Starting phenix.real_space_refine
on Thu Mar  6 04:12:18 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8sx3_40825/03_2025/8sx3_40825.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8sx3_40825/03_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_40825/03_2025/8sx3_40825.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8sx3_40825/03_2025/8sx3_40825.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8sx3_40825/03_2025/8sx3_40825.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8sx3_40825/03_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-5624/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: 4.27, per 1000 atoms: 0.89
  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: 1.17
  Conformation dependent library (CDL) restraints added in 567.9 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: 0.64
  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: 1.14

  Time building geometry restraints manager: 1.29 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:             3.470
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     15.850
  Find NCS groups from input model:        0.060
  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:           0.010
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.770
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.460
-------------------------------------------------------------------------------
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  : 0.561 
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: 0.1871
  time to fit residues: 35.4972
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  : 0.540 
-------------------------------------------------------------------------------
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 = 10170.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.095896 restraints weight = 6258.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.098193 restraints weight = 4396.569|
|-----------------------------------------------------------------------------|
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  : 0.545 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   13 GLN cc_start: 0.7985 (tm-30) cc_final: 0.7687 (tm-30)
REVERT: A   16 GLN cc_start: 0.7978 (mm-40) cc_final: 0.7157 (mm-40)
REVERT: A  102 GLU cc_start: 0.8578 (tm-30) cc_final: 0.8192 (tm-30)
REVERT: B   61 ARG cc_start: 0.7953 (ptt180) cc_final: 0.7687 (ptt180)
REVERT: B   83 PHE cc_start: 0.7667 (m-80) cc_final: 0.7454 (m-80)
REVERT: B   87 TYR cc_start: 0.8415 (m-80) cc_final: 0.8174 (m-80)
REVERT: L   60 PHE cc_start: 0.6570 (p90) cc_final: 0.6336 (p90)
  outliers start: 20
  outliers final: 10
  residues processed: 142
  average time/residue: 0.1677
  time to fit residues: 29.9500
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  : 0.543 
-------------------------------------------------------------------------------
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:    0.0670
   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:    0.8980
   chunk 35 optimal weight:    1.9990
   chunk 37 optimal weight:    6.9990
   chunk 5 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9990
   overall best weight:    1.1924

-------------------------------------------------------------------------------
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 = 0.3566 r_free = 0.3566 target = 0.107730 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.088190 restraints weight = 10302.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.091269 restraints weight = 6465.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.093513 restraints weight = 4599.547|
|-----------------------------------------------------------------------------|
r_work (final): 0.3365
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7855
moved from start:          0.2553

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   4933  Z= 0.304
  Angle     :  0.741  11.043   6693  Z= 0.373
  Chirality :  0.045   0.182    725
  Planarity :  0.005   0.062    857
  Dihedral  :  5.117  31.333    712
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 12.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  4.07 %
    Allowed  : 20.93 %
    Favored  : 75.00 %
  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:  0.82 (0.33), residues: 604
  helix:  0.61 (0.58), residues: 77
  sheet:  1.27 (0.33), residues: 220
  loop :  0.06 (0.36), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP B  35 
 HIS   0.006   0.002   HIS L  29 
 PHE   0.020   0.002   PHE C  91 
 TYR   0.017   0.002   TYR L  85 
 ARG   0.006   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
  140 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 119
  time to evaluate  : 0.523 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   56 ASP cc_start: 0.8625 (p0) cc_final: 0.7950 (p0)
REVERT: A  102 GLU cc_start: 0.8574 (tm-30) cc_final: 0.8243 (tm-30)
REVERT: B   36 TYR cc_start: 0.7995 (m-80) cc_final: 0.7286 (m-10)
REVERT: B   61 ARG cc_start: 0.7937 (ptt180) cc_final: 0.7687 (ptt180)
REVERT: B   83 PHE cc_start: 0.7834 (m-80) cc_final: 0.7521 (m-80)
REVERT: L   60 PHE cc_start: 0.6914 (p90) cc_final: 0.6662 (p90)
  outliers start: 21
  outliers final: 14
  residues processed: 129
  average time/residue: 0.1520
  time to fit residues: 25.5352
Evaluate side-chains
  121 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 107
  time to evaluate  : 0.519 
-------------------------------------------------------------------------------
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
Chi-restraints excluded: chain L residue   98 VAL
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:    0.8980
   chunk 56 optimal weight:    0.9990
   chunk 39 optimal weight:    1.9990
   chunk 52 optimal weight:    0.0020
   chunk 48 optimal weight:    6.9990
   chunk 8 optimal weight:    0.9980
   chunk 13 optimal weight:    2.9990
   chunk 10 optimal weight:    0.7980
   chunk 29 optimal weight:    1.9990
   overall best weight:    0.7390

