Starting phenix.real_space_refine
on Sun Dec 29 11:45:02 2024 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jxd_36697/12_2024/8jxd_36697.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jxd_36697/12_2024/8jxd_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_36697/12_2024/8jxd_36697.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jxd_36697/12_2024/8jxd_36697.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jxd_36697/12_2024/8jxd_36697.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jxd_36697/12_2024/8jxd_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-5532/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: 8.37, per 1000 atoms: 0.81
  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: 3.01
  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: 1.39
  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: 3.37

  Time building geometry restraints manager: 3.35 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: 0.00
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:             0.780
  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:          0.380
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     28.510
  Find NCS groups from input model:        0.310
  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:2.850
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.050
-------------------------------------------------------------------------------
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  : 1.299 
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: 0.2279
  time to fit residues: 42.9323
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  : 1.235 
-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7828
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  : 1.218 
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: 0.7483 (tp30) cc_final: 0.7139 (pt0)
REVERT: B   89 GLU cc_start: 0.7974 (mp0) cc_final: 0.7314 (pt0)
REVERT: B 3766 PHE cc_start: 0.7184 (t80) cc_final: 0.6902 (t80)
REVERT: F   89 GLU cc_start: 0.7922 (mp0) cc_final: 0.7303 (pt0)
REVERT: F 3766 PHE cc_start: 0.7410 (t80) cc_final: 0.7110 (t80)
REVERT: F 3767 ARG cc_start: 0.8337 (mmm-85) cc_final: 0.7671 (mmm-85)
REVERT: F 3772 GLN cc_start: 0.7895 (OUTLIER) cc_final: 0.7517 (pt0)
REVERT: F 3796 GLU cc_start: 0.8153 (tp30) cc_final: 0.7544 (tp30)
  outliers start: 47
  outliers final: 20
  residues processed: 144
  average time/residue: 0.2417
  time to fit residues: 48.8982
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  : 1.232 
-------------------------------------------------------------------------------
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 64 optimal weight:   10.0000
   chunk 36 optimal weight:    1.9990
   chunk 96 optimal weight:    1.9990
   chunk 79 optimal weight:    0.5980
   chunk 32 optimal weight:    1.9990
   chunk 116 optimal weight:   10.0000
   chunk 125 optimal weight:    0.5980
   chunk 103 optimal weight:    0.9980
   chunk 115 optimal weight:    0.7980
   chunk 39 optimal weight:    0.7980
   chunk 93 optimal weight:    1.9990
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7851
moved from start:          0.1621

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  10554  Z= 0.235
  Angle     :  0.599   7.134  14296  Z= 0.320
  Chirality :  0.047   0.167   1518
  Planarity :  0.005   0.042   1902
  Dihedral  :  7.169  62.841   1704
  Min Nonbonded Distance : 2.195

Molprobity Statistics.
  All-atom Clashscore : 8.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.14 %
    Favored  : 93.86 %
  Rotamer:
    Outliers :  4.28 %
    Allowed  : 17.92 %
    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: -0.83 (0.24), residues: 1286
  helix: -3.13 (1.62), residues: 12
  sheet: -0.70 (0.32), residues: 282
  loop : -0.46 (0.21), residues: 992

