Starting phenix.real_space_refine
on Fri Feb 14 17:31:52 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jxd_36697/02_2025/8jxd_36697.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jxd_36697/02_2025/8jxd_36697.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jxd_36697/02_2025/8jxd_36697.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jxd_36697/02_2025/8jxd_36697.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jxd_36697/02_2025/8jxd_36697.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jxd_36697/02_2025/8jxd_36697.cif"
  }
  resolution = 3.3
  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=   0.003
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: 5
    Type Number    sf(0)   Gaussians
     Ca     12      9.91       5
     S     124      5.16       5
     C    6330      2.51       5
     N    1762      2.21       5
     O    2106      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 36 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 10334
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 3896
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 493, 3896
          Classifications: {'peptide': 493}
          Link IDs: {'PTRANS': 26, 'TRANS': 466}
    Chain: "B"
      Number of atoms: 1170
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 156, 1170
          Classifications: {'peptide': 156}
          Link IDs: {'PTRANS': 10, 'TRANS': 145}
          Chain breaks: 1
    Chain: "C"
      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
    Chain: "D"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "A"
      Number of atoms: 16
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 16
          Unusual residues: {' CA': 2, 'NAG': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 18
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 18
          Unusual residues: {' CA': 4, 'A2G': 1}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Restraints were copied for chains:
    E, F, G, H
  Time building chain proxies: 8.07, per 1000 atoms: 0.78
  Number of scatterers: 10334
  At special positions: 0
  Unit cell: (150.977, 153.799, 86.071, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Ca     12     19.99
     S     124     16.00
     O    2106      8.00
     N    1762      7.00
     C    6330      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=27, symmetry=0
    Simple disulfide: pdb=" SG  CYS A3930 " - pdb=" SG  CYS A3942 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A3937 " - pdb=" SG  CYS A3955 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A3949 " - pdb=" SG  CYS A3964 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A3972 " - pdb=" SG  CYS A3981 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A3977 " - pdb=" SG  CYS A3991 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A3993 " - pdb=" SG  CYS A4007 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A4013 " - pdb=" SG  CYS A4023 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A4019 " - pdb=" SG  CYS A4032 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A4034 " - pdb=" SG  CYS A4049 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A4336 " - pdb=" SG  CYS A4344 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A4340 " - pdb=" SG  CYS A4353 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A4355 " - pdb=" SG  CYS A4369 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A4383 " - pdb=" SG  CYS A4391 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A4385 " - pdb=" SG  CYS A4401 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A4403 " - pdb=" SG  CYS A4412 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  28 " - pdb=" SG  CYS B  40 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  35 " - pdb=" SG  CYS B  53 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B  47 " - pdb=" SG  CYS B  62 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  67 " - pdb=" SG  CYS B  80 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  74 " - pdb=" SG  CYS B  93 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  87 " - pdb=" SG  CYS B 103 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B3761 " - pdb=" SG  CYS B3773 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B3768 " - pdb=" SG  CYS B3786 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B3780 " - pdb=" SG  CYS B3795 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B3800 " - pdb=" SG  CYS B3812 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B3807 " - pdb=" SG  CYS B3825 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B3819 " - pdb=" SG  CYS B3834 " 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=2, symmetry=0
  Links applied
    BETA1-3
      " NAG D   2 " - " BMA D   3 "
      " NAG H   2 " - " BMA H   3 "
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
      " NAG D   1 " - " NAG D   2 "
      " NAG G   1 " - " NAG G   2 "
      " NAG H   1 " - " NAG H   2 "
    NAG-ASN
      " NAG A4701 " - " ASN A3980 "
      " NAG C   1 " - " ASN A4070 "
      " NAG D   1 " - " ASN A4329 "
      " NAG E4701 " - " ASN E3980 "
      " NAG G   1 " - " ASN E4070 "
      " NAG H   1 " - " ASN E4329 "
  Number of additional bonds: simple=2, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.99
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  2572 Ramachandran restraints generated.
    1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2404

  Finding SS restraints...
    Secondary structure from input PDB file:
      16 helices and 34 sheets defined
      5.1% alpha, 24.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.26
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3946 through 3948
      No H-bonds generated for 'chain 'A' and resid 3946 through 3948'
    Processing helix  chain 'A' and resid 3958 through 3962
      removed outlier: 3.804A  pdb=" N   THR A3962 " --> pdb=" O   SER A3959 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3971 through 3975
    Processing helix  chain 'A' and resid 4011 through 4015
    Processing helix  chain 'B' and resid 44 through 46
      No H-bonds generated for 'chain 'B' and resid 44 through 46'
    Processing helix  chain 'B' and resid 97 through 102
    Processing helix  chain 'B' and resid 3777 through 3779
      No H-bonds generated for 'chain 'B' and resid 3777 through 3779'
    Processing helix  chain 'B' and resid 3816 through 3818
      No H-bonds generated for 'chain 'B' and resid 3816 through 3818'
    Processing helix  chain 'E' and resid 3946 through 3948
      No H-bonds generated for 'chain 'E' and resid 3946 through 3948'
    Processing helix  chain 'E' and resid 3958 through 3962
      removed outlier: 3.804A  pdb=" N   THR E3962 " --> pdb=" O   SER E3959 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 3971 through 3975
    Processing helix  chain 'E' and resid 4011 through 4015
    Processing helix  chain 'F' and resid 44 through 46
      No H-bonds generated for 'chain 'F' and resid 44 through 46'
    Processing helix  chain 'F' and resid 97 through 102
    Processing helix  chain 'F' and resid 3777 through 3779
      No H-bonds generated for 'chain 'F' and resid 3777 through 3779'
    Processing helix  chain 'F' and resid 3816 through 3818
      No H-bonds generated for 'chain 'F' and resid 3816 through 3818'
    Processing sheet with id=1, first strand: chain 'A' and resid 3934 through 3935
    Processing sheet with id=2, first strand: chain 'A' and resid 3981 through 3983
    Processing sheet with id=3, first strand: chain 'A' and resid 3997 through 3999
    Processing sheet with id=4, first strand: chain 'A' and resid 4024 through 4026
    Processing sheet with id=5, first strand: chain 'A' and resid 4040 through 4043
      removed outlier: 3.738A  pdb=" N   GLY A4046 " --> pdb=" O   THR A4043 " (cutoff:3.500A)
    Processing sheet with id=6, first strand: chain 'A' and resid 4075 through 4077
      removed outlier: 3.871A  pdb=" N   LYS A4075 " --> pdb=" O   ASN A4070 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   SER A4077 " --> pdb=" O   LYS A4068 " (cutoff:3.500A)
      removed outlier: 4.065A  pdb=" N   LYS A4068 " --> pdb=" O   SER A4077 " (cutoff:3.500A)
    Processing sheet with id=7, first strand: chain 'A' and resid 4086 through 4092
      removed outlier: 5.144A  pdb=" N   THR A4088 " --> pdb=" O   THR A4106 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   THR A4106 " --> pdb=" O   THR A4088 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   VAL A4136 " --> pdb=" O   ARG A4119 " (cutoff:3.500A)
    Processing sheet with id=8, first strand: chain 'A' and resid 4146 through 4152
      removed outlier: 3.713A  pdb=" N   GLY A4148 " --> pdb=" O   SER A4161 " (cutoff:3.500A)
      removed outlier: 6.139A  pdb=" N   VAL A4170 " --> pdb=" O   TRP A4180 " (cutoff:3.500A)
      removed outlier: 5.199A  pdb=" N   TRP A4180 " --> pdb=" O   VAL A4170 " (cutoff:3.500A)
    Processing sheet with id=9, first strand: chain 'A' and resid 4189 through 4195
      removed outlier: 4.452A  pdb=" N   THR A4204 " --> pdb=" O   ALA A4190 " (cutoff:3.500A)
      removed outlier: 4.650A  pdb=" N   ILE A4192 " --> pdb=" O   PHE A4202 " (cutoff:3.500A)
      removed outlier: 6.668A  pdb=" N   PHE A4202 " --> pdb=" O   ILE A4192 " (cutoff:3.500A)
      removed outlier: 4.891A  pdb=" N   VAL A4194 " --> pdb=" O   LEU A4200 " (cutoff:3.500A)
      removed outlier: 7.003A  pdb=" N   LEU A4200 " --> pdb=" O   VAL A4194 " (cutoff:3.500A)
      removed outlier: 6.705A  pdb=" N   ILE A4212 " --> pdb=" O   LEU A4225 " (cutoff:3.500A)
    Processing sheet with id=10, first strand: chain 'A' and resid 4233 through 4239
      removed outlier: 3.587A  pdb=" N   GLY A4235 " --> pdb=" O   SER A4249 " (cutoff:3.500A)
      removed outlier: 6.906A  pdb=" N   ILE A4256 " --> pdb=" O   ILE A4269 " (cutoff:3.500A)
    Processing sheet with id=11, first strand: chain 'A' and resid 4276 through 4282
      removed outlier: 6.568A  pdb=" N   VAL A4289 " --> pdb=" O   PHE A4277 " (cutoff:3.500A)
      removed outlier: 4.331A  pdb=" N   LEU A4279 " --> pdb=" O   TYR A4287 " (cutoff:3.500A)
      removed outlier: 6.832A  pdb=" N   TYR A4287 " --> pdb=" O   LEU A4279 " (cutoff:3.500A)
      removed outlier: 5.244A  pdb=" N   ILE A4281 " --> pdb=" O   LYS A4285 " (cutoff:3.500A)
      removed outlier: 7.353A  pdb=" N   LYS A4285 " --> pdb=" O   ILE A4281 " (cutoff:3.500A)
      removed outlier: 6.788A  pdb=" N   VAL A4296 " --> pdb=" O   VAL A4310 " (cutoff:3.500A)
    Processing sheet with id=12, first strand: chain 'A' and resid 4343 through 4347
    Processing sheet with id=13, first strand: chain 'A' and resid 4390 through 4393
      removed outlier: 3.753A  pdb=" N   ASN A4390 " --> pdb=" O   LYS A4402 " (cutoff:3.500A)
    Processing sheet with id=14, first strand: chain 'B' and resid 32 through 34
    Processing sheet with id=15, first strand: chain 'B' and resid 71 through 73
    Processing sheet with id=16, first strand: chain 'B' and resid 3765 through 3767
    Processing sheet with id=17, first strand: chain 'B' and resid 3804 through 3806
    Processing sheet with id=18, first strand: chain 'E' and resid 3934 through 3935
    Processing sheet with id=19, first strand: chain 'E' and resid 3981 through 3983
    Processing sheet with id=20, first strand: chain 'E' and resid 3997 through 3999
    Processing sheet with id=21, first strand: chain 'E' and resid 4024 through 4026
    Processing sheet with id=22, first strand: chain 'E' and resid 4040 through 4043
      removed outlier: 3.738A  pdb=" N   GLY E4046 " --> pdb=" O   THR E4043 " (cutoff:3.500A)
    Processing sheet with id=23, first strand: chain 'E' and resid 4075 through 4077
      removed outlier: 3.871A  pdb=" N   LYS E4075 " --> pdb=" O   ASN E4070 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   SER E4077 " --> pdb=" O   LYS E4068 " (cutoff:3.500A)
      removed outlier: 4.065A  pdb=" N   LYS E4068 " --> pdb=" O   SER E4077 " (cutoff:3.500A)
    Processing sheet with id=24, first strand: chain 'E' and resid 4086 through 4092
      removed outlier: 5.144A  pdb=" N   THR E4088 " --> pdb=" O   THR E4106 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   THR E4106 " --> pdb=" O   THR E4088 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   VAL E4136 " --> pdb=" O   ARG E4119 " (cutoff:3.500A)
    Processing sheet with id=25, first strand: chain 'E' and resid 4146 through 4152
      removed outlier: 3.713A  pdb=" N   GLY E4148 " --> pdb=" O   SER E4161 " (cutoff:3.500A)
      removed outlier: 6.139A  pdb=" N   VAL E4170 " --> pdb=" O   TRP E4180 " (cutoff:3.500A)
      removed outlier: 5.199A  pdb=" N   TRP E4180 " --> pdb=" O   VAL E4170 " (cutoff:3.500A)
    Processing sheet with id=26, first strand: chain 'E' and resid 4189 through 4195
      removed outlier: 4.452A  pdb=" N   THR E4204 " --> pdb=" O   ALA E4190 " (cutoff:3.500A)
      removed outlier: 4.650A  pdb=" N   ILE E4192 " --> pdb=" O   PHE E4202 " (cutoff:3.500A)
      removed outlier: 6.668A  pdb=" N   PHE E4202 " --> pdb=" O   ILE E4192 " (cutoff:3.500A)
      removed outlier: 4.891A  pdb=" N   VAL E4194 " --> pdb=" O   LEU E4200 " (cutoff:3.500A)
      removed outlier: 7.003A  pdb=" N   LEU E4200 " --> pdb=" O   VAL E4194 " (cutoff:3.500A)
      removed outlier: 6.705A  pdb=" N   ILE E4212 " --> pdb=" O   LEU E4225 " (cutoff:3.500A)
    Processing sheet with id=27, first strand: chain 'E' and resid 4233 through 4239
      removed outlier: 3.587A  pdb=" N   GLY E4235 " --> pdb=" O   SER E4249 " (cutoff:3.500A)
      removed outlier: 6.906A  pdb=" N   ILE E4256 " --> pdb=" O   ILE E4269 " (cutoff:3.500A)
    Processing sheet with id=28, first strand: chain 'E' and resid 4276 through 4282
      removed outlier: 6.568A  pdb=" N   VAL E4289 " --> pdb=" O   PHE E4277 " (cutoff:3.500A)
      removed outlier: 4.331A  pdb=" N   LEU E4279 " --> pdb=" O   TYR E4287 " (cutoff:3.500A)
      removed outlier: 6.832A  pdb=" N   TYR E4287 " --> pdb=" O   LEU E4279 " (cutoff:3.500A)
      removed outlier: 5.244A  pdb=" N   ILE E4281 " --> pdb=" O   LYS E4285 " (cutoff:3.500A)
      removed outlier: 7.353A  pdb=" N   LYS E4285 " --> pdb=" O   ILE E4281 " (cutoff:3.500A)
      removed outlier: 6.788A  pdb=" N   VAL E4296 " --> pdb=" O   VAL E4310 " (cutoff:3.500A)
    Processing sheet with id=29, first strand: chain 'E' and resid 4343 through 4347
    Processing sheet with id=30, first strand: chain 'E' and resid 4390 through 4393
      removed outlier: 3.753A  pdb=" N   ASN E4390 " --> pdb=" O   LYS E4402 " (cutoff:3.500A)
    Processing sheet with id=31, first strand: chain 'F' and resid 32 through 34
    Processing sheet with id=32, first strand: chain 'F' and resid 71 through 73
    Processing sheet with id=33, first strand: chain 'F' and resid 3765 through 3767
    Processing sheet with id=34, first strand: chain 'F' and resid 3804 through 3806