-------------------------------------------------------------------------------
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 = 0.3577 r_free = 0.3577 target = 0.108427 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.088907 restraints weight = 10201.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.091987 restraints weight = 6278.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.094231 restraints weight = 4459.299|
|-----------------------------------------------------------------------------|
r_work (final): 0.3381
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7834
moved from start:          0.2859

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   4933  Z= 0.226
  Angle     :  0.692  10.675   6693  Z= 0.343
  Chirality :  0.044   0.175    725
  Planarity :  0.004   0.040    857
  Dihedral  :  4.920  29.449    712
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 12.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 21.51 %
    Favored  : 75.39 %
  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:  0.70 (0.33), residues: 604
  helix:  0.77 (0.59), residues: 77
  sheet:  1.03 (0.32), residues: 225
  loop :  0.03 (0.36), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B  35 
 HIS   0.005   0.001   HIS L  29 
 PHE   0.014   0.002   PHE H 107 
 TYR   0.019   0.002   TYR L  85 
 ARG   0.004   0.001   ARG C  37 

*********************** 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
  136 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 120
  time to evaluate  : 0.503 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   56 ASP cc_start: 0.8608 (p0) cc_final: 0.7762 (p0)
REVERT: A  102 GLU cc_start: 0.8571 (tm-30) cc_final: 0.8277 (tm-30)
REVERT: B   36 TYR cc_start: 0.7800 (m-80) cc_final: 0.6979 (m-10)
REVERT: B   83 PHE cc_start: 0.7821 (m-80) cc_final: 0.7434 (m-80)
  outliers start: 16
  outliers final: 10
  residues processed: 126
  average time/residue: 0.1533
  time to fit residues: 24.8874
Evaluate side-chains
  116 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 106
  time to evaluate  : 0.501 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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   97 THR
Chi-restraints excluded: chain H residue   20 LEU
Chi-restraints excluded: chain L residue   97 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 30 optimal weight:    0.7980
   chunk 56 optimal weight:    0.8980
   chunk 15 optimal weight:    0.8980
   chunk 18 optimal weight:    5.9990
   chunk 48 optimal weight:    6.9990
   chunk 39 optimal weight:    0.9990
   chunk 44 optimal weight:    5.9990
   chunk 28 optimal weight:    5.9990
   chunk 6 optimal weight:    2.9990
   chunk 12 optimal weight:    9.9990
   chunk 17 optimal weight:    3.9990
   overall best weight:    1.3184

-------------------------------------------------------------------------------
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 = 0.3633 r_free = 0.3633 target = 0.109942 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.091542 restraints weight = 11065.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.094531 restraints weight = 7211.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.096573 restraints weight = 5250.912|
|-----------------------------------------------------------------------------|
r_work (final): 0.3425
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7938
moved from start:          0.3421

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   4933  Z= 0.321
  Angle     :  0.706  10.762   6693  Z= 0.356
  Chirality :  0.044   0.176    725
  Planarity :  0.004   0.039    857
  Dihedral  :  5.105  29.031    712
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 15.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.81 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  4.07 %
    Allowed  : 21.32 %
    Favored  : 74.61 %
  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:  0.65 (0.33), residues: 604
  helix:  0.81 (0.59), residues: 77
  sheet:  1.10 (0.32), residues: 221
  loop : -0.11 (0.36), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.044   0.002   TRP B  35 
 HIS   0.005   0.002   HIS L  29 
 PHE   0.018   0.002   PHE C 117 
 TYR   0.017   0.002   TYR L  85 
 ARG   0.005   0.001   ARG H 100 