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP E4288 
 HIS   0.003   0.001   HIS A3927 
 PHE   0.019   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
  139 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 90
  time to evaluate  : 1.186 
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   89 GLU cc_start: 0.7743 (mp0) cc_final: 0.7374 (pt0)
REVERT: B 3767 ARG cc_start: 0.8247 (mmm-85) cc_final: 0.7943 (mmt90)
REVERT: B 3771 GLN cc_start: 0.7662 (tm-30) cc_final: 0.6913 (tm-30)
REVERT: B 3783 GLU cc_start: 0.8424 (tm-30) cc_final: 0.7947 (tm-30)
REVERT: B 3796 GLU cc_start: 0.8164 (tp30) cc_final: 0.7422 (tp30)
REVERT: F   89 GLU cc_start: 0.8022 (mp0) cc_final: 0.7423 (pt0)
REVERT: F 3771 GLN cc_start: 0.8869 (tp-100) cc_final: 0.8569 (tp40)
REVERT: F 3772 GLN cc_start: 0.8442 (OUTLIER) cc_final: 0.8179 (pt0)
REVERT: F 3793 ARG cc_start: 0.7799 (ttp80) cc_final: 0.7562 (ttp80)
REVERT: F 3796 GLU cc_start: 0.8151 (tp30) cc_final: 0.7486 (tp30)
  outliers start: 49
  outliers final: 26
  residues processed: 133
  average time/residue: 0.2302
  time to fit residues: 44.2200
Evaluate side-chains
  110 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 83
  time to evaluate  : 1.271 
-------------------------------------------------------------------------------
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 115 optimal weight:    0.9990
   chunk 87 optimal weight:    1.9990
   chunk 60 optimal weight:    0.0670
   chunk 12 optimal weight:    2.9990
   chunk 55 optimal weight:    0.8980
   chunk 78 optimal weight:    0.5980
   chunk 116 optimal weight:    1.9990
   chunk 123 optimal weight:    3.9990
   chunk 61 optimal weight:    1.9990
   chunk 110 optimal weight:    0.0010
   chunk 33 optimal weight:    0.6980
   overall best weight:    0.4524

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

Flipped N/Q/H residues before XYZ refinement:
A4087 GLN
B 100 GLN
E4087 GLN
** E4314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 100 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7838
moved from start:          0.1955

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10554  Z= 0.177
  Angle     :  0.563   7.181  14296  Z= 0.300
  Chirality :  0.045   0.162   1518
  Planarity :  0.004   0.040   1902
  Dihedral  :  6.220  60.330   1702
  Min Nonbonded Distance : 2.214

Molprobity Statistics.
  All-atom Clashscore : 8.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.69 %
    Favored  : 93.31 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 18.36 %
    Favored  : 77.71 %
  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: -0.78 (0.24), residues: 1286
  helix: -3.22 (1.55), residues: 12
  sheet: -0.66 (0.32), residues: 282
  loop : -0.42 (0.21), residues: 992

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP E4288 
 HIS   0.003   0.001   HIS E3927 
 PHE   0.015   0.001   PHE F  33 
 TYR   0.011   0.001   TYR A4121 
 ARG   0.003   0.000   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
  144 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 99
  time to evaluate  : 1.028 
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: A 4218 ASN cc_start: 0.9045 (t0) cc_final: 0.8805 (t0)
REVERT: A 4272 GLU cc_start: 0.8024 (pm20) cc_final: 0.7629 (pm20)
REVERT: B   89 GLU cc_start: 0.7729 (mp0) cc_final: 0.7368 (pt0)
REVERT: B 3766 PHE cc_start: 0.7726 (t80) cc_final: 0.7509 (t80)
REVERT: B 3767 ARG cc_start: 0.8098 (mmm-85) cc_final: 0.7820 (mmm-85)
REVERT: B 3783 GLU cc_start: 0.8493 (tm-30) cc_final: 0.7885 (tm-30)
REVERT: B 3796 GLU cc_start: 0.8170 (tp30) cc_final: 0.7494 (tp30)
REVERT: E 4218 ASN cc_start: 0.9046 (t0) cc_final: 0.8831 (t0)
REVERT: E 4272 GLU cc_start: 0.8020 (pm20) cc_final: 0.7625 (pm20)
REVERT: F   89 GLU cc_start: 0.8008 (mp0) cc_final: 0.7398 (pt0)
REVERT: F 3767 ARG cc_start: 0.7924 (mmm-85) cc_final: 0.7621 (mmm-85)
REVERT: F 3772 GLN cc_start: 0.8160 (OUTLIER) cc_final: 0.7765 (pt0)
REVERT: F 3793 ARG cc_start: 0.7943 (ttp80) cc_final: 0.7713 (ttp80)
REVERT: F 3796 GLU cc_start: 0.8067 (tp30) cc_final: 0.7450 (tp30)
  outliers start: 45
  outliers final: 27
  residues processed: 137
  average time/residue: 0.2121
  time to fit residues: 42.1097
Evaluate side-chains
  119 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 91
  time to evaluate  : 1.234 
-------------------------------------------------------------------------------
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 3980 ASN
Chi-restraints excluded: chain A residue 4035 VAL
Chi-restraints excluded: chain A residue 4041 MET
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 4147 ASP
Chi-restraints excluded: chain A residue 4174 ASP
Chi-restraints excluded: chain A residue 4314 ASN
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 3980 ASN
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 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 103 optimal weight:    0.0770
   chunk 70 optimal weight:    6.9990
   chunk 1 optimal weight:    9.9990
   chunk 92 optimal weight:    0.9980
   chunk 51 optimal weight:    0.0270
   chunk 105 optimal weight:    0.8980
   chunk 85 optimal weight:    0.5980
   chunk 0 optimal weight:    8.9990
   chunk 63 optimal weight:   20.0000
   chunk 111 optimal weight:    0.9980
   chunk 31 optimal weight:    0.7980
   overall best weight:    0.4796