    212 hydrogen bonds defined for protein.
    504 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: 3.33

  Time building geometry restraints manager: 3.21 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3500
        1.34 -     1.46: 2278
        1.46 -     1.58: 4636
        1.58 -     1.70: 0
        1.70 -     1.82: 140
  Bond restraints: 10554
  Sorted by residual:
  bond pdb=" C1  A2G B4701 "
       pdb=" O5  A2G B4701 "
    ideal  model  delta    sigma   weight residual
    1.385  1.420 -0.035 2.00e-02 2.50e+03 3.07e+00
  bond pdb=" C1  A2G F4701 "
       pdb=" O5  A2G F4701 "
    ideal  model  delta    sigma   weight residual
    1.385  1.420 -0.035 2.00e-02 2.50e+03 3.07e+00
  bond pdb=" C2  BMA H   3 "
       pdb=" O2  BMA H   3 "
    ideal  model  delta    sigma   weight residual
    1.402  1.431 -0.029 2.00e-02 2.50e+03 2.17e+00
  bond pdb=" C2  BMA D   3 "
       pdb=" O2  BMA D   3 "
    ideal  model  delta    sigma   weight residual
    1.402  1.431 -0.029 2.00e-02 2.50e+03 2.17e+00
  bond pdb=" C3  NAG H   1 "
       pdb=" O3  NAG H   1 "
    ideal  model  delta    sigma   weight residual
    1.403  1.432 -0.029 2.00e-02 2.50e+03 2.11e+00
  ... (remaining 10549 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.96: 13968
        1.96 -     3.92: 288
        3.92 -     5.88: 32
        5.88 -     7.84: 6
        7.84 -     9.80: 2
  Bond angle restraints: 14296
  Sorted by residual:
  angle pdb=" CB  LYS B  91 "
        pdb=" CG  LYS B  91 "
        pdb=" CD  LYS B  91 "
      ideal   model   delta    sigma   weight residual
     111.30  121.10   -9.80 2.30e+00 1.89e-01 1.82e+01
  angle pdb=" CB  LYS F  91 "
        pdb=" CG  LYS F  91 "
        pdb=" CD  LYS F  91 "
      ideal   model   delta    sigma   weight residual
     111.30  121.10   -9.80 2.30e+00 1.89e-01 1.82e+01
  angle pdb=" C   ARG B3793 "
        pdb=" N   ASP B3794 "
        pdb=" CA  ASP B3794 "
      ideal   model   delta    sigma   weight residual
     122.46  126.92   -4.46 1.41e+00 5.03e-01 1.00e+01
  angle pdb=" C   ARG F3793 "
        pdb=" N   ASP F3794 "
        pdb=" CA  ASP F3794 "
      ideal   model   delta    sigma   weight residual
     122.46  126.92   -4.46 1.41e+00 5.03e-01 1.00e+01
  angle pdb=" N   ASP B3794 "
        pdb=" CA  ASP B3794 "
        pdb=" C   ASP B3794 "
      ideal   model   delta    sigma   weight residual
     111.30  115.57   -4.27 1.36e+00 5.41e-01 9.84e+00
  ... (remaining 14291 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.50: 5928
       21.50 -    42.99: 563
       42.99 -    64.49: 88
       64.49 -    85.99: 35
       85.99 -   107.48: 15
  Dihedral angle restraints: 6629
    sinusoidal: 2887
      harmonic: 3742
  Sorted by residual:
  dihedral pdb=" CB  CYS A3937 "
           pdb=" SG  CYS A3937 "
           pdb=" SG  CYS A3955 "
           pdb=" CB  CYS A3955 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -173.10   87.10     1      1.00e+01 1.00e-02 9.11e+01
  dihedral pdb=" CB  CYS A3972 "
           pdb=" SG  CYS A3972 "
           pdb=" SG  CYS A3981 "
           pdb=" CB  CYS A3981 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  165.57  -72.57     1      1.00e+01 1.00e-02 6.72e+01
  dihedral pdb=" CB  CYS A3930 "
           pdb=" SG  CYS A3930 "
           pdb=" SG  CYS A3942 "
           pdb=" CB  CYS A3942 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -156.88   70.88     1      1.00e+01 1.00e-02 6.46e+01
  ... (remaining 6626 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 982
       0.039 -    0.078: 366
       0.078 -    0.117: 136
       0.117 -    0.156: 26
       0.156 -    0.195: 8
  Chirality restraints: 1518
  Sorted by residual:
  chirality pdb=" C1  BMA H   3 "
            pdb=" O3  NAG H   2 "
            pdb=" C2  BMA H   3 "
            pdb=" O5  BMA H   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.28   -0.12 2.00e-02 2.50e+03 3.61e+01
  chirality pdb=" C1  BMA D   3 "
            pdb=" O3  NAG D   2 "
            pdb=" C2  BMA D   3 "
            pdb=" O5  BMA D   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.28   -0.12 2.00e-02 2.50e+03 3.61e+01
  chirality pdb=" C5  BMA D   3 "
            pdb=" C4  BMA D   3 "
            pdb=" C6  BMA D   3 "
            pdb=" O5  BMA D   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.47    0.20 2.00e-01 2.50e+01 9.52e-01
  ... (remaining 1515 not shown)

