Starting phenix.real_space_refine
on Thu Jul 24 11:50:58 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9uok_64380/07_2025/9uok_64380.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9uok_64380/07_2025/9uok_64380.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.05
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9uok_64380/07_2025/9uok_64380.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9uok_64380/07_2025/9uok_64380.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9uok_64380/07_2025/9uok_64380.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9uok_64380/07_2025/9uok_64380.cif"
  }
  resolution = 3.05
  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=   0.007
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      46      5.16       5
     C    3664      2.51       5
     N    1043      2.21       5
     O    1098      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 5851
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 840
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 110, 840
          Classifications: {'peptide': 110}
          Link IDs: {'PTRANS': 3, 'TRANS': 106}
    Chain: "C"
      Number of atoms: 3445
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 444, 3445
          Classifications: {'peptide': 444}
          Link IDs: {'PTRANS': 22, 'TRANS': 421}
    Chain: "E"
      Number of atoms: 784
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 784
          Classifications: {'peptide': 99}
          Link IDs: {'PTRANS': 5, 'TRANS': 93}
          Chain breaks: 1
    Chain: "F"
      Number of atoms: 782
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 782
          Classifications: {'peptide': 99}
          Link IDs: {'PTRANS': 5, 'TRANS': 93}
  Time building chain proxies: 6.42, per 1000 atoms: 1.10
  Number of scatterers: 5851
  At special positions: 0
  Unit cell: (112.455, 110.313, 107.1, 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      46     16.00
     O    1098      8.00
     N    1043      7.00
     C    3664      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=14, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 428 " - pdb=" SG  CYS A 501 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C  33 " - pdb=" SG  CYS C  43 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 339 " - pdb=" SG  CYS C 364 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  39 " - pdb=" SG  CYS E  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  55 " - pdb=" SG  CYS E 110 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  65 " - pdb=" SG  CYS E 126 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  69 " - pdb=" SG  CYS E 128 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  93 " - pdb=" SG  CYS F  95 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E  95 " - pdb=" SG  CYS F  93 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 131 " - pdb=" SG  CYS F 131 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  39 " - pdb=" SG  CYS F  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  55 " - pdb=" SG  CYS F 110 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  65 " - pdb=" SG  CYS F 126 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  69 " - pdb=" SG  CYS F 128 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.69
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1424

  Finding SS restraints...
    Secondary structure from input PDB file:
      8 helices and 13 sheets defined
      5.9% alpha, 26.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.85
  Creating SS restraints...
    Processing helix  chain 'A' and resid 467 through 470
    Processing helix  chain 'A' and resid 492 through 496
      removed outlier: 3.989A  pdb=" N   THR A 496 " --> pdb=" O   PRO A 493 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 121 through 126
      removed outlier: 3.704A  pdb=" N   ARG C 126 " --> pdb=" O   SER C 122 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 169 through 175
      removed outlier: 3.812A  pdb=" N   ASN C 175 " --> pdb=" O   HIS C 171 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 241 through 247
      removed outlier: 3.835A  pdb=" N   ILE C 244 " --> pdb=" O   PRO C 241 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   LYS C 245 " --> pdb=" O   GLN C 242 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 337 through 342
      removed outlier: 3.502A  pdb=" N   GLU C 341 " --> pdb=" O   ASN C 337 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 405 through 410
      removed outlier: 4.285A  pdb=" N   PHE C 409 " --> pdb=" O   SER C 406 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 111 through 113
      No H-bonds generated for 'chain 'F' and resid 111 through 113'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 424 through 426
    Processing sheet with id=AA2, first strand: chain 'A' and resid 463 through 465
      removed outlier: 5.430A  pdb=" N   GLY A 453 " --> pdb=" O   ARG A 444 " (cutoff:3.500A)
      removed outlier: 5.293A  pdb=" N   ARG A 444 " --> pdb=" O   GLY A 453 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 463 through 465
      removed outlier: 5.430A  pdb=" N   GLY A 453 " --> pdb=" O   ARG A 444 " (cutoff:3.500A)
      removed outlier: 5.293A  pdb=" N   ARG A 444 " --> pdb=" O   GLY A 453 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 40 through 42
      removed outlier: 7.033A  pdb=" N   LEU C 110 " --> pdb=" O   ARG C 135 " (cutoff:3.500A)
      removed outlier: 7.217A  pdb=" N   LEU C 134 " --> pdb=" O   TRP C 159 " (cutoff:3.500A)
      removed outlier: 7.207A  pdb=" N   LEU C 206 " --> pdb=" O   ASP C 231 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 71 through 72
    Processing sheet with id=AA6, first strand: chain 'C' and resid 191 through 192
      removed outlier: 3.713A  pdb=" N   ILE C 192 " --> pdb=" O   SER C 215 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'C' and resid 262 through 263
      removed outlier: 3.521A  pdb=" N   ILE C 263 " --> pdb=" O   PHE C 286 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'C' and resid 300 through 304
      removed outlier: 6.834A  pdb=" N   LEU C 348 " --> pdb=" O   SER C 371 " (cutoff:3.500A)
      removed outlier: 6.768A  pdb=" N   LEU C 418 " --> pdb=" O   LYS C 440 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   SER C 463 " --> pdb=" O   LEU C 439 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 40 through 46
      removed outlier: 3.593A  pdb=" N   GLU E  66 " --> pdb=" O   MET E  40 " (cutoff:3.500A)
      removed outlier: 7.827A  pdb=" N   ALA E  63 " --> pdb=" O   PRO F  77 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'E' and resid 89 through 92
      removed outlier: 7.685A  pdb=" N   ALA F  63 " --> pdb=" O   PRO E  77 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 94 through 97
      removed outlier: 3.592A  pdb=" N   HIS E 127 " --> pdb=" O   ARG E  97 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 101 through 109
      removed outlier: 3.522A  pdb=" N   LEU E 116 " --> pdb=" O   LEU E 108 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   THR E 119 " --> pdb=" O   SER F  80 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'F' and resid 94 through 109
      removed outlier: 6.750A  pdb=" N   HIS F  94 " --> pdb=" O   GLU F 130 " (cutoff:3.500A)
      removed outlier: 6.763A  pdb=" N   GLU F 130 " --> pdb=" O   HIS F  94 " (cutoff:3.500A)
      removed outlier: 6.426A  pdb=" N   CYS F  96 " --> pdb=" O   CYS F 128 " (cutoff:3.500A)
      removed outlier: 6.447A  pdb=" N   CYS F 128 " --> pdb=" O   CYS F  96 " (cutoff:3.500A)
      removed outlier: 6.205A  pdb=" N   CYS F 126 " --> pdb=" O   PRO F  98 " (cutoff:3.500A)
      removed outlier: 6.723A  pdb=" N   THR F 100 " --> pdb=" O   LEU F 124 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   LEU F 116 " --> pdb=" O   LEU F 108 " (cutoff:3.500A)

    129 hydrogen bonds defined for protein.
    330 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: 2.02