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

Flipped N/Q/H residues before XYZ refinement:
B 100 GLN
** E4314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 100 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7843
moved from start:          0.2126

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  10554  Z= 0.181
  Angle     :  0.566   8.536  14296  Z= 0.300
  Chirality :  0.045   0.161   1518
  Planarity :  0.004   0.039   1902
  Dihedral  :  5.937  58.352   1700
  Min Nonbonded Distance : 2.213

Molprobity Statistics.
  All-atom Clashscore : 7.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.84 %
    Favored  : 93.16 %
  Rotamer:
    Outliers :  4.46 %
    Allowed  : 17.31 %
    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: -0.74 (0.24), residues: 1286
  helix: -3.13 (1.61), residues: 12
  sheet: -0.69 (0.32), residues: 282
  loop : -0.38 (0.21), residues: 992

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP E4160 
 HIS   0.003   0.001   HIS E3927 
 PHE   0.013   0.001   PHE F  33 
 TYR   0.010   0.001   TYR E4159 
 ARG   0.003   0.000   ARG A3970 

*********************** 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
  147 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 96
  time to evaluate  : 1.029 
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: A 4041 MET cc_start: 0.7148 (OUTLIER) cc_final: 0.6667 (mpt)
REVERT: A 4217 MET cc_start: 0.9207 (OUTLIER) cc_final: 0.8970 (mpt)
REVERT: A 4218 ASN cc_start: 0.9023 (t0) cc_final: 0.8758 (t0)
REVERT: B   89 GLU cc_start: 0.7725 (mp0) cc_final: 0.7389 (pt0)
REVERT: B 3767 ARG cc_start: 0.8113 (mmm-85) cc_final: 0.7837 (mmm-85)
REVERT: B 3783 GLU cc_start: 0.8149 (tm-30) cc_final: 0.7728 (tm-30)
REVERT: B 3796 GLU cc_start: 0.8151 (tp30) cc_final: 0.7519 (tp30)
REVERT: E 4041 MET cc_start: 0.6965 (OUTLIER) cc_final: 0.6353 (mpt)
REVERT: E 4217 MET cc_start: 0.9170 (OUTLIER) cc_final: 0.8889 (mpt)
REVERT: E 4218 ASN cc_start: 0.9012 (t0) cc_final: 0.8794 (t0)
REVERT: F   89 GLU cc_start: 0.8016 (mp0) cc_final: 0.7422 (pt0)
REVERT: F 3772 GLN cc_start: 0.8486 (OUTLIER) cc_final: 0.8181 (pt0)
REVERT: F 3796 GLU cc_start: 0.8091 (tp30) cc_final: 0.7498 (tp30)
  outliers start: 51
  outliers final: 31
  residues processed: 139
  average time/residue: 0.2245
  time to fit residues: 44.6999
Evaluate side-chains
  123 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 87
  time to evaluate  : 1.091 
-------------------------------------------------------------------------------
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 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 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 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 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 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
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 41 optimal weight:    0.7980
   chunk 111 optimal weight:    6.9990
   chunk 24 optimal weight:    3.9990
   chunk 72 optimal weight:    0.6980
   chunk 30 optimal weight:    0.7980
   chunk 123 optimal weight:    6.9990
   chunk 102 optimal weight:    0.6980
   chunk 57 optimal weight:    0.0970
   chunk 10 optimal weight:    3.9990
   chunk 40 optimal weight:    2.9990
   chunk 65 optimal weight:   10.0000
   overall best weight:    0.6178