  Planarity restraints: 1908
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG C   2 "    0.156 2.00e-02 2.50e+03   1.28e-01 2.06e+02
        pdb=" C7  NAG C   2 "   -0.042 2.00e-02 2.50e+03
        pdb=" C8  NAG C   2 "    0.115 2.00e-02 2.50e+03
        pdb=" N2  NAG C   2 "   -0.206 2.00e-02 2.50e+03
        pdb=" O7  NAG C   2 "   -0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG G   2 "    0.156 2.00e-02 2.50e+03   1.28e-01 2.06e+02
        pdb=" C7  NAG G   2 "   -0.042 2.00e-02 2.50e+03
        pdb=" C8  NAG G   2 "    0.115 2.00e-02 2.50e+03
        pdb=" N2  NAG G   2 "   -0.206 2.00e-02 2.50e+03
        pdb=" O7  NAG G   2 "   -0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG C   1 "   -0.081 2.00e-02 2.50e+03   6.63e-02 5.49e+01
        pdb=" C7  NAG C   1 "    0.022 2.00e-02 2.50e+03
        pdb=" C8  NAG C   1 "   -0.061 2.00e-02 2.50e+03
        pdb=" N2  NAG C   1 "    0.105 2.00e-02 2.50e+03
        pdb=" O7  NAG C   1 "    0.015 2.00e-02 2.50e+03
  ... (remaining 1905 not shown)

  Histogram of nonbonded interaction distances:
        2.03 -     2.60: 221
        2.60 -     3.18: 9281
        3.18 -     3.75: 16055
        3.75 -     4.33: 21714
        4.33 -     4.90: 35540
  Nonbonded interactions: 82811
  Sorted by model distance:
  nonbonded pdb=" SG  CYS E3977 "
            pdb=" SG  CYS E3991 "
     model   vdw
     2.029 3.760
  nonbonded pdb=" SG  CYS F  87 "
            pdb=" SG  CYS F 103 "
     model   vdw
     2.029 3.760
  nonbonded pdb=" SG  CYS E4355 "
            pdb=" SG  CYS E4369 "
     model   vdw
     2.029 3.760
  nonbonded pdb=" SG  CYS E4340 "
            pdb=" SG  CYS E4353 "
     model   vdw
     2.029 3.760
  nonbonded pdb=" SG  CYS E4336 "
            pdb=" SG  CYS E4344 "
     model   vdw
     2.030 3.760
  ... (remaining 82806 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: 0.05
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'E'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'F'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'G'
}
ncs_group {
  reference = chain 'D'
  selection = chain 'H'
}

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:             1.190
  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:          0.330
  Check model and map are aligned:         0.080
  Set scattering table:                    0.080
  Process input model:                     27.480
  Find NCS groups from input model:        0.190
  Set up NCS constraints:                  0.040
  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:2.950
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.350
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7802
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      :  0.004   0.062  10554  Z= 0.244
  Angle     :  0.659   9.805  14296  Z= 0.349
  Chirality :  0.047   0.195   1518
  Planarity :  0.007   0.128   1902
  Dihedral  : 17.240 107.485   4144
  Min Nonbonded Distance : 2.029

Molprobity Statistics.
  All-atom Clashscore : 9.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.53 %
    Favored  : 93.47 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 22.55 %
    Favored  : 75.00 %
  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: -0.71 (0.24), residues: 1286
  helix: -3.96 (1.09), residues: 14
  sheet: -0.43 (0.31), residues: 298
  loop : -0.41 (0.21), residues: 974

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A4288 
 HIS   0.005   0.001   HIS A4221 
 PHE   0.007   0.001   PHE A4125 
 TYR   0.018   0.001   TYR A4392 
 ARG   0.004   0.000   ARG B  46 

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

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

  2572 Ramachandran restraints generated.
    1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2572 Ramachandran restraints generated.
    1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 106
  time to evaluate  : 1.001 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 4062 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.7517 (mp0)
REVERT: B   89 GLU cc_start: 0.7862 (mp0) cc_final: 0.7265 (pt0)
REVERT: B 3767 ARG cc_start: 0.8127 (mmm-85) cc_final: 0.7898 (mmm-85)
REVERT: B 3798 LYS cc_start: 0.9013 (ptpt) cc_final: 0.8806 (ptpt)
REVERT: E 4062 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.7519 (mp0)
REVERT: F   89 GLU cc_start: 0.7863 (mp0) cc_final: 0.7267 (pt0)
REVERT: F 3767 ARG cc_start: 0.8104 (mmm-85) cc_final: 0.7870 (mmm-85)
REVERT: F 3798 LYS cc_start: 0.9011 (ptpt) cc_final: 0.8805 (ptpt)
  outliers start: 28
  outliers final: 22
  residues processed: 132
  average time/residue: 0.2318
  time to fit residues: 43.6918
Evaluate side-chains
  112 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 88
  time to evaluate  : 1.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 3942 CYS
Chi-restraints excluded: chain A residue 3980 ASN
Chi-restraints excluded: chain A residue 4062 GLU
Chi-restraints excluded: chain A residue 4106 THR
Chi-restraints excluded: chain A residue 4108 LEU
Chi-restraints excluded: chain A residue 4237 SER
Chi-restraints excluded: chain A residue 4314 ASN
Chi-restraints excluded: chain A residue 4339 VAL
Chi-restraints excluded: chain A residue 4353 CYS
Chi-restraints excluded: chain A residue 4375 LEU
Chi-restraints excluded: chain B residue 3773 CYS
Chi-restraints excluded: chain B residue 3799 THR
Chi-restraints excluded: chain E residue 3942 CYS
Chi-restraints excluded: chain E residue 3980 ASN
Chi-restraints excluded: chain E residue 4062 GLU
Chi-restraints excluded: chain E residue 4106 THR
Chi-restraints excluded: chain E residue 4108 LEU
Chi-restraints excluded: chain E residue 4237 SER
Chi-restraints excluded: chain E residue 4314 ASN
Chi-restraints excluded: chain E residue 4339 VAL
Chi-restraints excluded: chain E residue 4353 CYS
Chi-restraints excluded: chain E residue 4375 LEU
Chi-restraints excluded: chain F residue 3773 CYS
Chi-restraints excluded: chain F residue 3799 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 108 optimal weight:    0.0670
   chunk 97 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9980
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:   10.0000
   chunk 51 optimal weight:    0.9980
   chunk 100 optimal weight:    1.9990
   chunk 38 optimal weight:    0.8980
   chunk 61 optimal weight:    5.9990
   chunk 74 optimal weight:    0.6980
   chunk 116 optimal weight:    0.0570
   overall best weight:    0.5436

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

Flipped N/Q/H residues before XYZ refinement:
A4131 ASN
A4221 HIS
** A4314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A4390 ASN
B 100 GLN
B3772 GLN
B3782 GLN
E4131 ASN
E4221 HIS
** E4314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E4390 ASN
F 100 GLN
F3782 GLN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4172 r_free = 0.4172 target = 0.148880 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.097539 restraints weight = 18547.802|
|-----------------------------------------------------------------------------|
r_work (start): 0.3416 rms_B_bonded: 3.24
r_work: 0.3256 rms_B_bonded: 3.57 restraints_weight: 0.5000
r_work (final): 0.3256
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7907
moved from start:          0.1187

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  10554  Z= 0.209
  Angle     :  0.629   7.246  14296  Z= 0.337
  Chirality :  0.046   0.165   1518
  Planarity :  0.005   0.052   1902
  Dihedral  :  9.589  67.778   1726
  Min Nonbonded Distance : 2.196

Molprobity Statistics.
  All-atom Clashscore : 8.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.53 %
    Favored  : 93.47 %
  Rotamer:
    Outliers :  4.11 %
    Allowed  : 20.02 %
    Favored  : 75.87 %
  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: -0.80 (0.24), residues: 1286
  helix: -3.43 (1.42), residues: 12
  sheet: -0.58 (0.32), residues: 278
  loop : -0.47 (0.20), residues: 996

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A4288 
 HIS   0.004   0.001   HIS A4221 
 PHE   0.014   0.001   PHE B3766 
 TYR   0.012   0.001   TYR E3935 
 ARG   0.004   0.001   ARG A3970 