*********************** 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
  129 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 108
  time to evaluate  : 0.499 
Fit side-chains
   revert: symmetry clash
REVERT: A   13 GLN cc_start: 0.7837 (tm-30) cc_final: 0.7428 (tm-30)
REVERT: A   56 ASP cc_start: 0.8613 (p0) cc_final: 0.7787 (p0)
REVERT: A   66 LYS cc_start: 0.7162 (OUTLIER) cc_final: 0.6900 (tppt)
REVERT: B   36 TYR cc_start: 0.8108 (m-80) cc_final: 0.7242 (m-10)
REVERT: B   83 PHE cc_start: 0.7689 (m-80) cc_final: 0.7218 (m-80)
  outliers start: 21
  outliers final: 16
  residues processed: 121
  average time/residue: 0.1601
  time to fit residues: 24.9785
Evaluate side-chains
  117 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 100
  time to evaluate  : 0.503 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 LYS
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   58 TYR
Chi-restraints excluded: chain C residue   76 SER
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 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   36 LYS
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:    0.9980
   chunk 34 optimal weight:    0.8980
   chunk 13 optimal weight:    4.9990
   chunk 33 optimal weight:    0.6980
   chunk 14 optimal weight:    0.8980
   chunk 0 optimal weight:    6.9990
   chunk 39 optimal weight:    0.7980
   chunk 20 optimal weight:    0.0970
   chunk 51 optimal weight:    0.9990
   chunk 54 optimal weight:    0.8980
   chunk 40 optimal weight:    2.9990
   overall best weight:    0.6778

-------------------------------------------------------------------------------
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 = 0.3523 r_free = 0.3523 target = 0.105306 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.085711 restraints weight = 10562.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.088894 restraints weight = 6596.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.091255 restraints weight = 4664.517|
|-----------------------------------------------------------------------------|
r_work (final): 0.3318
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7884
moved from start:          0.3464

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   4933  Z= 0.229
  Angle     :  0.695  11.936   6693  Z= 0.344
  Chirality :  0.044   0.164    725
  Planarity :  0.004   0.038    857
  Dihedral  :  4.934  26.587    712
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 13.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  4.46 %
    Allowed  : 23.64 %
    Favored  : 71.90 %
  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:  0.62 (0.34), residues: 604
  helix:  0.74 (0.60), residues: 77
  sheet:  1.06 (0.32), residues: 225
  loop : -0.11 (0.36), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP B  35 
 HIS   0.004   0.001   HIS L  29 
 PHE   0.014   0.002   PHE H 107 
 TYR   0.019   0.002   TYR L  85 
 ARG   0.002   0.000   ARG L  22 

*********************** 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
  131 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 108
  time to evaluate  : 0.517 
Fit side-chains
   revert: symmetry clash
REVERT: A   13 GLN cc_start: 0.7827 (tm-30) cc_final: 0.7466 (tm-30)
REVERT: A   56 ASP cc_start: 0.8604 (p0) cc_final: 0.7730 (p0)
REVERT: A   66 LYS cc_start: 0.7208 (OUTLIER) cc_final: 0.6900 (tppt)
REVERT: A  102 GLU cc_start: 0.8623 (tp30) cc_final: 0.8283 (tm-30)
REVERT: B   83 PHE cc_start: 0.7862 (m-80) cc_final: 0.7516 (m-80)
REVERT: B   87 TYR cc_start: 0.8393 (m-80) cc_final: 0.8184 (m-80)
  outliers start: 23
  outliers final: 20
  residues processed: 121
  average time/residue: 0.1501
  time to fit residues: 23.8062
Evaluate side-chains
  125 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 104
  time to evaluate  : 0.559 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 SER
Chi-restraints excluded: chain A residue   66 LYS
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   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   36 LYS
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 57 optimal weight:    3.9990
   chunk 49 optimal weight:    8.9990
   chunk 56 optimal weight:    1.9990
   chunk 7 optimal weight:    3.9990
   chunk 19 optimal weight:    1.9990
   chunk 37 optimal weight:    5.9990
   chunk 52 optimal weight:    0.7980
   chunk 41 optimal weight:    0.9980
   chunk 23 optimal weight:    0.0980
   chunk 55 optimal weight:    0.9980
   chunk 8 optimal weight:    0.8980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
C 155 HIS
L  35 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.105402 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.085538 restraints weight = 10579.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.088729 restraints weight = 6713.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.091057 restraints weight = 4808.965|
|-----------------------------------------------------------------------------|
r_work (final): 0.3314
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7897
moved from start:          0.3661