  Time building geometry restraints manager: 2.02 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 1954
        1.35 -     1.47: 1352
        1.47 -     1.59: 2604
        1.59 -     1.71: 0
        1.71 -     1.83: 58
  Bond restraints: 5968
  Sorted by residual:
  bond pdb=" CB  GLN F  71 "
       pdb=" CG  GLN F  71 "
    ideal  model  delta    sigma   weight residual
    1.520  1.558 -0.038 3.00e-02 1.11e+03 1.59e+00
  bond pdb=" CB  LYS A 449 "
       pdb=" CG  LYS A 449 "
    ideal  model  delta    sigma   weight residual
    1.520  1.554 -0.034 3.00e-02 1.11e+03 1.28e+00
  bond pdb=" CA  CYS F  39 "
       pdb=" CB  CYS F  39 "
    ideal  model  delta    sigma   weight residual
    1.524  1.537 -0.013 1.22e-02 6.72e+03 1.12e+00
  bond pdb=" CB  GLN A 523 "
       pdb=" CG  GLN A 523 "
    ideal  model  delta    sigma   weight residual
    1.520  1.551 -0.031 3.00e-02 1.11e+03 1.05e+00
  bond pdb=" CA  ARG E 107 "
       pdb=" CB  ARG E 107 "
    ideal  model  delta    sigma   weight residual
    1.524  1.538 -0.014 1.37e-02 5.33e+03 1.04e+00
  ... (remaining 5963 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.28: 7921
        2.28 -     4.57: 139
        4.57 -     6.85: 16
        6.85 -     9.14: 1
        9.14 -    11.42: 2
  Bond angle restraints: 8079
  Sorted by residual:
  angle pdb=" CB  MET C 308 "
        pdb=" CG  MET C 308 "
        pdb=" SD  MET C 308 "
      ideal   model   delta    sigma   weight residual
     112.70  124.12  -11.42 3.00e+00 1.11e-01 1.45e+01
  angle pdb=" CA  GLN F  71 "
        pdb=" CB  GLN F  71 "
        pdb=" CG  GLN F  71 "
      ideal   model   delta    sigma   weight residual
     114.10  120.71   -6.61 2.00e+00 2.50e-01 1.09e+01
  angle pdb=" N   ARG C 460 "
        pdb=" CA  ARG C 460 "
        pdb=" C   ARG C 460 "
      ideal   model   delta    sigma   weight residual
     111.71  107.33    4.38 1.34e+00 5.57e-01 1.07e+01
  angle pdb=" CA  GLN F  87 "
        pdb=" CB  GLN F  87 "
        pdb=" CG  GLN F  87 "
      ideal   model   delta    sigma   weight residual
     114.10  120.12   -6.02 2.00e+00 2.50e-01 9.06e+00
  angle pdb=" CB  GLN F  71 "
        pdb=" CG  GLN F  71 "
        pdb=" CD  GLN F  71 "
      ideal   model   delta    sigma   weight residual
     112.60  117.63   -5.03 1.70e+00 3.46e-01 8.77e+00
  ... (remaining 8074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.97: 3272
       17.97 -    35.93: 306
       35.93 -    53.89: 81
       53.89 -    71.86: 11
       71.86 -    89.82: 5
  Dihedral angle restraints: 3675
    sinusoidal: 1482
      harmonic: 2193
  Sorted by residual:
  dihedral pdb=" CB  CYS E  65 "
           pdb=" SG  CYS E  65 "
           pdb=" SG  CYS E 126 "
           pdb=" CB  CYS E 126 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  166.57  -73.57     1      1.00e+01 1.00e-02 6.89e+01
  dihedral pdb=" CB  CYS E  93 "
           pdb=" SG  CYS E  93 "
           pdb=" SG  CYS F  95 "
           pdb=" CB  CYS F  95 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   39.74   53.26     1      1.00e+01 1.00e-02 3.86e+01
  dihedral pdb=" CB  CYS C  33 "
           pdb=" SG  CYS C  33 "
           pdb=" SG  CYS C  43 "
           pdb=" CB  CYS C  43 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   48.62   44.38     1      1.00e+01 1.00e-02 2.74e+01
  ... (remaining 3672 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 525
       0.031 -    0.061: 253
       0.061 -    0.092: 81
       0.092 -    0.123: 52
       0.123 -    0.153: 9
  Chirality restraints: 920
  Sorted by residual:
  chirality pdb=" CA  ILE C 263 "
            pdb=" N   ILE C 263 "
            pdb=" C   ILE C 263 "
            pdb=" CB  ILE C 263 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.15 2.00e-01 2.50e+01 5.88e-01
  chirality pdb=" CA  ILE C  64 "
            pdb=" N   ILE C  64 "
            pdb=" C   ILE C  64 "
            pdb=" CB  ILE C  64 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.36e-01
  chirality pdb=" CA  LEU F  52 "
            pdb=" N   LEU F  52 "
            pdb=" C   LEU F  52 "
            pdb=" CB  LEU F  52 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.34e-01
  ... (remaining 917 not shown)

  Planarity restraints: 1044
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS F  50 "    0.026 5.00e-02 4.00e+02   4.02e-02 2.58e+00
        pdb=" N   PRO F  51 "   -0.069 5.00e-02 4.00e+02
        pdb=" CA  PRO F  51 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO F  51 "    0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR E  44 "    0.011 2.00e-02 2.50e+03   1.00e-02 2.02e+00
        pdb=" CG  TYR E  44 "   -0.025 2.00e-02 2.50e+03
        pdb=" CD1 TYR E  44 "    0.006 2.00e-02 2.50e+03
        pdb=" CD2 TYR E  44 "    0.005 2.00e-02 2.50e+03
        pdb=" CE1 TYR E  44 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TYR E  44 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR E  44 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR E  44 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 436 "   -0.023 5.00e-02 4.00e+02   3.44e-02 1.89e+00
        pdb=" N   PRO A 437 "    0.059 5.00e-02 4.00e+02
        pdb=" CA  PRO A 437 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A 437 "   -0.019 5.00e-02 4.00e+02
  ... (remaining 1041 not shown)

  Histogram of nonbonded interaction distances:
        2.50 -     2.98: 2820
        2.98 -     3.46: 5577
        3.46 -     3.94: 8935
        3.94 -     4.42: 10438
        4.42 -     4.90: 17611
  Nonbonded interactions: 45381
  Sorted by model distance:
  nonbonded pdb=" N   GLN F  71 "
            pdb=" OE1 GLN F  71 "
     model   vdw
     2.496 3.120
  nonbonded pdb=" O   SER A 490 "
            pdb=" OG  SER A 490 "
     model   vdw
     2.504 3.040
  nonbonded pdb=" O   THR A 483 "
            pdb=" OG1 THR A 483 "
     model   vdw
     2.547 3.040
  nonbonded pdb=" N   ASP A 458 "
            pdb=" OD1 ASP A 458 "
     model   vdw
     2.591 3.120
  nonbonded pdb=" N   ILE C  64 "
            pdb=" N   SER C  65 "
     model   vdw
     2.597 2.560
  ... (remaining 45376 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
Found NCS groups:
ncs_group {
  reference = (chain 'E' and resid 35 through 133)
  selection = (chain 'F' and (resid 35 through 112 or resid 114 through 133))
}