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

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

  2572 Ramachandran restraints generated.
    1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2572 Ramachandran restraints generated.
    1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 102
  time to evaluate  : 1.163 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   77 GLU cc_start: 0.7522 (tp30) cc_final: 0.7148 (pt0)
REVERT: B   89 GLU cc_start: 0.7991 (mp0) cc_final: 0.7277 (pt0)
REVERT: B 3766 PHE cc_start: 0.7031 (t80) cc_final: 0.6743 (t80)
REVERT: F   89 GLU cc_start: 0.7937 (mp0) cc_final: 0.7266 (pt0)
REVERT: F 3766 PHE cc_start: 0.7308 (t80) cc_final: 0.7008 (t80)
REVERT: F 3767 ARG cc_start: 0.8312 (mmm-85) cc_final: 0.7773 (mmm-85)
REVERT: F 3772 GLN cc_start: 0.7976 (OUTLIER) cc_final: 0.7589 (pt0)
REVERT: F 3796 GLU cc_start: 0.8430 (tp30) cc_final: 0.7854 (tp30)
  outliers start: 47
  outliers final: 20
  residues processed: 144
  average time/residue: 0.2491
  time to fit residues: 50.8132
Evaluate side-chains
  105 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 84
  time to evaluate  : 1.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 3980 ASN
Chi-restraints excluded: chain A residue 4035 VAL
Chi-restraints excluded: chain A residue 4047 GLU
Chi-restraints excluded: chain A residue 4102 VAL
Chi-restraints excluded: chain A residue 4106 THR
Chi-restraints excluded: chain A residue 4174 ASP
Chi-restraints excluded: chain A residue 4314 ASN
Chi-restraints excluded: chain A residue 4339 VAL
Chi-restraints excluded: chain B residue 3773 CYS
Chi-restraints excluded: chain B residue 3774 ILE
Chi-restraints excluded: chain B residue 3797 MET
Chi-restraints excluded: chain E residue 3980 ASN
Chi-restraints excluded: chain E residue 4047 GLU
Chi-restraints excluded: chain E residue 4102 VAL
Chi-restraints excluded: chain E residue 4106 THR
Chi-restraints excluded: chain E residue 4174 ASP
Chi-restraints excluded: chain E residue 4314 ASN
Chi-restraints excluded: chain E residue 4339 VAL
Chi-restraints excluded: chain E residue 4353 CYS
Chi-restraints excluded: chain F residue 3772 GLN
Chi-restraints excluded: chain F residue 3797 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 47 optimal weight:    1.9990
   chunk 64 optimal weight:   10.0000
   chunk 119 optimal weight:    0.4980
   chunk 31 optimal weight:    0.8980
   chunk 19 optimal weight:    3.9990
   chunk 90 optimal weight:    0.7980
   chunk 68 optimal weight:    3.9990
   chunk 11 optimal weight:    2.9990
   chunk 51 optimal weight:    0.7980
   chunk 113 optimal weight:    0.0670
   chunk 50 optimal weight:    0.9990
   overall best weight:    0.6118

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

Flipped N/Q/H residues before XYZ refinement:
B 100 GLN
F 100 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4163 r_free = 0.4163 target = 0.148049 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.097159 restraints weight = 18843.009|
|-----------------------------------------------------------------------------|
r_work (start): 0.3405 rms_B_bonded: 3.22
r_work: 0.3244 rms_B_bonded: 3.55 restraints_weight: 0.5000
r_work (final): 0.3244
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7915
moved from start:          0.1596

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  10554  Z= 0.207
  Angle     :  0.587   7.143  14296  Z= 0.313
  Chirality :  0.046   0.171   1518
  Planarity :  0.005   0.042   1902
  Dihedral  :  7.162  63.310   1704
  Min Nonbonded Distance : 2.207

Molprobity Statistics.
  All-atom Clashscore : 7.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.14 %
    Favored  : 93.86 %
  Rotamer:
    Outliers :  4.20 %
    Allowed  : 18.01 %
    Favored  : 77.80 %
  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: -0.81 (0.24), residues: 1286
  helix: -3.15 (1.61), residues: 12
  sheet: -0.67 (0.32), residues: 282
  loop : -0.46 (0.21), residues: 992

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A4288 
 HIS   0.003   0.001   HIS A3927 
 PHE   0.020   0.002   PHE F  33 
 TYR   0.012   0.001   TYR A4142 
 ARG   0.012   0.001   ARG F3767 

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

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

  2572 Ramachandran restraints generated.
    1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2572 Ramachandran restraints generated.
    1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 90
  time to evaluate  : 1.236 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   89 GLU cc_start: 0.7754 (mp0) cc_final: 0.7319 (pt0)
REVERT: B 3783 GLU cc_start: 0.8421 (tm-30) cc_final: 0.7943 (tm-30)
REVERT: B 3796 GLU cc_start: 0.8465 (tp30) cc_final: 0.7770 (tp30)
REVERT: F   89 GLU cc_start: 0.8027 (mp0) cc_final: 0.7374 (pt0)
REVERT: F 3772 GLN cc_start: 0.8474 (OUTLIER) cc_final: 0.8192 (pt0)
REVERT: F 3793 ARG cc_start: 0.7808 (ttp80) cc_final: 0.7563 (ttp80)
REVERT: F 3796 GLU cc_start: 0.8402 (tp30) cc_final: 0.7761 (tp30)
  outliers start: 48
  outliers final: 26
  residues processed: 132
  average time/residue: 0.2174
  time to fit residues: 41.7817
Evaluate side-chains
  108 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 81
  time to evaluate  : 1.208 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 3926 THR
Chi-restraints excluded: chain A residue 3942 CYS
Chi-restraints excluded: chain A residue 3964 CYS
Chi-restraints excluded: chain A residue 3980 ASN
Chi-restraints excluded: chain A residue 4035 VAL
Chi-restraints excluded: chain A residue 4047 GLU
Chi-restraints excluded: chain A residue 4089 ILE
Chi-restraints excluded: chain A residue 4102 VAL
Chi-restraints excluded: chain A residue 4106 THR
Chi-restraints excluded: chain A residue 4174 ASP
Chi-restraints excluded: chain A residue 4314 ASN
Chi-restraints excluded: chain A residue 4339 VAL
Chi-restraints excluded: chain A residue 4400 LYS
Chi-restraints excluded: chain B residue 3773 CYS
Chi-restraints excluded: chain B residue 3774 ILE
Chi-restraints excluded: chain B residue 3797 MET
Chi-restraints excluded: chain E residue 3926 THR
Chi-restraints excluded: chain E residue 3980 ASN
Chi-restraints excluded: chain E residue 4047 GLU
Chi-restraints excluded: chain E residue 4089 ILE
Chi-restraints excluded: chain E residue 4102 VAL
Chi-restraints excluded: chain E residue 4106 THR
Chi-restraints excluded: chain E residue 4174 ASP
Chi-restraints excluded: chain E residue 4314 ASN
Chi-restraints excluded: chain F residue 3772 GLN
Chi-restraints excluded: chain F residue 3774 ILE
Chi-restraints excluded: chain F residue 3797 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 105 optimal weight:    0.9980
   chunk 101 optimal weight:    0.7980
   chunk 7 optimal weight:    6.9990
   chunk 55 optimal weight:    0.5980
   chunk 124 optimal weight:    4.9990
   chunk 57 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   chunk 71 optimal weight:    5.9990
   chunk 53 optimal weight:    7.9990
   chunk 60 optimal weight:    3.9990
   chunk 98 optimal weight:    0.9980
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
A4087 GLN
A4130 ASN
** B 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E4087 GLN
E4130 ASN
** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4139 r_free = 0.4139 target = 0.146375 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.094783 restraints weight = 18694.848|
|-----------------------------------------------------------------------------|
r_work (start): 0.3362 rms_B_bonded: 3.21
r_work: 0.3203 rms_B_bonded: 3.55 restraints_weight: 0.5000
r_work (final): 0.3203
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7961
moved from start:          0.1976

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046  10554  Z= 0.299
  Angle     :  0.610   7.138  14296  Z= 0.326
  Chirality :  0.047   0.159   1518
  Planarity :  0.005   0.041   1902
  Dihedral  :  6.410  59.669   1702
  Min Nonbonded Distance : 2.166

Molprobity Statistics.
  All-atom Clashscore : 8.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.92 %
    Favored  : 93.08 %
  Rotamer:
    Outliers :  4.63 %
    Allowed  : 17.13 %
    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: -0.83 (0.24), residues: 1286
  helix: -3.06 (1.66), residues: 12
  sheet: -0.80 (0.32), residues: 282
  loop : -0.42 (0.21), residues: 992

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP E4288 
 HIS   0.003   0.001   HIS E4324 
 PHE   0.014   0.002   PHE F  33 
 TYR   0.012   0.002   TYR E4247 
 ARG   0.010   0.001   ARG B  65 

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

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

  2572 Ramachandran restraints generated.
    1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2572 Ramachandran restraints generated.
    1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 94
  time to evaluate  : 1.083 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   89 GLU cc_start: 0.8022 (mp0) cc_final: 0.7354 (pt0)
REVERT: B 3767 ARG cc_start: 0.8160 (mmm-85) cc_final: 0.7530 (mmm-85)
REVERT: B 3783 GLU cc_start: 0.8559 (tm-30) cc_final: 0.7992 (tm-30)
REVERT: B 3796 GLU cc_start: 0.8525 (tp30) cc_final: 0.7898 (tp30)
REVERT: E 4041 MET cc_start: 0.7145 (OUTLIER) cc_final: 0.6604 (mpt)
REVERT: F   89 GLU cc_start: 0.8086 (mp0) cc_final: 0.7452 (pt0)
REVERT: F 3772 GLN cc_start: 0.8563 (OUTLIER) cc_final: 0.8306 (pt0)
REVERT: F 3793 ARG cc_start: 0.8115 (ttp80) cc_final: 0.7908 (ttp80)
REVERT: F 3796 GLU cc_start: 0.8499 (tp30) cc_final: 0.7906 (tp30)
  outliers start: 53
  outliers final: 30
  residues processed: 138
  average time/residue: 0.2260
  time to fit residues: 44.9914
Evaluate side-chains
  120 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 88
  time to evaluate  : 1.192 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 3926 THR
Chi-restraints excluded: chain A residue 3942 CYS
Chi-restraints excluded: chain A residue 3964 CYS
Chi-restraints excluded: chain A residue 3980 ASN
Chi-restraints excluded: chain A residue 4041 MET
Chi-restraints excluded: chain A residue 4047 GLU
Chi-restraints excluded: chain A residue 4088 THR
Chi-restraints excluded: chain A residue 4089 ILE
Chi-restraints excluded: chain A residue 4102 VAL
Chi-restraints excluded: chain A residue 4106 THR
Chi-restraints excluded: chain A residue 4174 ASP
Chi-restraints excluded: chain A residue 4314 ASN
Chi-restraints excluded: chain A residue 4339 VAL
Chi-restraints excluded: chain A residue 4375 LEU
Chi-restraints excluded: chain B residue   92 ASP
Chi-restraints excluded: chain B residue 3774 ILE
Chi-restraints excluded: chain B residue 3797 MET
Chi-restraints excluded: chain E residue 3926 THR
Chi-restraints excluded: chain E residue 3980 ASN
Chi-restraints excluded: chain E residue 4041 MET
Chi-restraints excluded: chain E residue 4047 GLU
Chi-restraints excluded: chain E residue 4088 THR
Chi-restraints excluded: chain E residue 4089 ILE
Chi-restraints excluded: chain E residue 4102 VAL
Chi-restraints excluded: chain E residue 4106 THR
Chi-restraints excluded: chain E residue 4174 ASP
Chi-restraints excluded: chain E residue 4314 ASN
Chi-restraints excluded: chain E residue 4375 LEU
Chi-restraints excluded: chain E residue 4400 LYS
Chi-restraints excluded: chain F residue 3772 GLN
Chi-restraints excluded: chain F residue 3774 ILE
Chi-restraints excluded: chain F residue 3797 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 38 optimal weight:    1.9990
   chunk 40 optimal weight:    1.9990
   chunk 110 optimal weight:    0.9980
   chunk 13 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9990
   chunk 83 optimal weight:    2.9990
   chunk 77 optimal weight:    1.9990
   chunk 119 optimal weight:    5.9990
   chunk 80 optimal weight:    0.5980
   chunk 53 optimal weight:    4.9990
   chunk 124 optimal weight:    3.9990
   overall best weight:    1.3186