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   4933  Z= 0.242
  Angle     :  0.689  11.013   6693  Z= 0.342
  Chirality :  0.043   0.166    725
  Planarity :  0.004   0.037    857
  Dihedral  :  4.895  25.536    712
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 14.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.81 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  4.46 %
    Allowed  : 24.61 %
    Favored  : 70.93 %
  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:  0.57 (0.34), residues: 604
  helix:  0.71 (0.59), residues: 77
  sheet:  1.03 (0.32), residues: 225
  loop : -0.14 (0.36), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B  35 
 HIS   0.004   0.001   HIS L  29 
 PHE   0.014   0.002   PHE B  83 
 TYR   0.020   0.002   TYR L  85 
 ARG   0.002   0.000   ARG L  22 

*********************** 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
  129 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 106
  time to evaluate  : 0.550 
Fit side-chains
   revert: symmetry clash
REVERT: A   13 GLN cc_start: 0.7810 (tm-30) cc_final: 0.7549 (tm-30)
REVERT: A   56 ASP cc_start: 0.8606 (p0) cc_final: 0.7710 (p0)
REVERT: A   66 LYS cc_start: 0.7207 (OUTLIER) cc_final: 0.6902 (tppt)
REVERT: A  104 TYR cc_start: 0.8300 (m-80) cc_final: 0.7759 (m-10)
REVERT: B   83 PHE cc_start: 0.7808 (m-80) cc_final: 0.7198 (m-80)
REVERT: C   22 MET cc_start: 0.8403 (mmp) cc_final: 0.8065 (mmp)
REVERT: L   45 LEU cc_start: 0.8448 (tp) cc_final: 0.8117 (tt)
  outliers start: 23
  outliers final: 19
  residues processed: 121
  average time/residue: 0.1450
  time to fit residues: 23.0049
Evaluate side-chains
  119 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 99
  time to evaluate  : 0.546 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 LYS
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   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:    1.9990
   chunk 38 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9980
   chunk 43 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9980
   chunk 53 optimal weight:    1.9990
   chunk 42 optimal weight:    0.6980
   chunk 57 optimal weight:    3.9990
   chunk 23 optimal weight:    1.9990
   chunk 50 optimal weight:    0.6980
   chunk 0 optimal weight:    6.9990
   overall best weight:    0.8580

-------------------------------------------------------------------------------
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 = 0.3518 r_free = 0.3518 target = 0.104792 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.084734 restraints weight = 10695.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.087853 restraints weight = 6750.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.090154 restraints weight = 4853.444|
|-----------------------------------------------------------------------------|
r_work (final): 0.3298
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7908
moved from start:          0.3733