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 individual isotropic
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:             94.700
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     21.690
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  119.800
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7901
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5982  Z= 0.132
  Angle     :  0.725  11.422   8107  Z= 0.371
  Chirality :  0.045   0.153    920
  Planarity :  0.004   0.045   1044
  Dihedral  : 15.034  89.824   2209
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 4.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.99 %
    Favored  : 95.01 %
  Rotamer:
    Outliers :  0.60 %
    Allowed  : 18.77 %
    Favored  : 80.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.40 (0.31), residues: 742
  helix: -2.68 (1.31), residues: 19
  sheet: -1.06 (0.37), residues: 207
  loop : -0.79 (0.28), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 442 
 HIS   0.005   0.001   HIS E  50 
 PHE   0.015   0.001   PHE C  58 
 TYR   0.025   0.002   TYR E  44 
 ARG   0.005   0.001   ARG F  97 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.20616 (  115)
  hydrogen bonds       : angle       7.38083 (  330)
  SS BOND              : bond        0.00409 (   14)
  SS BOND              : angle       1.91185 (   28)
  covalent geometry    : bond        0.00283 ( 5968)
  covalent geometry    : angle       0.71772 ( 8079)

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

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

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 83
  time to evaluate  : 0.739 
Fit side-chains
   revert: symmetry clash
REVERT: A  458 ASP cc_start: 0.8070 (p0) cc_final: 0.7588 (p0)
REVERT: C   75 ASP cc_start: 0.8278 (OUTLIER) cc_final: 0.7823 (t0)
REVERT: C  308 MET cc_start: 0.8795 (mpp) cc_final: 0.8349 (mtm)
REVERT: C  436 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8132 (mp)
REVERT: E   87 GLN cc_start: 0.8781 (tp40) cc_final: 0.8374 (tp-100)
REVERT: F   46 ASP cc_start: 0.9383 (t0) cc_final: 0.9171 (t0)
REVERT: F  130 GLU cc_start: 0.9060 (mm-30) cc_final: 0.8533 (tp30)
  outliers start: 4
  outliers final: 2
  residues processed: 84
  average time/residue: 0.1787
  time to fit residues: 20.3605
Evaluate side-chains
  75 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 71
  time to evaluate  : 0.671 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   75 ASP
Chi-restraints excluded: chain C residue  315 LEU
Chi-restraints excluded: chain C residue  436 LEU
Chi-restraints excluded: chain F residue   86 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 61 optimal weight:    0.5980
   chunk 55 optimal weight:    5.9990
   chunk 30 optimal weight:    2.9990
   chunk 18 optimal weight:    2.9990
   chunk 37 optimal weight:    2.9990
   chunk 29 optimal weight:    0.8980
   chunk 57 optimal weight:    2.9990
   chunk 22 optimal weight:    0.8980
   chunk 34 optimal weight:    1.9990
   chunk 42 optimal weight:    0.8980
   chunk 66 optimal weight:    4.9990
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
A 482 ASN
C 417 ASN
C 438 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.087376 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.071241 restraints weight = 17326.549|
|-----------------------------------------------------------------------------|
r_work (start): 0.3351 rms_B_bonded: 3.45
r_work: 0.3231 rms_B_bonded: 3.80 restraints_weight: 0.5000
r_work (final): 0.3231
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8149
moved from start:          0.1212

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.045   5982  Z= 0.238
  Angle     :  0.671   5.839   8107  Z= 0.345
  Chirality :  0.046   0.142    920
  Planarity :  0.004   0.037   1044
  Dihedral  :  6.077  57.756    822
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 5.93
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  7.14 %
    Favored  : 92.72 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 16.22 %
    Favored  : 80.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.43 (0.32), residues: 742
  helix: -3.56 (1.40), residues: 13
  sheet: -0.97 (0.38), residues: 200
  loop : -0.88 (0.28), residues: 529

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP C 159 
 HIS   0.006   0.001   HIS C 293 
 PHE   0.011   0.001   PHE A 518 
 TYR   0.029   0.002   TYR C 468 
 ARG   0.006   0.001   ARG A 472 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04498 (  115)
  hydrogen bonds       : angle       6.04946 (  330)
  SS BOND              : bond        0.00318 (   14)
  SS BOND              : angle       1.45351 (   28)
  covalent geometry    : bond        0.00553 ( 5968)
  covalent geometry    : angle       0.66671 ( 8079)

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

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

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 70
  time to evaluate  : 0.658 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   75 ASP cc_start: 0.8320 (OUTLIER) cc_final: 0.7948 (t0)
REVERT: C  344 MET cc_start: 0.8686 (tpp) cc_final: 0.8427 (tpt)
REVERT: E   42 HIS cc_start: 0.7779 (m170) cc_final: 0.7556 (m170)
REVERT: E   87 GLN cc_start: 0.8760 (tp40) cc_final: 0.8520 (tp-100)
REVERT: E  114 MET cc_start: 0.6805 (OUTLIER) cc_final: 0.6215 (mmm)
REVERT: F   46 ASP cc_start: 0.9191 (t0) cc_final: 0.8937 (t0)
REVERT: F  130 GLU cc_start: 0.8847 (mm-30) cc_final: 0.8549 (tp30)
  outliers start: 21
  outliers final: 13
  residues processed: 81
  average time/residue: 0.2028
  time to fit residues: 21.9580
Evaluate side-chains
  79 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 64
  time to evaluate  : 0.878 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  434 THR
Chi-restraints excluded: chain A residue  458 ASP
Chi-restraints excluded: chain A residue  485 TYR
Chi-restraints excluded: chain A residue  486 LEU
Chi-restraints excluded: chain A residue  511 CYS
Chi-restraints excluded: chain C residue   75 ASP
Chi-restraints excluded: chain C residue  287 VAL
Chi-restraints excluded: chain C residue  315 LEU
Chi-restraints excluded: chain E residue   45 VAL
Chi-restraints excluded: chain E residue   84 VAL
Chi-restraints excluded: chain E residue  114 MET
Chi-restraints excluded: chain E residue  116 LEU
Chi-restraints excluded: chain F residue   86 LYS
Chi-restraints excluded: chain F residue  119 THR
Chi-restraints excluded: chain F residue  123 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 29 optimal weight:    0.8980
   chunk 14 optimal weight:    1.9990
   chunk 31 optimal weight:    0.6980
   chunk 3 optimal weight:    0.2980
   chunk 52 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 63 optimal weight:    0.0980
   chunk 19 optimal weight:    1.9990
   chunk 70 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9990
   chunk 11 optimal weight:    3.9990
   overall best weight:    0.5982

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

Flipped N/Q/H residues before XYZ refinement:
** C 423 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 = 0.3702 r_free = 0.3702 target = 0.088585 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.073448 restraints weight = 17624.583|
|-----------------------------------------------------------------------------|
r_work (start): 0.3393 rms_B_bonded: 3.59
r_work: 0.3265 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.3265
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8095
moved from start:          0.1371

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   5982  Z= 0.146
  Angle     :  0.593   7.373   8107  Z= 0.300
  Chirality :  0.044   0.153    920
  Planarity :  0.004   0.041   1044
  Dihedral  :  5.645  59.711    820
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.99 %
    Favored  : 94.88 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 16.52 %
    Favored  : 80.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.29 (0.32), residues: 742
  helix: -3.71 (1.34), residues: 14
  sheet: -0.82 (0.37), residues: 207
  loop : -0.78 (0.29), residues: 521