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

Flipped N/Q/H residues before XYZ refinement:
A4130 ASN
** B 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E4130 ASN
** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4114 r_free = 0.4114 target = 0.144555 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.093049 restraints weight = 18531.720|
|-----------------------------------------------------------------------------|
r_work (start): 0.3333 rms_B_bonded: 3.17
r_work: 0.3175 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.3175
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7984
moved from start:          0.2378

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038  10554  Z= 0.347
  Angle     :  0.643   8.701  14296  Z= 0.343
  Chirality :  0.048   0.161   1518
  Planarity :  0.005   0.042   1902
  Dihedral  :  6.321  58.793   1701
  Min Nonbonded Distance : 2.150

Molprobity Statistics.
  All-atom Clashscore : 8.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.23 %
    Favored  : 92.77 %
  Rotamer:
    Outliers :  4.98 %
    Allowed  : 16.96 %
    Favored  : 78.06 %
  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: -0.89 (0.24), residues: 1286
  helix: -3.13 (1.62), residues: 12
  sheet: -0.88 (0.32), residues: 278
  loop : -0.46 (0.21), residues: 996

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A4288 
 HIS   0.004   0.001   HIS A4324 
 PHE   0.021   0.002   PHE E4033 
 TYR   0.013   0.002   TYR A4247 
 ARG   0.005   0.001   ARG A4048 

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

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

  2572 Ramachandran restraints generated.
    1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2572 Ramachandran restraints generated.
    1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 96
  time to evaluate  : 1.198 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 4217 MET cc_start: 0.9249 (OUTLIER) cc_final: 0.8999 (mpt)
REVERT: B   77 GLU cc_start: 0.6238 (tm-30) cc_final: 0.5874 (pp20)
REVERT: B   89 GLU cc_start: 0.8049 (mp0) cc_final: 0.7446 (pt0)
REVERT: B 3767 ARG cc_start: 0.8223 (mmm-85) cc_final: 0.7913 (mmm-85)
REVERT: B 3796 GLU cc_start: 0.8608 (tp30) cc_final: 0.8088 (tp30)
REVERT: E 4217 MET cc_start: 0.9240 (OUTLIER) cc_final: 0.8990 (mpt)
REVERT: F   89 GLU cc_start: 0.8154 (mp0) cc_final: 0.7492 (pt0)
REVERT: F 3767 ARG cc_start: 0.8220 (mmm-85) cc_final: 0.7925 (tpt-90)
REVERT: F 3771 GLN cc_start: 0.8763 (tp40) cc_final: 0.8030 (tp40)
REVERT: F 3772 GLN cc_start: 0.8546 (OUTLIER) cc_final: 0.8238 (pt0)
REVERT: F 3796 GLU cc_start: 0.8676 (tp30) cc_final: 0.8082 (tp30)
  outliers start: 57
  outliers final: 44
  residues processed: 142
  average time/residue: 0.2161
  time to fit residues: 44.5826
Evaluate side-chains
  136 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 89
  time to evaluate  : 1.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 3926 THR
Chi-restraints excluded: chain A residue 3942 CYS
Chi-restraints excluded: chain A residue 3964 CYS
Chi-restraints excluded: chain A residue 3980 ASN
Chi-restraints excluded: chain A residue 4035 VAL
Chi-restraints excluded: chain A residue 4041 MET
Chi-restraints excluded: chain A residue 4047 GLU
Chi-restraints excluded: chain A residue 4089 ILE
Chi-restraints excluded: chain A residue 4102 VAL
Chi-restraints excluded: chain A residue 4106 THR
Chi-restraints excluded: chain A residue 4108 LEU
Chi-restraints excluded: chain A residue 4136 VAL
Chi-restraints excluded: chain A residue 4147 ASP
Chi-restraints excluded: chain A residue 4174 ASP
Chi-restraints excluded: chain A residue 4217 MET
Chi-restraints excluded: chain A residue 4314 ASN
Chi-restraints excluded: chain A residue 4339 VAL
Chi-restraints excluded: chain A residue 4375 LEU
Chi-restraints excluded: chain A residue 4400 LYS
Chi-restraints excluded: chain B residue   92 ASP
Chi-restraints excluded: chain B residue 3773 CYS
Chi-restraints excluded: chain B residue 3774 ILE
Chi-restraints excluded: chain B residue 3797 MET
Chi-restraints excluded: chain B residue 3799 THR
Chi-restraints excluded: chain E residue 3926 THR
Chi-restraints excluded: chain E residue 3980 ASN
Chi-restraints excluded: chain E residue 4007 CYS
Chi-restraints excluded: chain E residue 4033 PHE
Chi-restraints excluded: chain E residue 4041 MET
Chi-restraints excluded: chain E residue 4047 GLU
Chi-restraints excluded: chain E residue 4089 ILE
Chi-restraints excluded: chain E residue 4102 VAL
Chi-restraints excluded: chain E residue 4106 THR
Chi-restraints excluded: chain E residue 4108 LEU
Chi-restraints excluded: chain E residue 4136 VAL
Chi-restraints excluded: chain E residue 4147 ASP
Chi-restraints excluded: chain E residue 4174 ASP
Chi-restraints excluded: chain E residue 4217 MET
Chi-restraints excluded: chain E residue 4314 ASN
Chi-restraints excluded: chain E residue 4339 VAL
Chi-restraints excluded: chain E residue 4375 LEU
Chi-restraints excluded: chain E residue 4400 LYS
Chi-restraints excluded: chain F residue   84 SER
Chi-restraints excluded: chain F residue 3772 GLN
Chi-restraints excluded: chain F residue 3774 ILE
Chi-restraints excluded: chain F residue 3797 MET
Chi-restraints excluded: chain F residue 3799 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 119 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9990
   chunk 98 optimal weight:    4.9990
   chunk 80 optimal weight:    0.8980
   chunk 24 optimal weight:    0.8980
   chunk 117 optimal weight:    0.7980
   chunk 66 optimal weight:    6.9990
   chunk 68 optimal weight:    7.9990
   chunk 59 optimal weight:    0.8980
   chunk 112 optimal weight:    4.9990
   chunk 10 optimal weight:    3.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
A4130 ASN
B 100 GLN
E4130 ASN
F 100 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4118 r_free = 0.4118 target = 0.145069 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.093726 restraints weight = 18635.751|
|-----------------------------------------------------------------------------|
r_work (start): 0.3345 rms_B_bonded: 3.20
r_work: 0.3189 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.3189
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7965
moved from start:          0.2557

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  10554  Z= 0.257
  Angle     :  0.600   7.211  14296  Z= 0.320
  Chirality :  0.046   0.163   1518
  Planarity :  0.004   0.041   1902
  Dihedral  :  6.141  59.715   1701
  Min Nonbonded Distance : 2.169

Molprobity Statistics.
  All-atom Clashscore : 8.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.08 %
    Favored  : 92.92 %
  Rotamer:
    Outliers :  4.81 %
    Allowed  : 18.09 %
    Favored  : 77.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.83 (0.24), residues: 1286
  helix: -3.11 (1.63), residues: 12
  sheet: -0.70 (0.34), residues: 258
  loop : -0.48 (0.21), residues: 1016

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A4288 
 HIS   0.002   0.001   HIS E3927 
 PHE   0.027   0.002   PHE A4033 
 TYR   0.012   0.002   TYR E4247 
 ARG   0.004   0.000   ARG B3793 