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   4933  Z= 0.253
  Angle     :  0.691  10.946   6693  Z= 0.342
  Chirality :  0.044   0.166    725
  Planarity :  0.004   0.036    857
  Dihedral  :  4.902  24.457    712
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 14.96
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  3.81 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  4.46 %
    Allowed  : 25.19 %
    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:  0.56 (0.34), residues: 604
  helix:  0.69 (0.59), residues: 77
  sheet:  1.01 (0.33), residues: 225
  loop : -0.15 (0.36), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B  35 
 HIS   0.004   0.001   HIS L  29 
 PHE   0.014   0.002   PHE A  81 
 TYR   0.017   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
  127 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 104
  time to evaluate  : 0.544 
Fit side-chains
   revert: symmetry clash
REVERT: A   16 GLN cc_start: 0.7293 (mm-40) cc_final: 0.7059 (mm-40)
REVERT: A   56 ASP cc_start: 0.8643 (p0) cc_final: 0.7745 (p0)
REVERT: A   66 LYS cc_start: 0.7210 (OUTLIER) cc_final: 0.6867 (tppt)
REVERT: A   79 GLN cc_start: 0.7355 (mm-40) cc_final: 0.7138 (mm110)
REVERT: A  104 TYR cc_start: 0.8330 (m-80) cc_final: 0.7994 (m-80)
REVERT: B   42 LYS cc_start: 0.8302 (mmtt) cc_final: 0.8011 (mptt)
REVERT: B   83 PHE cc_start: 0.7843 (m-80) cc_final: 0.7223 (m-80)
REVERT: C   22 MET cc_start: 0.8434 (mmp) cc_final: 0.8133 (mmp)
REVERT: L   45 LEU cc_start: 0.8528 (tp) cc_final: 0.8201 (tt)
  outliers start: 23
  outliers final: 21
  residues processed: 119
  average time/residue: 0.1499
  time to fit residues: 23.2234
Evaluate side-chains
  121 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 99
  time to evaluate  : 0.506 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 SER
Chi-restraints excluded: chain A residue   66 LYS
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   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   36 LYS
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:    0.6980
   chunk 25 optimal weight:    0.0870
   chunk 40 optimal weight:    1.9990
   chunk 20 optimal weight:    0.0370
   chunk 35 optimal weight:    0.9990
   chunk 23 optimal weight:    0.0970
   chunk 50 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9990
   chunk 57 optimal weight:    3.9990
   chunk 51 optimal weight:    2.9990
   chunk 49 optimal weight:   10.0000
   overall best weight:    0.3836

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

Flipped N/Q/H residues before XYZ refinement:
A  52 HIS
L  35 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.107368 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.087612 restraints weight = 10585.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.090802 restraints weight = 6672.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.093176 restraints weight = 4782.886|
|-----------------------------------------------------------------------------|
r_work (final): 0.3348
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7839
moved from start:          0.3831

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   4933  Z= 0.194
  Angle     :  0.691  10.393   6693  Z= 0.340
  Chirality :  0.044   0.161    725
  Planarity :  0.004   0.034    857
  Dihedral  :  4.710  23.181    712
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 13.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 25.00 %
    Favored  : 71.12 %
  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:  0.57 (0.34), residues: 604
  helix:  0.73 (0.59), residues: 77
  sheet:  1.05 (0.32), residues: 223
  loop : -0.18 (0.36), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B  35 
 HIS   0.004   0.001   HIS L  29 
 PHE   0.013   0.002   PHE H 107 
 TYR   0.021   0.001   TYR L  85 
 ARG   0.003   0.000   ARG L  22 

*********************** 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
  139 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 119
  time to evaluate  : 0.573 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   56 ASP cc_start: 0.8520 (p0) cc_final: 0.7563 (p0)
REVERT: A   66 LYS cc_start: 0.7148 (OUTLIER) cc_final: 0.6858 (tppt)
REVERT: A  104 TYR cc_start: 0.8223 (m-80) cc_final: 0.7881 (m-80)
REVERT: C   22 MET cc_start: 0.8406 (mmp) cc_final: 0.8167 (mmp)
REVERT: L   85 TYR cc_start: 0.8884 (m-80) cc_final: 0.8615 (m-10)
  outliers start: 20
  outliers final: 19
  residues processed: 130
  average time/residue: 0.1701
  time to fit residues: 28.0925
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  : 0.452 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 LYS
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   58 TYR
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  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   35 GLN
Chi-restraints excluded: chain L residue   36 LYS
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 16 optimal weight:    0.8980
   chunk 12 optimal weight:    6.9990
   chunk 32 optimal weight:    2.9990
   chunk 50 optimal weight:    2.9990
   chunk 0 optimal weight:    6.9990
   chunk 29 optimal weight:    0.9980
   chunk 26 optimal weight:    5.9990
   chunk 43 optimal weight:    4.9990
   chunk 35 optimal weight:    1.9990
   chunk 15 optimal weight:    4.9990
   chunk 51 optimal weight:    0.9990
   overall best weight:    1.5786