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7855
moved from start:          0.2316

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10554  Z= 0.203
  Angle     :  0.570   8.913  14296  Z= 0.302
  Chirality :  0.045   0.162   1518
  Planarity :  0.004   0.038   1902
  Dihedral  :  5.825  55.935   1700
  Min Nonbonded Distance : 2.209

Molprobity Statistics.
  All-atom Clashscore : 8.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.00 %
    Favored  : 93.00 %
  Rotamer:
    Outliers :  4.11 %
    Allowed  : 17.31 %
    Favored  : 78.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.68 (0.24), residues: 1286
  helix: -3.14 (1.61), residues: 12
  sheet: -0.68 (0.32), residues: 282
  loop : -0.32 (0.21), residues: 992

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP E4288 
 HIS   0.003   0.001   HIS E3927 
 PHE   0.010   0.001   PHE F  33 
 TYR   0.010   0.001   TYR E4159 
 ARG   0.003   0.000   ARG B3767 

*********************** 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
  143 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 96
  time to evaluate  : 1.164 
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 3970 ARG cc_start: 0.0028 (OUTLIER) cc_final: -0.1270 (mtm180)
REVERT: A 4041 MET cc_start: 0.7113 (OUTLIER) cc_final: 0.6636 (mpt)
REVERT: A 4217 MET cc_start: 0.9212 (OUTLIER) cc_final: 0.8988 (mpt)
REVERT: A 4218 ASN cc_start: 0.9042 (t0) cc_final: 0.8805 (t0)
REVERT: B   77 GLU cc_start: 0.6025 (tm-30) cc_final: 0.5655 (pp20)
REVERT: B   89 GLU cc_start: 0.7713 (mp0) cc_final: 0.7330 (pt0)
REVERT: B 3796 GLU cc_start: 0.8250 (tp30) cc_final: 0.7703 (tp30)
REVERT: E 4041 MET cc_start: 0.7039 (OUTLIER) cc_final: 0.6435 (mpt)
REVERT: E 4217 MET cc_start: 0.9170 (OUTLIER) cc_final: 0.8826 (mpt)
REVERT: E 4218 ASN cc_start: 0.8996 (t0) cc_final: 0.8774 (t0)
REVERT: F   89 GLU cc_start: 0.8018 (mp0) cc_final: 0.7450 (pt0)
REVERT: F 3767 ARG cc_start: 0.8268 (mmm-85) cc_final: 0.8008 (mmm-85)
REVERT: F 3772 GLN cc_start: 0.8577 (OUTLIER) cc_final: 0.8269 (pt0)
REVERT: F 3796 GLU cc_start: 0.8171 (tp30) cc_final: 0.7633 (tp30)
  outliers start: 47
  outliers final: 31
  residues processed: 135
  average time/residue: 0.2185
  time to fit residues: 43.0136
Evaluate side-chains
  127 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 90
  time to evaluate  : 1.150 
-------------------------------------------------------------------------------
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 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 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 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 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 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
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 119 optimal weight:    0.9990
   chunk 13 optimal weight:    0.0980
   chunk 70 optimal weight:    8.9990
   chunk 90 optimal weight:    0.8980
   chunk 104 optimal weight:    1.9990
   chunk 69 optimal weight:    0.8980
   chunk 123 optimal weight:    0.5980
   chunk 77 optimal weight:    0.3980
   chunk 75 optimal weight:    1.9990
   chunk 56 optimal weight:    7.9990
   chunk 76 optimal weight:    0.9990
   overall best weight:    0.5780