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 159 
 HIS   0.005   0.001   HIS C 293 
 PHE   0.008   0.001   PHE A 518 
 TYR   0.018   0.002   TYR C 468 
 ARG   0.004   0.000   ARG F 109 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03567 (  115)
  hydrogen bonds       : angle       5.51625 (  330)
  SS BOND              : bond        0.00231 (   14)
  SS BOND              : angle       1.17642 (   28)
  covalent geometry    : bond        0.00342 ( 5968)
  covalent geometry    : angle       0.58963 ( 8079)

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

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

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 72
  time to evaluate  : 0.692 
Fit side-chains
REVERT: A  458 ASP cc_start: 0.8291 (OUTLIER) cc_final: 0.8017 (p0)
REVERT: C   75 ASP cc_start: 0.8386 (OUTLIER) cc_final: 0.7966 (t0)
REVERT: C  217 SER cc_start: 0.8699 (OUTLIER) cc_final: 0.8382 (t)
REVERT: C  344 MET cc_start: 0.8709 (tpp) cc_final: 0.8372 (tpt)
REVERT: E   42 HIS cc_start: 0.7719 (m170) cc_final: 0.7518 (m170)
REVERT: E  114 MET cc_start: 0.6771 (OUTLIER) cc_final: 0.6225 (mmm)
REVERT: F   46 ASP cc_start: 0.9194 (t0) cc_final: 0.8936 (t0)
REVERT: F  102 LYS cc_start: 0.9210 (tppp) cc_final: 0.8781 (tppp)
REVERT: F  114 MET cc_start: 0.8543 (ppp) cc_final: 0.7728 (tmm)
REVERT: F  130 GLU cc_start: 0.8857 (mm-30) cc_final: 0.8576 (tp30)
  outliers start: 23
  outliers final: 12
  residues processed: 85
  average time/residue: 0.1889
  time to fit residues: 21.9869
Evaluate side-chains
  84 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 68
  time to evaluate  : 0.726 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  427 SER
Chi-restraints excluded: chain A residue  434 THR
Chi-restraints excluded: chain A residue  458 ASP
Chi-restraints excluded: chain A residue  486 LEU
Chi-restraints excluded: chain A residue  511 CYS
Chi-restraints excluded: chain A residue  529 VAL
Chi-restraints excluded: chain C residue   75 ASP
Chi-restraints excluded: chain C residue  217 SER
Chi-restraints excluded: chain C residue  289 ASN
Chi-restraints excluded: chain C residue  315 LEU
Chi-restraints excluded: chain E residue   84 VAL
Chi-restraints excluded: chain E residue  114 MET
Chi-restraints excluded: chain E residue  116 LEU
Chi-restraints excluded: chain F residue   86 LYS
Chi-restraints excluded: chain F residue  119 THR
Chi-restraints excluded: chain F residue  123 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 70 optimal weight:    0.1980
   chunk 63 optimal weight:    0.7980
   chunk 16 optimal weight:    0.8980
   chunk 41 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9980
   chunk 35 optimal weight:    0.8980
   chunk 72 optimal weight:    1.9990
   chunk 71 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   chunk 57 optimal weight:    1.9990
   chunk 18 optimal weight:    0.5980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
C 373 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.087980 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.073256 restraints weight = 17841.157|
|-----------------------------------------------------------------------------|
r_work (start): 0.3389 rms_B_bonded: 3.44
r_work: 0.3263 rms_B_bonded: 3.63 restraints_weight: 0.5000
r_work (final): 0.3263
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8112
moved from start:          0.1562

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   5982  Z= 0.164
  Angle     :  0.592   7.071   8107  Z= 0.302
  Chirality :  0.043   0.142    920
  Planarity :  0.004   0.037   1044
  Dihedral  :  5.576  54.831    820
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 5.67
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  6.74 %
    Favored  : 93.13 %
  Rotamer:
    Outliers :  3.75 %
    Allowed  : 16.67 %
    Favored  : 79.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.37 (0.31), residues: 742
  helix: -3.70 (1.34), residues: 14
  sheet: -0.85 (0.40), residues: 180
  loop : -0.87 (0.28), residues: 548

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 159 
 HIS   0.005   0.001   HIS C 293 
 PHE   0.008   0.001   PHE A 518 
 TYR   0.019   0.002   TYR C 468 
 ARG   0.004   0.000   ARG F  97 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03467 (  115)
  hydrogen bonds       : angle       5.42952 (  330)
  SS BOND              : bond        0.00222 (   14)
  SS BOND              : angle       1.15729 (   28)
  covalent geometry    : bond        0.00386 ( 5968)
  covalent geometry    : angle       0.58918 ( 8079)

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

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

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 70
  time to evaluate  : 0.655 
Fit side-chains
REVERT: A  458 ASP cc_start: 0.8269 (OUTLIER) cc_final: 0.7782 (p0)
REVERT: C   75 ASP cc_start: 0.8442 (OUTLIER) cc_final: 0.8076 (t0)
REVERT: C  217 SER cc_start: 0.8704 (OUTLIER) cc_final: 0.8400 (t)
REVERT: C  344 MET cc_start: 0.8745 (tpp) cc_final: 0.8408 (tpt)
REVERT: E   42 HIS cc_start: 0.7833 (m170) cc_final: 0.7633 (m170)
REVERT: E  114 MET cc_start: 0.6778 (OUTLIER) cc_final: 0.6260 (mmm)
REVERT: F   46 ASP cc_start: 0.9162 (t0) cc_final: 0.8962 (t0)
REVERT: F  102 LYS cc_start: 0.9245 (tppp) cc_final: 0.8807 (tppp)
REVERT: F  130 GLU cc_start: 0.8856 (mm-30) cc_final: 0.8467 (tp30)
  outliers start: 25
  outliers final: 17
  residues processed: 84
  average time/residue: 0.1538
  time to fit residues: 17.9861
Evaluate side-chains
  87 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 66
  time to evaluate  : 0.649 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  423 SER
Chi-restraints excluded: chain A residue  427 SER
Chi-restraints excluded: chain A residue  434 THR
Chi-restraints excluded: chain A residue  458 ASP
Chi-restraints excluded: chain A residue  470 LYS
Chi-restraints excluded: chain A residue  485 TYR
Chi-restraints excluded: chain A residue  486 LEU
Chi-restraints excluded: chain A residue  511 CYS
Chi-restraints excluded: chain A residue  529 VAL
Chi-restraints excluded: chain C residue   75 ASP
Chi-restraints excluded: chain C residue  217 SER
Chi-restraints excluded: chain C residue  289 ASN
Chi-restraints excluded: chain C residue  315 LEU
Chi-restraints excluded: chain C residue  436 LEU
Chi-restraints excluded: chain E residue   45 VAL
Chi-restraints excluded: chain E residue   84 VAL
Chi-restraints excluded: chain E residue  114 MET
Chi-restraints excluded: chain E residue  116 LEU
Chi-restraints excluded: chain F residue   86 LYS
Chi-restraints excluded: chain F residue  119 THR
Chi-restraints excluded: chain F residue  123 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 10 optimal weight:    0.5980
   chunk 38 optimal weight:    0.6980
   chunk 28 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9990
   chunk 36 optimal weight:    0.5980
   chunk 15 optimal weight:    0.9990
   chunk 1 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9980
   chunk 59 optimal weight:    1.9990
   chunk 68 optimal weight:    2.9990
   chunk 51 optimal weight:    0.1980
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 = 0.3695 r_free = 0.3695 target = 0.088174 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.072988 restraints weight = 17673.741|
|-----------------------------------------------------------------------------|
r_work (start): 0.3385 rms_B_bonded: 3.60
r_work: 0.3255 rms_B_bonded: 3.80 restraints_weight: 0.5000
r_work (final): 0.3255
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8097
moved from start:          0.1727