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

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

  2572 Ramachandran restraints generated.
    1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2572 Ramachandran restraints generated.
    1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 96
  time to evaluate  : 1.240 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 3970 ARG cc_start: 0.0544 (OUTLIER) cc_final: -0.0528 (mtm180)
REVERT: A 4217 MET cc_start: 0.9214 (OUTLIER) cc_final: 0.9011 (mpt)
REVERT: B   77 GLU cc_start: 0.5974 (tm-30) cc_final: 0.5499 (pp20)
REVERT: B   89 GLU cc_start: 0.8040 (mp0) cc_final: 0.7452 (pt0)
REVERT: B 3767 ARG cc_start: 0.8231 (mmm-85) cc_final: 0.7956 (mmm-85)
REVERT: B 3796 GLU cc_start: 0.8646 (tp30) cc_final: 0.8006 (tp30)
REVERT: E 4041 MET cc_start: 0.7071 (OUTLIER) cc_final: 0.6465 (mpt)
REVERT: E 4217 MET cc_start: 0.9203 (OUTLIER) cc_final: 0.8993 (mpt)
REVERT: F   89 GLU cc_start: 0.8121 (mp0) cc_final: 0.7486 (pt0)
REVERT: F 3772 GLN cc_start: 0.8723 (OUTLIER) cc_final: 0.8495 (pt0)
REVERT: F 3796 GLU cc_start: 0.8655 (tp30) cc_final: 0.8056 (tp30)
  outliers start: 55
  outliers final: 40
  residues processed: 141
  average time/residue: 0.2182
  time to fit residues: 44.3650
Evaluate side-chains
  137 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 92
  time to evaluate  : 1.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 3926 THR
Chi-restraints excluded: chain A residue 3942 CYS
Chi-restraints excluded: chain A residue 3964 CYS
Chi-restraints excluded: chain A residue 3970 ARG
Chi-restraints excluded: chain A residue 3980 ASN
Chi-restraints excluded: chain A residue 4041 MET
Chi-restraints excluded: chain A residue 4047 GLU
Chi-restraints excluded: chain A residue 4088 THR
Chi-restraints excluded: chain A residue 4089 ILE
Chi-restraints excluded: chain A residue 4102 VAL
Chi-restraints excluded: chain A residue 4106 THR
Chi-restraints excluded: chain A residue 4136 VAL
Chi-restraints excluded: chain A residue 4147 ASP
Chi-restraints excluded: chain A residue 4174 ASP
Chi-restraints excluded: chain A residue 4217 MET
Chi-restraints excluded: chain A residue 4255 VAL
Chi-restraints excluded: chain A residue 4314 ASN
Chi-restraints excluded: chain A residue 4375 LEU
Chi-restraints excluded: chain A residue 4400 LYS
Chi-restraints excluded: chain B residue   92 ASP
Chi-restraints excluded: chain B residue 3773 CYS
Chi-restraints excluded: chain B residue 3774 ILE
Chi-restraints excluded: chain B residue 3797 MET
Chi-restraints excluded: chain E residue 3926 THR
Chi-restraints excluded: chain E residue 3980 ASN
Chi-restraints excluded: chain E residue 4007 CYS
Chi-restraints excluded: chain E residue 4033 PHE
Chi-restraints excluded: chain E residue 4041 MET
Chi-restraints excluded: chain E residue 4047 GLU
Chi-restraints excluded: chain E residue 4088 THR
Chi-restraints excluded: chain E residue 4089 ILE
Chi-restraints excluded: chain E residue 4102 VAL
Chi-restraints excluded: chain E residue 4106 THR
Chi-restraints excluded: chain E residue 4136 VAL
Chi-restraints excluded: chain E residue 4147 ASP
Chi-restraints excluded: chain E residue 4174 ASP
Chi-restraints excluded: chain E residue 4217 MET
Chi-restraints excluded: chain E residue 4255 VAL
Chi-restraints excluded: chain E residue 4314 ASN
Chi-restraints excluded: chain E residue 4339 VAL
Chi-restraints excluded: chain E residue 4375 LEU
Chi-restraints excluded: chain E residue 4400 LYS
Chi-restraints excluded: chain F residue   84 SER
Chi-restraints excluded: chain F residue 3772 GLN
Chi-restraints excluded: chain F residue 3797 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 112 optimal weight:    0.0970
   chunk 102 optimal weight:    0.9980
   chunk 51 optimal weight:    1.9990
   chunk 78 optimal weight:    0.9980
   chunk 87 optimal weight:    0.9990
   chunk 66 optimal weight:    5.9990
   chunk 50 optimal weight:    0.7980
   chunk 33 optimal weight:    0.3980
   chunk 13 optimal weight:    0.8980
   chunk 65 optimal weight:    3.9990
   chunk 67 optimal weight:    0.4980
   overall best weight:    0.5378

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

Flipped N/Q/H residues before XYZ refinement:
A4130 ASN
B 100 GLN
E4005 ASN
E4130 ASN
** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4129 r_free = 0.4129 target = 0.146142 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.094448 restraints weight = 18852.899|
|-----------------------------------------------------------------------------|
r_work (start): 0.3362 rms_B_bonded: 3.29
r_work: 0.3204 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.3204
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7949
moved from start:          0.2655

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  10554  Z= 0.187
  Angle     :  0.576   8.294  14296  Z= 0.307
  Chirality :  0.046   0.165   1518
  Planarity :  0.004   0.039   1902
  Dihedral  :  5.956  59.364   1700
  Min Nonbonded Distance : 2.190

Molprobity Statistics.
  All-atom Clashscore : 8.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.77 %
    Favored  : 93.23 %
  Rotamer:
    Outliers :  4.46 %
    Allowed  : 18.27 %
    Favored  : 77.27 %
  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: -0.75 (0.24), residues: 1286
  helix: -3.14 (1.60), residues: 12
  sheet: -0.70 (0.34), residues: 258
  loop : -0.39 (0.21), residues: 1016

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP E4160 
 HIS   0.002   0.001   HIS E3927 
 PHE   0.021   0.002   PHE A4033 
 TYR   0.012   0.001   TYR A4407 
 ARG   0.003   0.000   ARG A4048 

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

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

  2572 Ramachandran restraints generated.
    1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2572 Ramachandran restraints generated.
    1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 102
  time to evaluate  : 1.250 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 3970 ARG cc_start: 0.0673 (OUTLIER) cc_final: -0.0366 (mtm180)
REVERT: A 4041 MET cc_start: 0.7057 (OUTLIER) cc_final: 0.6447 (mpt)
REVERT: A 4217 MET cc_start: 0.9188 (OUTLIER) cc_final: 0.8915 (mpt)
REVERT: B   77 GLU cc_start: 0.6006 (tm-30) cc_final: 0.5533 (pp20)
REVERT: B   89 GLU cc_start: 0.8061 (mp0) cc_final: 0.7407 (pt0)
REVERT: B 3796 GLU cc_start: 0.8802 (tp30) cc_final: 0.8112 (tp30)
REVERT: E 4041 MET cc_start: 0.6858 (OUTLIER) cc_final: 0.6213 (mpt)
REVERT: E 4217 MET cc_start: 0.9182 (OUTLIER) cc_final: 0.8916 (mpt)
REVERT: F   89 GLU cc_start: 0.7909 (mp0) cc_final: 0.7319 (pt0)
REVERT: F 3766 PHE cc_start: 0.7893 (t80) cc_final: 0.7398 (t80)
REVERT: F 3767 ARG cc_start: 0.8453 (mmm-85) cc_final: 0.8083 (mmm-85)
REVERT: F 3772 GLN cc_start: 0.8705 (OUTLIER) cc_final: 0.8399 (pt0)
REVERT: F 3796 GLU cc_start: 0.8629 (tp30) cc_final: 0.8033 (tp30)
  outliers start: 51
  outliers final: 35
  residues processed: 142
  average time/residue: 0.2189
  time to fit residues: 44.7903
Evaluate side-chains
  134 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 93
  time to evaluate  : 1.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 3926 THR
Chi-restraints excluded: chain A residue 3942 CYS
Chi-restraints excluded: chain A residue 3964 CYS
Chi-restraints excluded: chain A residue 3970 ARG
Chi-restraints excluded: chain A residue 3980 ASN
Chi-restraints excluded: chain A residue 4035 VAL
Chi-restraints excluded: chain A residue 4041 MET
Chi-restraints excluded: chain A residue 4089 ILE
Chi-restraints excluded: chain A residue 4102 VAL
Chi-restraints excluded: chain A residue 4106 THR
Chi-restraints excluded: chain A residue 4108 LEU
Chi-restraints excluded: chain A residue 4136 VAL
Chi-restraints excluded: chain A residue 4147 ASP
Chi-restraints excluded: chain A residue 4174 ASP
Chi-restraints excluded: chain A residue 4217 MET
Chi-restraints excluded: chain A residue 4314 ASN
Chi-restraints excluded: chain A residue 4400 LYS
Chi-restraints excluded: chain B residue   92 ASP
Chi-restraints excluded: chain B residue 3773 CYS
Chi-restraints excluded: chain B residue 3774 ILE
Chi-restraints excluded: chain B residue 3797 MET
Chi-restraints excluded: chain E residue 3926 THR
Chi-restraints excluded: chain E residue 3980 ASN
Chi-restraints excluded: chain E residue 4007 CYS
Chi-restraints excluded: chain E residue 4033 PHE
Chi-restraints excluded: chain E residue 4041 MET
Chi-restraints excluded: chain E residue 4089 ILE
Chi-restraints excluded: chain E residue 4102 VAL
Chi-restraints excluded: chain E residue 4106 THR
Chi-restraints excluded: chain E residue 4108 LEU
Chi-restraints excluded: chain E residue 4136 VAL
Chi-restraints excluded: chain E residue 4147 ASP
Chi-restraints excluded: chain E residue 4174 ASP
Chi-restraints excluded: chain E residue 4217 MET
Chi-restraints excluded: chain E residue 4314 ASN
Chi-restraints excluded: chain E residue 4400 LYS
Chi-restraints excluded: chain F residue   81 ILE
Chi-restraints excluded: chain F residue   84 SER
Chi-restraints excluded: chain F residue 3772 GLN
Chi-restraints excluded: chain F residue 3781 ASP
Chi-restraints excluded: chain F residue 3797 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 18 optimal weight:    0.9980
   chunk 68 optimal weight:    0.5980
   chunk 6 optimal weight:    2.9990
   chunk 3 optimal weight:    8.9990
   chunk 65 optimal weight:    7.9990
   chunk 92 optimal weight:    0.6980
   chunk 37 optimal weight:    1.9990
   chunk 97 optimal weight:    1.9990
   chunk 22 optimal weight:    0.0970
   chunk 70 optimal weight:    0.0010
   chunk 85 optimal weight:    0.5980
   overall best weight:    0.3984

