAL
Chi-restraints excluded: chain C residue   89 VAL
Chi-restraints excluded: chain C residue   93 LEU
Chi-restraints excluded: chain C residue   97 THR
Chi-restraints excluded: chain C residue  102 VAL
Chi-restraints excluded: chain C residue  105 LEU
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   20 LEU
Chi-restraints excluded: chain H residue  117 TYR
Chi-restraints excluded: chain L residue   44 LEU
Chi-restraints excluded: chain L residue   86 CYS
Chi-restraints excluded: chain L residue   97 SER
Chi-restraints excluded: chain L residue   98 VAL
Chi-restraints excluded: chain L residue  108 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 16 optimal weight:    0.0040
   chunk 12 optimal weight:    2.9990
   chunk 32 optimal weight:    0.8980
   chunk 50 optimal weight:    0.6980
   chunk 0 optimal weight:    6.9990
   chunk 29 optimal weight:    2.9990
   chunk 26 optimal weight:    6.9990
   chunk 43 optimal weight:    4.9990
   chunk 35 optimal weight:    0.9980
   chunk 15 optimal weight:    0.7980
   chunk 51 optimal weight:    0.9980
   overall best weight:    0.6792

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

Flipped N/Q/H residues before XYZ refinement:
** H  76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.104975 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.084923 restraints weight = 10375.719|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.087979 restraints weight = 6592.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.090295 restraints weight = 4739.412|
|-----------------------------------------------------------------------------|
r_work (final): 0.3306
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7900
moved from start:          0.4076

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   4933  Z= 0.230
  Angle     :  0.714  10.232   6693  Z= 0.350
  Chirality :  0.044   0.164    725
  Planarity :  0.004   0.034    857
  Dihedral  :  4.936  25.941    712
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 15.17
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  3.15 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 25.97 %
    Favored  : 70.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.48 (0.34), residues: 604
  helix:  0.62 (0.59), residues: 77
  sheet:  1.11 (0.34), residues: 217
  loop : -0.30 (0.36), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP B  35 
 HIS   0.004   0.001   HIS L  29 
 PHE   0.015   0.002   PHE H 107 
 TYR   0.023   0.002   TYR B  87 
 ARG   0.002   0.000   ARG C 131 

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

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

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 114
  time to evaluate  : 0.480 
Fit side-chains
   revert: symmetry clash
REVERT: A   56 ASP cc_start: 0.8655 (p0) cc_final: 0.7692 (p0)
REVERT: A   66 LYS cc_start: 0.7246 (pttm) cc_final: 0.6809 (tppt)
REVERT: A   81 PHE cc_start: 0.8317 (m-80) cc_final: 0.7840 (m-10)
REVERT: A  104 TYR cc_start: 0.8278 (m-80) cc_final: 0.7999 (m-80)
REVERT: B   42 LYS cc_start: 0.8453 (mmtt) cc_final: 0.8174 (mptt)
REVERT: B   62 PHE cc_start: 0.8120 (m-80) cc_final: 0.7871 (m-10)
REVERT: B   83 PHE cc_start: 0.7885 (m-80) cc_final: 0.7253 (m-80)
  outliers start: 18
  outliers final: 17
  residues processed: 128
  average time/residue: 0.1702
  time to fit residues: 27.4870
Evaluate side-chains
  119 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 102
  time to evaluate  : 0.594 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   15 VAL
Chi-restraints excluded: chain B residue   54 LEU
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain C residue   58 TYR
Chi-restraints excluded: chain C residue   80 GLN
Chi-restraints excluded: chain C residue   85 VAL
Chi-restraints excluded: chain C residue   89 VAL
Chi-restraints excluded: chain C residue   93 LEU
Chi-restraints excluded: chain C residue   97 THR
Chi-restraints excluded: chain C residue  105 LEU
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   20 LEU
Chi-restraints excluded: chain H residue  117 TYR
Chi-restraints excluded: chain L residue   44 LEU
Chi-restraints excluded: chain L residue   86 CYS
Chi-restraints excluded: chain L residue   97 SER
Chi-restraints excluded: chain L residue  108 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 45 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 57 optimal weight:    1.9990
   chunk 50 optimal weight:    0.3980
   chunk 47 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9990
   chunk 52 optimal weight:    0.9980
   chunk 38 optimal weight:    0.8980
   chunk 19 optimal weight:    4.9990
   chunk 1 optimal weight:    2.9990
   chunk 54 optimal weight:    0.8980
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
** H  76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.103943 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.083744 restraints weight = 10626.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.086759 restraints weight = 6720.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.089012 restraints weight = 4844.248|
|-----------------------------------------------------------------------------|
r_work (final): 0.3284
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7924
moved from start:          0.4229

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   4933  Z= 0.254
  Angle     :  0.742  10.562   6693  Z= 0.366
  Chirality :  0.044   0.166    725
  Planarity :  0.004   0.033    857
  Dihedral  :  4.960  24.845    712
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 14.96
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  3.31 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  4.07 %
    Allowed  : 25.78 %
    Favored  : 70.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.39 (0.34), residues: 604
  helix:  0.54 (0.58), residues: 77
  sheet:  1.02 (0.34), residues: 220
  loop : -0.34 (0.36), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B  35 
 HIS   0.004   0.001   HIS L  29 
 PHE   0.017   0.002   PHE H 107 
 TYR   0.022   0.002   TYR B  87 
 ARG   0.006   0.001   ARG H  69 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1912.86 seconds
wall clock time: 35 minutes 48.35 seconds (2148.35 seconds total)