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

Flipped N/Q/H residues before XYZ refinement:
B  30 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.102387 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.082391 restraints weight = 10438.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.085326 restraints weight = 6624.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.087475 restraints weight = 4782.426|
|-----------------------------------------------------------------------------|
r_work (final): 0.3255
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7969
moved from start:          0.4135

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.049   4933  Z= 0.364
  Angle     :  0.750  10.267   6693  Z= 0.379
  Chirality :  0.045   0.178    725
  Planarity :  0.004   0.036    857
  Dihedral  :  5.145  23.730    712
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 18.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  5.04 %
    Allowed  : 25.00 %
    Favored  : 69.96 %
  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:  0.34 (0.33), residues: 604
  helix:  0.51 (0.58), residues: 77
  sheet:  0.93 (0.33), residues: 221
  loop : -0.33 (0.36), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A  49 
 HIS   0.004   0.002   HIS L  29 
 PHE   0.018   0.003   PHE C 117 
 TYR   0.018   0.002   TYR H 117 
 ARG   0.003   0.001   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
  135 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 109
  time to evaluate  : 0.715 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   66 LYS cc_start: 0.7135 (OUTLIER) cc_final: 0.6768 (tppt)
REVERT: A  104 TYR cc_start: 0.8432 (m-80) cc_final: 0.8133 (m-80)
REVERT: B   42 LYS cc_start: 0.8527 (mmtt) cc_final: 0.8225 (mptt)
REVERT: B   83 PHE cc_start: 0.7897 (m-80) cc_final: 0.7232 (m-80)
REVERT: C   22 MET cc_start: 0.8471 (mmp) cc_final: 0.8224 (mmp)
  outliers start: 26
  outliers final: 19
  residues processed: 126
  average time/residue: 0.1955
  time to fit residues: 31.4612
Evaluate side-chains
  121 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 101
  time to evaluate  : 1.078 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 SER
Chi-restraints excluded: chain A residue   66 LYS
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  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   36 LYS
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:    0.9990
   chunk 24 optimal weight:    1.9990
   chunk 57 optimal weight:    0.9980
   chunk 50 optimal weight:    3.9990
   chunk 47 optimal weight:    0.8980
   chunk 56 optimal weight:    1.9990
   chunk 52 optimal weight:    0.6980
   chunk 38 optimal weight:    0.7980
   chunk 19 optimal weight:    4.9990
   chunk 1 optimal weight:    1.9990
   chunk 54 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:
** 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 = 0.3497 r_free = 0.3497 target = 0.103337 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.083549 restraints weight = 10559.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.086434 restraints weight = 6746.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.088673 restraints weight = 4915.593|
|-----------------------------------------------------------------------------|
r_work (final): 0.3278
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7930
moved from start:          0.4306

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= 0.269
  Angle     :  0.753  10.766   6693  Z= 0.373
  Chirality :  0.044   0.168    725
  Planarity :  0.004   0.037    857
  Dihedral  :  5.054  23.605    712
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 16.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  4.07 %
    Allowed  : 26.36 %
    Favored  : 69.57 %
  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:  0.30 (0.33), residues: 604
  helix:  0.59 (0.58), residues: 77
  sheet:  0.92 (0.33), residues: 219
  loop : -0.40 (0.35), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B  35 
 HIS   0.004   0.001   HIS L  29 
 PHE   0.018   0.002   PHE H 107 
 TYR   0.019   0.002   TYR L  85 
 ARG   0.005   0.000   ARG H 100 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2577.58 seconds
wall clock time: 46 minutes 33.45 seconds (2793.45 seconds total)