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7855
moved from start:          0.2433

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10554  Z= 0.194
  Angle     :  0.565   9.284  14296  Z= 0.299
  Chirality :  0.045   0.164   1518
  Planarity :  0.004   0.037   1902
  Dihedral  :  5.752  55.802   1700
  Min Nonbonded Distance : 2.211

Molprobity Statistics.
  All-atom Clashscore : 8.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.45 %
    Favored  : 93.55 %
  Rotamer:
    Outliers :  4.63 %
    Allowed  : 17.05 %
    Favored  : 78.32 %
  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: -3.14 (1.61), residues: 12
  sheet: -0.69 (0.32), residues: 282
  loop : -0.31 (0.21), residues: 992

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP E4288 
 HIS   0.003   0.001   HIS E3927 
 PHE   0.020   0.001   PHE E4033 
 TYR   0.010   0.001   TYR E4159 
 ARG   0.002   0.000   ARG A3970 

*********************** 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
  149 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 96
  time to evaluate  : 1.210 
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 3970 ARG cc_start: 0.0214 (OUTLIER) cc_final: -0.1021 (mtm180)
REVERT: A 4041 MET cc_start: 0.7047 (OUTLIER) cc_final: 0.6558 (mpt)
REVERT: A 4217 MET cc_start: 0.9212 (OUTLIER) cc_final: 0.8905 (mpt)
REVERT: A 4218 ASN cc_start: 0.9032 (t0) cc_final: 0.8809 (t0)
REVERT: B   77 GLU cc_start: 0.6073 (tm-30) cc_final: 0.5696 (pp20)
REVERT: B   89 GLU cc_start: 0.7757 (mp0) cc_final: 0.7325 (pt0)
REVERT: B 3796 GLU cc_start: 0.8392 (tp30) cc_final: 0.7794 (tp30)
REVERT: E 4041 MET cc_start: 0.7024 (OUTLIER) cc_final: 0.6428 (mpt)
REVERT: E 4217 MET cc_start: 0.9199 (OUTLIER) cc_final: 0.8849 (mpt)
REVERT: E 4218 ASN cc_start: 0.8991 (t0) cc_final: 0.8752 (t0)
REVERT: F   89 GLU cc_start: 0.8020 (mp0) cc_final: 0.7514 (pt0)
REVERT: F 3767 ARG cc_start: 0.8294 (mmm-85) cc_final: 0.7898 (mmm-85)
REVERT: F 3772 GLN cc_start: 0.8456 (OUTLIER) cc_final: 0.8138 (pt0)
REVERT: F 3796 GLU cc_start: 0.8266 (tp30) cc_final: 0.7694 (tp30)
  outliers start: 53
  outliers final: 39
  residues processed: 141
  average time/residue: 0.2405
  time to fit residues: 49.3849
Evaluate side-chains
  136 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 91
  time to evaluate  : 1.119 
-------------------------------------------------------------------------------
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 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 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 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 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 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 49 optimal weight:    0.6980
   chunk 73 optimal weight:    2.9990
   chunk 37 optimal weight:    2.9990
   chunk 24 optimal weight:    3.9990
   chunk 23 optimal weight:    0.9990
   chunk 78 optimal weight:    0.7980
   chunk 84 optimal weight:    1.9990
   chunk 60 optimal weight:    4.9990
   chunk 11 optimal weight:    0.9980
   chunk 96 optimal weight:    0.8980
   chunk 112 optimal weight:    0.0060
   overall best weight:    0.6796

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7864
moved from start:          0.2571