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

Flipped N/Q/H residues before XYZ refinement:
A4130 ASN
** B 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E4130 ASN
** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4141 r_free = 0.4141 target = 0.146905 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.095342 restraints weight = 18612.417|
|-----------------------------------------------------------------------------|
r_work (start): 0.3378 rms_B_bonded: 3.27
r_work: 0.3219 rms_B_bonded: 3.55 restraints_weight: 0.5000
r_work (final): 0.3219
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7937
moved from start:          0.2778

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  10554  Z= 0.175
  Angle     :  0.576  10.572  14296  Z= 0.304
  Chirality :  0.045   0.166   1518
  Planarity :  0.004   0.038   1902
  Dihedral  :  5.804  57.742   1700
  Min Nonbonded Distance : 2.200

Molprobity Statistics.
  All-atom Clashscore : 8.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.61 %
    Favored  : 93.39 %
  Rotamer:
    Outliers :  4.46 %
    Allowed  : 18.01 %
    Favored  : 77.53 %
  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: -0.66 (0.24), residues: 1286
  helix: -3.24 (1.53), residues: 12
  sheet: -0.79 (0.33), residues: 278
  loop : -0.27 (0.21), residues: 996

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.002   TRP F3778 
 HIS   0.002   0.001   HIS E3927 
 PHE   0.021   0.002   PHE E4033 
 TYR   0.011   0.001   TYR E4159 
 ARG   0.003   0.000   ARG A4048 

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

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

  2572 Ramachandran restraints generated.
    1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2572 Ramachandran restraints generated.
    1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 98
  time to evaluate  : 1.368 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 3970 ARG cc_start: 0.0627 (OUTLIER) cc_final: -0.0240 (mtm180)
REVERT: A 4217 MET cc_start: 0.9156 (OUTLIER) cc_final: 0.8921 (mpt)
REVERT: B   77 GLU cc_start: 0.6123 (tm-30) cc_final: 0.5792 (pp20)
REVERT: B   89 GLU cc_start: 0.8049 (mp0) cc_final: 0.7409 (pt0)
REVERT: B 3766 PHE cc_start: 0.7521 (t80) cc_final: 0.7078 (t80)
REVERT: B 3796 GLU cc_start: 0.8786 (tp30) cc_final: 0.8197 (tp30)
REVERT: E 3970 ARG cc_start: 0.0117 (OUTLIER) cc_final: -0.1038 (mtm180)
REVERT: E 4041 MET cc_start: 0.6783 (OUTLIER) cc_final: 0.6292 (mpt)
REVERT: E 4217 MET cc_start: 0.9148 (OUTLIER) cc_final: 0.8928 (mpt)
REVERT: F   89 GLU cc_start: 0.7873 (mp0) cc_final: 0.7327 (pt0)
REVERT: F 3767 ARG cc_start: 0.8435 (mmm-85) cc_final: 0.7963 (mmm-85)
REVERT: F 3772 GLN cc_start: 0.8645 (OUTLIER) cc_final: 0.8307 (pt0)
REVERT: F 3796 GLU cc_start: 0.8648 (tp30) cc_final: 0.8046 (tp30)
  outliers start: 51
  outliers final: 35
  residues processed: 138
  average time/residue: 0.2424
  time to fit residues: 48.3901
Evaluate side-chains
  131 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 90
  time to evaluate  : 1.510 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 3926 THR
Chi-restraints excluded: chain A residue 3942 CYS
Chi-restraints excluded: chain A residue 3964 CYS
Chi-restraints excluded: chain A residue 3970 ARG
Chi-restraints excluded: chain A residue 3980 ASN
Chi-restraints excluded: chain A residue 4035 VAL
Chi-restraints excluded: chain A residue 4089 ILE
Chi-restraints excluded: chain A residue 4102 VAL
Chi-restraints excluded: chain A residue 4106 THR
Chi-restraints excluded: chain A residue 4108 LEU
Chi-restraints excluded: chain A residue 4136 VAL
Chi-restraints excluded: chain A residue 4174 ASP
Chi-restraints excluded: chain A residue 4217 MET
Chi-restraints excluded: chain A residue 4255 VAL
Chi-restraints excluded: chain A residue 4314 ASN
Chi-restraints excluded: chain A residue 4375 LEU
Chi-restraints excluded: chain A residue 4400 LYS
Chi-restraints excluded: chain B residue   92 ASP
Chi-restraints excluded: chain B residue 3773 CYS
Chi-restraints excluded: chain B residue 3774 ILE
Chi-restraints excluded: chain B residue 3797 MET
Chi-restraints excluded: chain E residue 3926 THR
Chi-restraints excluded: chain E residue 3970 ARG
Chi-restraints excluded: chain E residue 3980 ASN
Chi-restraints excluded: chain E residue 4007 CYS
Chi-restraints excluded: chain E residue 4041 MET
Chi-restraints excluded: chain E residue 4089 ILE
Chi-restraints excluded: chain E residue 4102 VAL
Chi-restraints excluded: chain E residue 4106 THR
Chi-restraints excluded: chain E residue 4108 LEU
Chi-restraints excluded: chain E residue 4136 VAL
Chi-restraints excluded: chain E residue 4174 ASP
Chi-restraints excluded: chain E residue 4217 MET
Chi-restraints excluded: chain E residue 4255 VAL
Chi-restraints excluded: chain E residue 4314 ASN
Chi-restraints excluded: chain E residue 4339 VAL
Chi-restraints excluded: chain E residue 4375 LEU
Chi-restraints excluded: chain E residue 4400 LYS
Chi-restraints excluded: chain F residue   81 ILE
Chi-restraints excluded: chain F residue 3772 GLN
Chi-restraints excluded: chain F residue 3781 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 59 optimal weight:    4.9990
   chunk 88 optimal weight:    1.9990
   chunk 75 optimal weight:    0.7980
   chunk 65 optimal weight:   10.0000
   chunk 29 optimal weight:    2.9990
   chunk 90 optimal weight:    1.9990
   chunk 77 optimal weight:    0.6980
   chunk 10 optimal weight:    4.9990
   chunk 61 optimal weight:    3.9990
   chunk 20 optimal weight:    0.4980
   chunk 2 optimal weight:    0.8980
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
A4130 ASN
** B 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E4130 ASN
** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4155 r_free = 0.4155 target = 0.151263 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.098426 restraints weight = 18662.774|
|-----------------------------------------------------------------------------|
r_work (start): 0.3334 rms_B_bonded: 3.10
r_work: 0.3158 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.3158
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7940
moved from start:          0.2972

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  10554  Z= 0.281
  Angle     :  0.609   9.539  14296  Z= 0.322
  Chirality :  0.047   0.182   1518
  Planarity :  0.004   0.039   1902
  Dihedral  :  5.936  58.007   1700
  Min Nonbonded Distance : 2.178

Molprobity Statistics.
  All-atom Clashscore : 9.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.15 %
    Favored  : 92.85 %
  Rotamer:
    Outliers :  4.55 %
    Allowed  : 17.57 %
    Favored  : 77.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.75 (0.24), residues: 1286
  helix: -3.11 (1.63), residues: 12
  sheet: -0.80 (0.34), residues: 258
  loop : -0.36 (0.21), residues: 1016

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A4288 
 HIS   0.003   0.001   HIS A4324 
 PHE   0.019   0.002   PHE B3766 
 TYR   0.016   0.002   TYR E4287 
 ARG   0.010   0.001   ARG F  65 