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   5982  Z= 0.150
  Angle     :  0.582   6.763   8107  Z= 0.293
  Chirality :  0.043   0.146    920
  Planarity :  0.004   0.036   1044
  Dihedral  :  5.430  50.363    820
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 5.33
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.39 %
    Favored  : 94.47 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  : 17.57 %
    Favored  : 78.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.28 (0.32), residues: 742
  helix: -3.70 (1.34), residues: 14
  sheet: -0.80 (0.37), residues: 202
  loop : -0.79 (0.28), residues: 526

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 159 
 HIS   0.005   0.001   HIS C 293 
 PHE   0.008   0.001   PHE A 518 
 TYR   0.018   0.002   TYR C 468 
 ARG   0.003   0.000   ARG A 472 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03273 (  115)
  hydrogen bonds       : angle       5.24829 (  330)
  SS BOND              : bond        0.00211 (   14)
  SS BOND              : angle       1.06134 (   28)
  covalent geometry    : bond        0.00352 ( 5968)
  covalent geometry    : angle       0.57963 ( 8079)

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

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

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 71
  time to evaluate  : 0.643 
Fit side-chains
   revert: symmetry clash
REVERT: A  452 GLU cc_start: 0.7642 (pp20) cc_final: 0.7357 (pp20)
REVERT: A  458 ASP cc_start: 0.8282 (OUTLIER) cc_final: 0.7779 (p0)
REVERT: A  482 ASN cc_start: 0.5894 (OUTLIER) cc_final: 0.5611 (m-40)
REVERT: C  217 SER cc_start: 0.8717 (OUTLIER) cc_final: 0.8407 (t)
REVERT: C  344 MET cc_start: 0.8812 (tpp) cc_final: 0.8430 (tpt)
REVERT: E   42 HIS cc_start: 0.7905 (m170) cc_final: 0.7693 (m170)
REVERT: E  114 MET cc_start: 0.6599 (OUTLIER) cc_final: 0.6087 (mmm)
REVERT: F   35 ASP cc_start: 0.8405 (t0) cc_final: 0.8092 (t0)
REVERT: F   46 ASP cc_start: 0.9215 (t0) cc_final: 0.8959 (t0)
REVERT: F  102 LYS cc_start: 0.9255 (tppp) cc_final: 0.8823 (tppp)
REVERT: F  130 GLU cc_start: 0.8894 (mm-30) cc_final: 0.8437 (tp30)
  outliers start: 26
  outliers final: 18
  residues processed: 89
  average time/residue: 0.1608
  time to fit residues: 20.1218
Evaluate side-chains
  91 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 69
  time to evaluate  : 0.713 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  423 SER
Chi-restraints excluded: chain A residue  427 SER
Chi-restraints excluded: chain A residue  434 THR
Chi-restraints excluded: chain A residue  458 ASP
Chi-restraints excluded: chain A residue  470 LYS
Chi-restraints excluded: chain A residue  482 ASN
Chi-restraints excluded: chain A residue  485 TYR
Chi-restraints excluded: chain A residue  486 LEU
Chi-restraints excluded: chain A residue  511 CYS
Chi-restraints excluded: chain A residue  529 VAL
Chi-restraints excluded: chain C residue  217 SER
Chi-restraints excluded: chain C residue  287 VAL
Chi-restraints excluded: chain C residue  289 ASN
Chi-restraints excluded: chain C residue  315 LEU
Chi-restraints excluded: chain C residue  436 LEU
Chi-restraints excluded: chain E residue   45 VAL
Chi-restraints excluded: chain E residue   84 VAL
Chi-restraints excluded: chain E residue  114 MET
Chi-restraints excluded: chain E residue  116 LEU
Chi-restraints excluded: chain F residue   86 LYS
Chi-restraints excluded: chain F residue  119 THR
Chi-restraints excluded: chain F residue  123 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 59 optimal weight:    1.9990
   chunk 51 optimal weight:    0.5980
   chunk 37 optimal weight:    0.8980
   chunk 34 optimal weight:    0.0970
   chunk 29 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 63 optimal weight:    0.0070
   chunk 6 optimal weight:    0.9980
   chunk 35 optimal weight:    0.6980
   overall best weight:    0.4596

-------------------------------------------------------------------------------
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 = 0.3711 r_free = 0.3711 target = 0.088999 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.072604 restraints weight = 17531.527|
|-----------------------------------------------------------------------------|
r_work (start): 0.3386 rms_B_bonded: 3.61
r_work: 0.3267 rms_B_bonded: 3.96 restraints_weight: 0.5000
r_work (final): 0.3267
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8103
moved from start:          0.1811

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   5982  Z= 0.123
  Angle     :  0.571   7.166   8107  Z= 0.282
  Chirality :  0.043   0.149    920
  Planarity :  0.004   0.035   1044
  Dihedral  :  4.954  31.058    818
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 4.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.99 %
    Favored  : 95.01 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 17.42 %
    Favored  : 78.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.27 (0.31), residues: 742
  helix: -3.67 (1.36), residues: 14
  sheet: -0.79 (0.42), residues: 170
  loop : -0.80 (0.27), residues: 558

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 159 
 HIS   0.004   0.001   HIS C 293 
 PHE   0.007   0.001   PHE A 518 
 TYR   0.015   0.001   TYR C 468 
 ARG   0.003   0.000   ARG A 472 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03046 (  115)
  hydrogen bonds       : angle       5.16053 (  330)
  SS BOND              : bond        0.00177 (   14)
  SS BOND              : angle       1.10203 (   28)
  covalent geometry    : bond        0.00290 ( 5968)
  covalent geometry    : angle       0.56866 ( 8079)