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10554  Z= 0.213
  Angle     :  0.571   8.850  14296  Z= 0.302
  Chirality :  0.045   0.165   1518
  Planarity :  0.004   0.037   1902
  Dihedral  :  5.742  55.977   1700
  Min Nonbonded Distance : 2.145

Molprobity Statistics.
  All-atom Clashscore : 8.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.92 %
    Favored  : 93.08 %
  Rotamer:
    Outliers :  4.28 %
    Allowed  : 17.22 %
    Favored  : 78.50 %
  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: -0.65 (0.24), residues: 1286
  helix: -3.11 (1.63), residues: 12
  sheet: -0.64 (0.33), residues: 278
  loop : -0.31 (0.21), residues: 996

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP E4288 
 HIS   0.003   0.001   HIS E3927 
 PHE   0.017   0.001   PHE E4033 
 TYR   0.009   0.001   TYR E4392 
 ARG   0.004   0.000   ARG B3793 

*********************** 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
  144 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 95
  time to evaluate  : 1.238 
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: 0.0659 (OUTLIER) cc_final: -0.0401 (mtm180)
REVERT: A 4217 MET cc_start: 0.9217 (OUTLIER) cc_final: 0.8917 (mpt)
REVERT: B   77 GLU cc_start: 0.6358 (tm-30) cc_final: 0.5966 (pp20)
REVERT: B   89 GLU cc_start: 0.7769 (mp0) cc_final: 0.7373 (pt0)
REVERT: B 3783 GLU cc_start: 0.8622 (mm-30) cc_final: 0.8416 (mm-30)
REVERT: B 3796 GLU cc_start: 0.8379 (tp30) cc_final: 0.7809 (tp30)
REVERT: E 4041 MET cc_start: 0.6817 (OUTLIER) cc_final: 0.6196 (mpt)
REVERT: E 4217 MET cc_start: 0.9211 (OUTLIER) cc_final: 0.8863 (mpt)
REVERT: E 4218 ASN cc_start: 0.8999 (t0) cc_final: 0.8774 (t0)
REVERT: F   89 GLU cc_start: 0.8009 (mp0) cc_final: 0.7458 (pt0)
REVERT: F 3767 ARG cc_start: 0.8285 (mmm-85) cc_final: 0.7906 (mmm-85)
REVERT: F 3772 GLN cc_start: 0.8447 (OUTLIER) cc_final: 0.8113 (pt0)
REVERT: F 3796 GLU cc_start: 0.8272 (tp30) cc_final: 0.7693 (tp30)
  outliers start: 49
  outliers final: 38
  residues processed: 136
  average time/residue: 0.2110
  time to fit residues: 41.8740
Evaluate side-chains
  134 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 91
  time to evaluate  : 1.231 
-------------------------------------------------------------------------------
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 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 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 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 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 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 3781 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 118 optimal weight:    0.9990
   chunk 107 optimal weight:    2.9990
   chunk 114 optimal weight:    0.6980
   chunk 69 optimal weight:   10.0000
   chunk 50 optimal weight:    0.0980
   chunk 90 optimal weight:    0.5980
   chunk 35 optimal weight:    2.9990
   chunk 103 optimal weight:    2.9990
   chunk 108 optimal weight:    0.0170
   chunk 75 optimal weight:    1.9990
   chunk 121 optimal weight:    2.9990
   overall best weight:    0.4820

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

Flipped N/Q/H residues before XYZ refinement:
A4130 ASN
B 100 GLN
** E4008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E4130 ASN
** E4314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7856
moved from start:          0.2714

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10554  Z= 0.175
  Angle     :  0.564   9.728  14296  Z= 0.297
  Chirality :  0.045   0.165   1518
  Planarity :  0.004   0.037   1902
  Dihedral  :  5.652  55.534   1700
  Min Nonbonded Distance : 2.200