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

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

  2572 Ramachandran restraints generated.
    1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2572 Ramachandran restraints generated.
    1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 95
  time to evaluate  : 1.329 
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: symmetry clash
   revert: symmetry clash
REVERT: A 3970 ARG cc_start: 0.1271 (OUTLIER) cc_final: 0.0611 (mtm180)
REVERT: B   77 GLU cc_start: 0.5932 (tm-30) cc_final: 0.5522 (pp20)
REVERT: B   89 GLU cc_start: 0.8052 (mp0) cc_final: 0.7443 (pt0)
REVERT: B 3766 PHE cc_start: 0.7553 (t80) cc_final: 0.7112 (t80)
REVERT: B 3767 ARG cc_start: 0.8429 (mmm-85) cc_final: 0.7889 (mmm-85)
REVERT: B 3796 GLU cc_start: 0.8805 (tp30) cc_final: 0.8224 (tp30)
REVERT: E 3970 ARG cc_start: 0.0270 (OUTLIER) cc_final: -0.0821 (mtm180)
REVERT: E 4041 MET cc_start: 0.6642 (OUTLIER) cc_final: 0.5977 (mpt)
REVERT: F   89 GLU cc_start: 0.7923 (mp0) cc_final: 0.7360 (pt0)
REVERT: F 3767 ARG cc_start: 0.8469 (mmm-85) cc_final: 0.7986 (mmm-85)
REVERT: F 3772 GLN cc_start: 0.8718 (OUTLIER) cc_final: 0.8362 (pt0)
REVERT: F 3796 GLU cc_start: 0.8714 (tp30) cc_final: 0.8125 (tp30)
  outliers start: 52
  outliers final: 39
  residues processed: 138
  average time/residue: 0.2234
  time to fit residues: 44.2031
Evaluate side-chains
  132 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 89
  time to evaluate  : 1.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 3926 THR
Chi-restraints excluded: chain A residue 3942 CYS
Chi-restraints excluded: chain A residue 3964 CYS
Chi-restraints excluded: chain A residue 3970 ARG
Chi-restraints excluded: chain A residue 3980 ASN
Chi-restraints excluded: chain A residue 4035 VAL
Chi-restraints excluded: chain A residue 4088 THR
Chi-restraints excluded: chain A residue 4089 ILE
Chi-restraints excluded: chain A residue 4102 VAL
Chi-restraints excluded: chain A residue 4106 THR
Chi-restraints excluded: chain A residue 4108 LEU
Chi-restraints excluded: chain A residue 4136 VAL
Chi-restraints excluded: chain A residue 4174 ASP
Chi-restraints excluded: chain A residue 4255 VAL
Chi-restraints excluded: chain A residue 4314 ASN
Chi-restraints excluded: chain A residue 4375 LEU
Chi-restraints excluded: chain A residue 4400 LYS
Chi-restraints excluded: chain B residue   92 ASP
Chi-restraints excluded: chain B residue 3773 CYS
Chi-restraints excluded: chain B residue 3774 ILE
Chi-restraints excluded: chain B residue 3797 MET
Chi-restraints excluded: chain E residue 3926 THR
Chi-restraints excluded: chain E residue 3970 ARG
Chi-restraints excluded: chain E residue 3980 ASN
Chi-restraints excluded: chain E residue 4007 CYS
Chi-restraints excluded: chain E residue 4041 MET
Chi-restraints excluded: chain E residue 4088 THR
Chi-restraints excluded: chain E residue 4089 ILE
Chi-restraints excluded: chain E residue 4102 VAL
Chi-restraints excluded: chain E residue 4106 THR
Chi-restraints excluded: chain E residue 4108 LEU
Chi-restraints excluded: chain E residue 4136 VAL
Chi-restraints excluded: chain E residue 4174 ASP
Chi-restraints excluded: chain E residue 4255 VAL
Chi-restraints excluded: chain E residue 4314 ASN
Chi-restraints excluded: chain E residue 4339 VAL
Chi-restraints excluded: chain E residue 4375 LEU
Chi-restraints excluded: chain E residue 4400 LYS
Chi-restraints excluded: chain F residue   81 ILE
Chi-restraints excluded: chain F residue   84 SER
Chi-restraints excluded: chain F residue 3772 GLN
Chi-restraints excluded: chain F residue 3781 ASP
Chi-restraints excluded: chain F residue 3797 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 12 optimal weight:    1.9990
   chunk 24 optimal weight:    0.5980
   chunk 10 optimal weight:    0.7980
   chunk 84 optimal weight:    0.0770
   chunk 105 optimal weight:    0.9980
   chunk 48 optimal weight:   10.0000
   chunk 66 optimal weight:    0.0670
   chunk 73 optimal weight:    0.9990
   chunk 17 optimal weight:    0.6980
   chunk 87 optimal weight:    0.5980
   chunk 33 optimal weight:    0.9990
   overall best weight:    0.4076

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

Flipped N/Q/H residues before XYZ refinement:
A4130 ASN
B 100 GLN
E4130 ASN
** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4157 r_free = 0.4157 target = 0.148109 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.095863 restraints weight = 18442.786|
|-----------------------------------------------------------------------------|
r_work (start): 0.3363 rms_B_bonded: 3.11
r_work: 0.3192 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.3192
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7886
moved from start:          0.3041

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  10554  Z= 0.174
  Angle     :  0.588  10.512  14296  Z= 0.309
  Chirality :  0.045   0.182   1518
  Planarity :  0.004   0.038   1902
  Dihedral  :  5.775  57.612   1700
  Min Nonbonded Distance : 2.202

Molprobity Statistics.
  All-atom Clashscore : 8.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.61 %
    Favored  : 93.39 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 19.14 %
    Favored  : 77.45 %
  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: -0.70 (0.24), residues: 1286
  helix: -3.26 (1.52), residues: 12
  sheet: -0.73 (0.34), residues: 258
  loop : -0.34 (0.21), residues: 1016

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP F3778 
 HIS   0.002   0.001   HIS A3927 
 PHE   0.026   0.001   PHE A4033 
 TYR   0.012   0.001   TYR E4159 
 ARG   0.006   0.000   ARG F  65 

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

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

  2572 Ramachandran restraints generated.
    1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2572 Ramachandran restraints generated.
    1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 98
  time to evaluate  : 1.169 
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: symmetry clash
   revert: symmetry clash
REVERT: A 3970 ARG cc_start: 0.0796 (OUTLIER) cc_final: 0.0017 (mtm180)
REVERT: B   77 GLU cc_start: 0.5995 (tm-30) cc_final: 0.5563 (pp20)
REVERT: B   89 GLU cc_start: 0.8019 (mp0) cc_final: 0.7413 (pt0)
REVERT: B 3766 PHE cc_start: 0.7505 (t80) cc_final: 0.7060 (t80)
REVERT: B 3767 ARG cc_start: 0.8488 (mmm-85) cc_final: 0.8225 (mmt90)
REVERT: B 3796 GLU cc_start: 0.8816 (tp30) cc_final: 0.8236 (tp30)
REVERT: E 3970 ARG cc_start: 0.0042 (OUTLIER) cc_final: -0.1113 (mtm180)
REVERT: E 4041 MET cc_start: 0.6823 (OUTLIER) cc_final: 0.6145 (mpt)
REVERT: E 4217 MET cc_start: 0.9129 (OUTLIER) cc_final: 0.8699 (mpt)
REVERT: F   89 GLU cc_start: 0.7907 (mp0) cc_final: 0.7339 (pt0)
REVERT: F 3767 ARG cc_start: 0.8450 (mmm-85) cc_final: 0.8077 (mmm-85)
REVERT: F 3772 GLN cc_start: 0.8669 (OUTLIER) cc_final: 0.8363 (pt0)
REVERT: F 3796 GLU cc_start: 0.8692 (tp30) cc_final: 0.8075 (tp30)
  outliers start: 39
  outliers final: 29
  residues processed: 131
  average time/residue: 0.2329
  time to fit residues: 44.0254
Evaluate side-chains
  128 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 94
  time to evaluate  : 1.455 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 3942 CYS
Chi-restraints excluded: chain A residue 3964 CYS
Chi-restraints excluded: chain A residue 3970 ARG
Chi-restraints excluded: chain A residue 3980 ASN
Chi-restraints excluded: chain A residue 4035 VAL
Chi-restraints excluded: chain A residue 4089 ILE
Chi-restraints excluded: chain A residue 4102 VAL
Chi-restraints excluded: chain A residue 4106 THR
Chi-restraints excluded: chain A residue 4108 LEU
Chi-restraints excluded: chain A residue 4136 VAL
Chi-restraints excluded: chain A residue 4174 ASP
Chi-restraints excluded: chain A residue 4314 ASN
Chi-restraints excluded: chain A residue 4400 LYS
Chi-restraints excluded: chain B residue   92 ASP
Chi-restraints excluded: chain B residue 3773 CYS
Chi-restraints excluded: chain B residue 3774 ILE
Chi-restraints excluded: chain B residue 3797 MET
Chi-restraints excluded: chain E residue 3970 ARG
Chi-restraints excluded: chain E residue 3980 ASN
Chi-restraints excluded: chain E residue 4007 CYS
Chi-restraints excluded: chain E residue 4041 MET
Chi-restraints excluded: chain E residue 4089 ILE
Chi-restraints excluded: chain E residue 4102 VAL
Chi-restraints excluded: chain E residue 4106 THR
Chi-restraints excluded: chain E residue 4108 LEU
Chi-restraints excluded: chain E residue 4136 VAL
Chi-restraints excluded: chain E residue 4174 ASP
Chi-restraints excluded: chain E residue 4217 MET
Chi-restraints excluded: chain E residue 4314 ASN
Chi-restraints excluded: chain E residue 4339 VAL
Chi-restraints excluded: chain E residue 4400 LYS
Chi-restraints excluded: chain F residue   81 ILE
Chi-restraints excluded: chain F residue 3772 GLN
Chi-restraints excluded: chain F residue 3781 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 88 optimal weight:    0.6980
   chunk 41 optimal weight:    0.6980
   chunk 115 optimal weight:    3.9990
   chunk 5 optimal weight:   10.0000
   chunk 49 optimal weight:    0.0570
   chunk 68 optimal weight:    0.0070
   chunk 50 optimal weight:    0.7980
   chunk 103 optimal weight:    0.8980
   chunk 90 optimal weight:    0.7980
   chunk 113 optimal weight:    2.9990
   chunk 1 optimal weight:    6.9990
   overall best weight:    0.4516

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

Flipped N/Q/H residues before XYZ refinement:
A4130 ASN
** B 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E4130 ASN
** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4156 r_free = 0.4156 target = 0.148038 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.095644 restraints weight = 18388.467|
|-----------------------------------------------------------------------------|
r_work (start): 0.3364 rms_B_bonded: 3.11
r_work: 0.3191 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.3191
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7889
moved from start:          0.3126

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  10554  Z= 0.181
  Angle     :  0.576  10.257  14296  Z= 0.302
  Chirality :  0.045   0.172   1518
  Planarity :  0.004   0.038   1902
  Dihedral  :  5.712  57.255   1700
  Min Nonbonded Distance : 2.193

Molprobity Statistics.
  All-atom Clashscore : 8.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.22 %
    Favored  : 93.78 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 18.97 %
    Favored  : 77.36 %
  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: -0.68 (0.24), residues: 1286
  helix: -3.30 (1.48), residues: 12
  sheet: -0.71 (0.34), residues: 258
  loop : -0.32 (0.21), residues: 1016

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A4288 
 HIS   0.002   0.001   HIS A3927 
 PHE   0.022   0.001   PHE A4033 
 TYR   0.011   0.001   TYR E4287 
 ARG   0.003   0.000   ARG B  51 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5455.85 seconds
wall clock time: 97 minutes 50.40 seconds (5870.40 seconds total)