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

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

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 70
  time to evaluate  : 0.736 
Fit side-chains
REVERT: A  452 GLU cc_start: 0.7587 (pp20) cc_final: 0.7288 (pp20)
REVERT: A  458 ASP cc_start: 0.8284 (OUTLIER) cc_final: 0.7803 (p0)
REVERT: A  482 ASN cc_start: 0.5804 (OUTLIER) cc_final: 0.5510 (m-40)
REVERT: C  217 SER cc_start: 0.8700 (OUTLIER) cc_final: 0.8415 (t)
REVERT: C  344 MET cc_start: 0.8782 (tpp) cc_final: 0.8470 (tpt)
REVERT: E  114 MET cc_start: 0.6794 (OUTLIER) cc_final: 0.6268 (mmm)
REVERT: F   35 ASP cc_start: 0.8187 (t0) cc_final: 0.7849 (t0)
REVERT: F   46 ASP cc_start: 0.9158 (t0) cc_final: 0.8933 (t0)
REVERT: F   53 TYR cc_start: 0.8723 (m-80) cc_final: 0.8426 (m-10)
REVERT: F  102 LYS cc_start: 0.9226 (tppp) cc_final: 0.8801 (tppp)
REVERT: F  114 MET cc_start: 0.8577 (ppp) cc_final: 0.7887 (tmm)
REVERT: F  130 GLU cc_start: 0.8851 (mm-30) cc_final: 0.8529 (tp30)
  outliers start: 24
  outliers final: 17
  residues processed: 87
  average time/residue: 0.1618
  time to fit residues: 19.7195
Evaluate side-chains
  90 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 69
  time to evaluate  : 1.013 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  427 SER
Chi-restraints excluded: chain A residue  434 THR
Chi-restraints excluded: chain A residue  458 ASP
Chi-restraints excluded: chain A residue  470 LYS
Chi-restraints excluded: chain A residue  482 ASN
Chi-restraints excluded: chain A residue  485 TYR
Chi-restraints excluded: chain A residue  486 LEU
Chi-restraints excluded: chain A residue  511 CYS
Chi-restraints excluded: chain A residue  529 VAL
Chi-restraints excluded: chain C residue  217 SER
Chi-restraints excluded: chain C residue  287 VAL
Chi-restraints excluded: chain C residue  289 ASN
Chi-restraints excluded: chain C residue  315 LEU
Chi-restraints excluded: chain C residue  436 LEU
Chi-restraints excluded: chain E residue   45 VAL
Chi-restraints excluded: chain E residue   84 VAL
Chi-restraints excluded: chain E residue  114 MET
Chi-restraints excluded: chain E residue  116 LEU
Chi-restraints excluded: chain F residue   86 LYS
Chi-restraints excluded: chain F residue  119 THR
Chi-restraints excluded: chain F residue  123 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 45 optimal weight:    1.9990
   chunk 69 optimal weight:    2.9990
   chunk 67 optimal weight:    6.9990
   chunk 13 optimal weight:    1.9990
   chunk 27 optimal weight:    0.8980
   chunk 53 optimal weight:    0.7980
   chunk 25 optimal weight:    0.0870
   chunk 21 optimal weight:    2.9990
   chunk 12 optimal weight:    2.9990
   chunk 29 optimal weight:    0.8980
   chunk 60 optimal weight:    0.5980
   overall best weight:    0.6558

-------------------------------------------------------------------------------
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 = 0.3700 r_free = 0.3700 target = 0.088357 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.073279 restraints weight = 17685.595|
|-----------------------------------------------------------------------------|
r_work (start): 0.3392 rms_B_bonded: 3.52
r_work: 0.3267 rms_B_bonded: 3.67 restraints_weight: 0.5000
r_work (final): 0.3267
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8105
moved from start:          0.1940

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   5982  Z= 0.158
  Angle     :  0.583   6.894   8107  Z= 0.292
  Chirality :  0.043   0.141    920
  Planarity :  0.004   0.034   1044
  Dihedral  :  5.050  31.103    818
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  6.06 %
    Favored  : 93.80 %
  Rotamer:
    Outliers :  3.75 %
    Allowed  : 17.72 %
    Favored  : 78.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.28 (0.32), residues: 742
  helix: -3.69 (1.35), residues: 14
  sheet: -0.77 (0.38), residues: 202
  loop : -0.80 (0.28), residues: 526

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 159 
 HIS   0.008   0.001   HIS E  42 
 PHE   0.010   0.001   PHE C  58 
 TYR   0.019   0.002   TYR C 468 
 ARG   0.003   0.000   ARG A 472 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03234 (  115)
  hydrogen bonds       : angle       5.17111 (  330)
  SS BOND              : bond        0.00229 (   14)
  SS BOND              : angle       1.15322 (   28)
  covalent geometry    : bond        0.00368 ( 5968)
  covalent geometry    : angle       0.57984 ( 8079)

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

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

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 69
  time to evaluate  : 0.689 
Fit side-chains
REVERT: A  458 ASP cc_start: 0.8275 (OUTLIER) cc_final: 0.7797 (p0)
REVERT: A  482 ASN cc_start: 0.5741 (OUTLIER) cc_final: 0.5409 (m-40)
REVERT: C  217 SER cc_start: 0.8703 (OUTLIER) cc_final: 0.8403 (t)
REVERT: C  344 MET cc_start: 0.8791 (tpp) cc_final: 0.8481 (tpt)
REVERT: E  114 MET cc_start: 0.6753 (OUTLIER) cc_final: 0.6222 (mmm)
REVERT: F   35 ASP cc_start: 0.8306 (t0) cc_final: 0.7978 (t0)
REVERT: F   46 ASP cc_start: 0.9105 (t0) cc_final: 0.8883 (t0)
REVERT: F   53 TYR cc_start: 0.8709 (m-80) cc_final: 0.8430 (m-80)
REVERT: F  102 LYS cc_start: 0.9238 (tppp) cc_final: 0.8811 (tppp)
REVERT: F  114 MET cc_start: 0.8539 (ppp) cc_final: 0.7891 (tmm)
REVERT: F  130 GLU cc_start: 0.8798 (mm-30) cc_final: 0.8530 (tp30)
  outliers start: 25
  outliers final: 20
  residues processed: 86
  average time/residue: 0.2032
  time to fit residues: 24.5452
Evaluate side-chains
  92 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 68
  time to evaluate  : 0.674 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  423 SER
Chi-restraints excluded: chain A residue  427 SER
Chi-restraints excluded: chain A residue  434 THR
Chi-restraints excluded: chain A residue  458 ASP
Chi-restraints excluded: chain A residue  469 VAL
Chi-restraints excluded: chain A residue  470 LYS
Chi-restraints excluded: chain A residue  482 ASN
Chi-restraints excluded: chain A residue  485 TYR
Chi-restraints excluded: chain A residue  486 LEU
Chi-restraints excluded: chain A residue  511 CYS
Chi-restraints excluded: chain A residue  529 VAL
Chi-restraints excluded: chain C residue  204 VAL
Chi-restraints excluded: chain C residue  217 SER
Chi-restraints excluded: chain C residue  287 VAL
Chi-restraints excluded: chain C residue  289 ASN
Chi-restraints excluded: chain C residue  315 LEU
Chi-restraints excluded: chain C residue  436 LEU
Chi-restraints excluded: chain E residue   45 VAL
Chi-restraints excluded: chain E residue   84 VAL
Chi-restraints excluded: chain E residue  114 MET
Chi-restraints excluded: chain E residue  116 LEU
Chi-restraints excluded: chain F residue   86 LYS
Chi-restraints excluded: chain F residue  119 THR
Chi-restraints excluded: chain F residue  123 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 41 optimal weight:    0.9990
   chunk 14 optimal weight:    2.9990
   chunk 69 optimal weight:    0.6980
   chunk 48 optimal weight:    0.0670
   chunk 59 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 36 optimal weight:    0.8980
   chunk 53 optimal weight:    2.9990
   chunk 6 optimal weight:    1.9990
   chunk 4 optimal weight:    0.0870
   chunk 51 optimal weight:    0.0970
   overall best weight:    0.3694