Molprobity Statistics.
  All-atom Clashscore : 7.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.83 %
    Favored  : 94.17 %
  Rotamer:
    Outliers :  4.37 %
    Allowed  : 17.40 %
    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: -0.60 (0.24), residues: 1286
  helix: -3.18 (1.57), residues: 12
  sheet: -0.64 (0.33), residues: 278
  loop : -0.26 (0.21), residues: 996

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A4288 
 HIS   0.002   0.001   HIS A3927 
 PHE   0.017   0.001   PHE E4033 
 TYR   0.011   0.001   TYR E4159 
 ARG   0.002   0.000   ARG A3970 

*********************** 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
  149 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 99
  time to evaluate  : 1.225 
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 4217 MET cc_start: 0.9201 (OUTLIER) cc_final: 0.8859 (mpt)
REVERT: A 4218 ASN cc_start: 0.9027 (t0) cc_final: 0.8819 (t0)
REVERT: B   77 GLU cc_start: 0.6378 (tm-30) cc_final: 0.5856 (pp20)
REVERT: B   89 GLU cc_start: 0.7776 (mp0) cc_final: 0.7399 (pt0)
REVERT: B 3766 PHE cc_start: 0.7820 (t80) cc_final: 0.7594 (t80)
REVERT: B 3783 GLU cc_start: 0.8625 (mm-30) cc_final: 0.8403 (mm-30)
REVERT: B 3796 GLU cc_start: 0.8422 (tp30) cc_final: 0.7787 (tp30)
REVERT: E 4041 MET cc_start: 0.6826 (OUTLIER) cc_final: 0.6361 (mpt)
REVERT: E 4047 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.7885 (mp0)
REVERT: E 4217 MET cc_start: 0.9160 (OUTLIER) cc_final: 0.8769 (mpt)
REVERT: F   89 GLU cc_start: 0.7997 (mp0) cc_final: 0.7501 (pt0)
REVERT: F 3767 ARG cc_start: 0.8279 (mmm-85) cc_final: 0.7916 (mmm-85)
REVERT: F 3772 GLN cc_start: 0.8465 (OUTLIER) cc_final: 0.8124 (pt0)
REVERT: F 3796 GLU cc_start: 0.8292 (tp30) cc_final: 0.7731 (tp30)
  outliers start: 50
  outliers final: 36
  residues processed: 141
  average time/residue: 0.2130
  time to fit residues: 44.2700
Evaluate side-chains
  133 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 92
  time to evaluate  : 1.352 
-------------------------------------------------------------------------------
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 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 4217 MET
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 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 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 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 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 74 optimal weight:    3.9990
   chunk 57 optimal weight:    0.8980
   chunk 84 optimal weight:    1.9990
   chunk 127 optimal weight:    6.9990
   chunk 117 optimal weight:    7.9990
   chunk 101 optimal weight:    0.1980
   chunk 10 optimal weight:    1.9990
   chunk 78 optimal weight:    0.8980
   chunk 62 optimal weight:    3.9990
   chunk 80 optimal weight:    0.9990
   chunk 108 optimal weight:    0.3980
   overall best weight:    0.6782

-------------------------------------------------------------------------------
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**
** E4008 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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7869
moved from start:          0.2875

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  10554  Z= 0.216
  Angle     :  0.585   9.531  14296  Z= 0.308
  Chirality :  0.046   0.206   1518
  Planarity :  0.004   0.037   1902
  Dihedral  :  5.709  55.817   1700
  Min Nonbonded Distance : 2.208

Molprobity Statistics.
  All-atom Clashscore : 8.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.53 %
    Favored  : 93.47 %
  Rotamer:
    Outliers :  4.46 %
    Allowed  : 17.05 %
    Favored  : 78.50 %
  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: -0.64 (0.25), residues: 1286
  helix: -3.21 (1.56), residues: 12
  sheet: -0.86 (0.33), residues: 290
  loop : -0.20 (0.21), residues: 984