-------------------------------------------------------------------------------
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 = 0.3719 r_free = 0.3719 target = 0.089461 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.073109 restraints weight = 17459.049|
|-----------------------------------------------------------------------------|
r_work (start): 0.3396 rms_B_bonded: 3.63
r_work: 0.3277 rms_B_bonded: 3.97 restraints_weight: 0.5000
r_work (final): 0.3277
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8084
moved from start:          0.1957

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5982  Z= 0.108
  Angle     :  0.571   8.151   8107  Z= 0.281
  Chirality :  0.042   0.152    920
  Planarity :  0.004   0.035   1044
  Dihedral  :  4.806  30.940    818
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 5.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.58 %
    Favored  : 95.42 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 18.47 %
    Favored  : 78.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.22 (0.32), residues: 742
  helix: -3.65 (1.36), residues: 14
  sheet: -0.69 (0.38), residues: 201
  loop : -0.77 (0.28), residues: 527

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C 159 
 HIS   0.007   0.001   HIS E  42 
 PHE   0.015   0.001   PHE A 473 
 TYR   0.013   0.001   TYR C 468 
 ARG   0.003   0.000   ARG A 472 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02860 (  115)
  hydrogen bonds       : angle       4.98854 (  330)
  SS BOND              : bond        0.00178 (   14)
  SS BOND              : angle       1.01009 (   28)
  covalent geometry    : bond        0.00254 ( 5968)
  covalent geometry    : angle       0.56907 ( 8079)

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

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

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 72
  time to evaluate  : 1.280 
Fit side-chains
REVERT: A  458 ASP cc_start: 0.8283 (OUTLIER) cc_final: 0.7815 (p0)
REVERT: C  217 SER cc_start: 0.8717 (OUTLIER) cc_final: 0.8430 (t)
REVERT: C  344 MET cc_start: 0.8781 (tpp) cc_final: 0.8514 (tpp)
REVERT: E  114 MET cc_start: 0.6678 (OUTLIER) cc_final: 0.6212 (mmm)
REVERT: E  132 ASN cc_start: 0.9049 (m-40) cc_final: 0.8712 (m-40)
REVERT: F   35 ASP cc_start: 0.8227 (t0) cc_final: 0.7979 (t70)
REVERT: F   46 ASP cc_start: 0.9133 (t0) cc_final: 0.8913 (t0)
REVERT: F   53 TYR cc_start: 0.8667 (m-80) cc_final: 0.8340 (m-10)
REVERT: F  114 MET cc_start: 0.8527 (ppp) cc_final: 0.7852 (tmm)
REVERT: F  130 GLU cc_start: 0.8759 (mm-30) cc_final: 0.8502 (tp30)
  outliers start: 22
  outliers final: 15
  residues processed: 86
  average time/residue: 0.1853
  time to fit residues: 22.0149
Evaluate side-chains
  86 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 68
  time to evaluate  : 0.700 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  427 SER
Chi-restraints excluded: chain A residue  434 THR
Chi-restraints excluded: chain A residue  458 ASP
Chi-restraints excluded: chain A residue  469 VAL
Chi-restraints excluded: chain A residue  485 TYR
Chi-restraints excluded: chain A residue  486 LEU
Chi-restraints excluded: chain A residue  511 CYS
Chi-restraints excluded: chain A residue  529 VAL
Chi-restraints excluded: chain C residue  217 SER
Chi-restraints excluded: chain C residue  315 LEU
Chi-restraints excluded: chain C residue  436 LEU
Chi-restraints excluded: chain E residue   45 VAL
Chi-restraints excluded: chain E residue   84 VAL
Chi-restraints excluded: chain E residue  114 MET
Chi-restraints excluded: chain E residue  116 LEU
Chi-restraints excluded: chain F residue   86 LYS
Chi-restraints excluded: chain F residue  119 THR
Chi-restraints excluded: chain F residue  123 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 57 optimal weight:    0.6980
   chunk 31 optimal weight:    1.9990
   chunk 12 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9980
   chunk 50 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   chunk 27 optimal weight:    0.7980
   chunk 0 optimal weight:    1.9990
   chunk 62 optimal weight:    0.0980
   chunk 20 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** E  43 HIS ** 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 = 0.3698 r_free = 0.3698 target = 0.088209 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.071998 restraints weight = 17382.067|
|-----------------------------------------------------------------------------|
r_work (start): 0.3372 rms_B_bonded: 3.58
r_work: 0.3250 rms_B_bonded: 3.93 restraints_weight: 0.5000
r_work (final): 0.3250
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8129
moved from start:          0.2077

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   5982  Z= 0.171
  Angle     :  0.601   7.646   8107  Z= 0.299
  Chirality :  0.043   0.137    920
  Planarity :  0.004   0.035   1044
  Dihedral  :  5.076  31.309    818
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  6.47 %
    Favored  : 93.40 %
  Rotamer:
    Outliers :  3.75 %
    Allowed  : 18.17 %
    Favored  : 78.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.28 (0.32), residues: 742
  helix: -3.70 (1.33), residues: 14
  sheet: -0.74 (0.38), residues: 201
  loop : -0.82 (0.28), residues: 527

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 159 
 HIS   0.007   0.001   HIS E  42 
 PHE   0.016   0.001   PHE A 473 
 TYR   0.020   0.002   TYR C 468 
 ARG   0.004   0.000   ARG A 472 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03220 (  115)
  hydrogen bonds       : angle       5.09447 (  330)
  SS BOND              : bond        0.00215 (   14)
  SS BOND              : angle       1.10467 (   28)
  covalent geometry    : bond        0.00399 ( 5968)
  covalent geometry    : angle       0.59835 ( 8079)

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

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

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 68
  time to evaluate  : 0.721 
Fit side-chains
   revert: symmetry clash
REVERT: A  458 ASP cc_start: 0.8255 (OUTLIER) cc_final: 0.7815 (p0)
REVERT: C  217 SER cc_start: 0.8709 (OUTLIER) cc_final: 0.8418 (t)
REVERT: C  344 MET cc_start: 0.8818 (tpp) cc_final: 0.8490 (tpt)
REVERT: E  114 MET cc_start: 0.6800 (OUTLIER) cc_final: 0.6262 (mmm)
REVERT: F   35 ASP cc_start: 0.8160 (t0) cc_final: 0.7881 (t0)
REVERT: F   46 ASP cc_start: 0.9147 (t0) cc_final: 0.8940 (t0)
REVERT: F  114 MET cc_start: 0.8515 (ppp) cc_final: 0.7898 (tmm)
  outliers start: 25
  outliers final: 20
  residues processed: 86
  average time/residue: 0.1728
  time to fit residues: 20.3183
Evaluate side-chains
  89 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 66
  time to evaluate  : 1.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  427 SER
Chi-restraints excluded: chain A residue  434 THR
Chi-restraints excluded: chain A residue  458 ASP
Chi-restraints excluded: chain A residue  469 VAL
Chi-restraints excluded: chain A residue  470 LYS
Chi-restraints excluded: chain A residue  485 TYR
Chi-restraints excluded: chain A residue  486 LEU
Chi-restraints excluded: chain A residue  511 CYS
Chi-restraints excluded: chain A residue  529 VAL
Chi-restraints excluded: chain C residue  204 VAL
Chi-restraints excluded: chain C residue  217 SER
Chi-restraints excluded: chain C residue  287 VAL
Chi-restraints excluded: chain C residue  289 ASN
Chi-restraints excluded: chain C residue  315 LEU
Chi-restraints excluded: chain C residue  436 LEU
Chi-restraints excluded: chain E residue   45 VAL
Chi-restraints excluded: chain E residue   84 VAL
Chi-restraints excluded: chain E residue  114 MET
Chi-restraints excluded: chain E residue  116 LEU
Chi-restraints excluded: chain F residue   86 LYS
Chi-restraints excluded: chain F residue  119 THR
Chi-restraints excluded: chain F residue  123 ILE
Chi-restraints excluded: chain F residue  129 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 11 optimal weight:    0.0060
   chunk 21 optimal weight:    1.9990
   chunk 47 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   chunk 23 optimal weight:    0.6980
   chunk 43 optimal weight:    0.0270
   chunk 6 optimal weight:    0.9980
   chunk 9 optimal weight:    0.3980
   chunk 61 optimal weight:    1.9990
   chunk 48 optimal weight:    0.5980
   overall best weight:    0.3454

-------------------------------------------------------------------------------
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 = 0.3729 r_free = 0.3729 target = 0.089801 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.075033 restraints weight = 17640.517|
|-----------------------------------------------------------------------------|
r_work (start): 0.3430 rms_B_bonded: 3.51
r_work: 0.3306 rms_B_bonded: 3.65 restraints_weight: 0.5000
r_work (final): 0.3306
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8062
moved from start:          0.2086

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   5982  Z= 0.107
  Angle     :  0.577   7.857   8107  Z= 0.285
  Chirality :  0.042   0.154    920
  Planarity :  0.004   0.033   1044
  Dihedral  :  4.773  30.945    818
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 4.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.99 %
    Favored  : 95.01 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 18.77 %
    Favored  : 78.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.23 (0.32), residues: 742
  helix: -3.61 (1.38), residues: 14
  sheet: -0.73 (0.40), residues: 191
  loop : -0.78 (0.28), residues: 537

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C 159 
 HIS   0.007   0.001   HIS E  42 
 PHE   0.013   0.001   PHE A 473 
 TYR   0.013   0.001   TYR C 468 
 ARG   0.003   0.000   ARG A 472 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02802 (  115)
  hydrogen bonds       : angle       4.86999 (  330)
  SS BOND              : bond        0.00178 (   14)
  SS BOND              : angle       0.99396 (   28)
  covalent geometry    : bond        0.00252 ( 5968)
  covalent geometry    : angle       0.57542 ( 8079)

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

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

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 69
  time to evaluate  : 0.675 
Fit side-chains
   revert: symmetry clash
REVERT: A  458 ASP cc_start: 0.8225 (OUTLIER) cc_final: 0.7778 (p0)
REVERT: C  217 SER cc_start: 0.8690 (OUTLIER) cc_final: 0.8411 (t)
REVERT: C  344 MET cc_start: 0.8724 (tpp) cc_final: 0.8477 (tpp)
REVERT: E  114 MET cc_start: 0.6654 (OUTLIER) cc_final: 0.6189 (mmm)
REVERT: E  132 ASN cc_start: 0.9055 (m-40) cc_final: 0.8721 (m-40)
REVERT: F   35 ASP cc_start: 0.8247 (t0) cc_final: 0.7897 (t0)
REVERT: F   46 ASP cc_start: 0.9160 (t0) cc_final: 0.8949 (t0)
REVERT: F  114 MET cc_start: 0.8469 (ppp) cc_final: 0.7869 (tmm)
  outliers start: 20
  outliers final: 14
  residues processed: 82
  average time/residue: 0.1655
  time to fit residues: 18.9107
Evaluate side-chains
  83 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 66
  time to evaluate  : 0.585 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  427 SER
Chi-restraints excluded: chain A residue  434 THR
Chi-restraints excluded: chain A residue  458 ASP
Chi-restraints excluded: chain A residue  469 VAL
Chi-restraints excluded: chain A residue  485 TYR
Chi-restraints excluded: chain A residue  511 CYS
Chi-restraints excluded: chain A residue  529 VAL
Chi-restraints excluded: chain C residue  217 SER
Chi-restraints excluded: chain C residue  315 LEU
Chi-restraints excluded: chain C residue  436 LEU
Chi-restraints excluded: chain E residue   45 VAL
Chi-restraints excluded: chain E residue   84 VAL
Chi-restraints excluded: chain E residue  114 MET
Chi-restraints excluded: chain E residue  116 LEU
Chi-restraints excluded: chain F residue   86 LYS
Chi-restraints excluded: chain F residue  119 THR
Chi-restraints excluded: chain F residue  123 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 18 optimal weight:    0.5980
   chunk 19 optimal weight:    1.9990
   chunk 34 optimal weight:    0.6980
   chunk 42 optimal weight:    0.8980
   chunk 50 optimal weight:    1.9990
   chunk 39 optimal weight:    0.5980
   chunk 67 optimal weight:    4.9990
   chunk 61 optimal weight:    0.0030
   chunk 70 optimal weight:    1.9990
   chunk 48 optimal weight:    0.6980
   chunk 37 optimal weight:    0.8980
   overall best weight:    0.5190

-------------------------------------------------------------------------------
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 = 0.3717 r_free = 0.3717 target = 0.089110 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.074238 restraints weight = 17732.262|
|-----------------------------------------------------------------------------|
r_work (start): 0.3417 rms_B_bonded: 3.50
r_work: 0.3292 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.3292
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8061
moved from start:          0.2175

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   5982  Z= 0.137
  Angle     :  0.598   9.406   8107  Z= 0.295
  Chirality :  0.042   0.142    920
  Planarity :  0.004   0.039   1044
  Dihedral  :  4.838  31.209    818
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 5.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.66 %
    Favored  : 94.34 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 19.22 %
    Favored  : 78.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.26 (0.32), residues: 742
  helix: -3.63 (1.36), residues: 14
  sheet: -0.77 (0.40), residues: 191
  loop : -0.79 (0.28), residues: 537

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 159 
 HIS   0.007   0.001   HIS E  42 
 PHE   0.016   0.001   PHE C  58 
 TYR   0.015   0.001   TYR C 468 
 ARG   0.003   0.000   ARG A 472 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03010 (  115)
  hydrogen bonds       : angle       4.88087 (  330)
  SS BOND              : bond        0.00205 (   14)
  SS BOND              : angle       1.01683 (   28)
  covalent geometry    : bond        0.00325 ( 5968)
  covalent geometry    : angle       0.59561 ( 8079)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4224.65 seconds
wall clock time: 75 minutes 31.87 seconds (4531.87 seconds total)