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP E4288 
 HIS   0.003   0.001   HIS A3927 
 PHE   0.015   0.001   PHE E4033 
 TYR   0.010   0.001   TYR A4392 
 ARG   0.017   0.001   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
  140 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 89
  time to evaluate  : 1.147 
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: 0.0578 (OUTLIER) cc_final: -0.0284 (mtm180)
REVERT: A 4217 MET cc_start: 0.9222 (OUTLIER) cc_final: 0.8927 (mpt)
REVERT: B   77 GLU cc_start: 0.6176 (tm-30) cc_final: 0.5647 (pp20)
REVERT: B   89 GLU cc_start: 0.7768 (mp0) cc_final: 0.7436 (pt0)
REVERT: B 3783 GLU cc_start: 0.8656 (mm-30) cc_final: 0.8449 (mm-30)
REVERT: B 3796 GLU cc_start: 0.8438 (tp30) cc_final: 0.7818 (tp30)
REVERT: E 4041 MET cc_start: 0.6701 (OUTLIER) cc_final: 0.6047 (mpt)
REVERT: E 4047 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.7885 (mp0)
REVERT: E 4217 MET cc_start: 0.9190 (OUTLIER) cc_final: 0.8830 (mpt)
REVERT: F   89 GLU cc_start: 0.8018 (mp0) cc_final: 0.7548 (pt0)
REVERT: F 3767 ARG cc_start: 0.8370 (mmm-85) cc_final: 0.8014 (mmm-85)
REVERT: F 3772 GLN cc_start: 0.8441 (OUTLIER) cc_final: 0.8131 (pt0)
REVERT: F 3796 GLU cc_start: 0.8327 (tp30) cc_final: 0.7744 (tp30)
  outliers start: 51
  outliers final: 39
  residues processed: 132
  average time/residue: 0.2282
  time to fit residues: 43.6142
Evaluate side-chains
  130 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 85
  time to evaluate  : 1.581 
-------------------------------------------------------------------------------
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 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 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 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   50 THR
Chi-restraints excluded: chain F residue   73 LEU
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 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 31 optimal weight:    0.0370
   chunk 93 optimal weight:    0.9980
   chunk 14 optimal weight:    0.8980
   chunk 28 optimal weight:    0.9980
   chunk 101 optimal weight:    0.2980
   chunk 42 optimal weight:    0.9980
   chunk 104 optimal weight:    1.9990
   chunk 12 optimal weight:    6.9990
   chunk 18 optimal weight:    1.9990
   chunk 89 optimal weight:    1.9990
   chunk 5 optimal weight:    9.9990
   overall best weight:    0.6458

-------------------------------------------------------------------------------
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**
** E4008 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 = 0.4161 r_free = 0.4161 target = 0.152065 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.101174 restraints weight = 18507.799|
|-----------------------------------------------------------------------------|
r_work (start): 0.3391 rms_B_bonded: 3.06
r_work: 0.3225 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.3225
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7933
moved from start:          0.2932

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  10554  Z= 0.208
  Angle     :  0.586   9.507  14296  Z= 0.308
  Chirality :  0.046   0.176   1518
  Planarity :  0.004   0.037   1902
  Dihedral  :  5.703  55.954   1700
  Min Nonbonded Distance : 2.193

Molprobity Statistics.
  All-atom Clashscore : 8.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.45 %
    Favored  : 93.55 %
  Rotamer:
    Outliers :  4.28 %
    Allowed  : 17.22 %
    Favored  : 78.50 %
  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: -0.69 (0.24), residues: 1286
  helix: -3.24 (1.54), residues: 12
  sheet: -0.81 (0.34), residues: 270
  loop : -0.29 (0.21), residues: 1004

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP E4288 
 HIS   0.003   0.001   HIS A3927 
 PHE   0.034   0.002   PHE B3766 
 TYR   0.010   0.001   TYR E4159 
 ARG   0.004   0.000   ARG B3777 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2326.69 seconds
wall clock time: 43 minutes 56.73 seconds (2636.73 seconds total)