Starting phenix.real_space_refine
on Mon May 12 20:03:25 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jxj_36703/05_2025/8jxj_36703.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jxj_36703/05_2025/8jxj_36703.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jxj_36703/05_2025/8jxj_36703.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jxj_36703/05_2025/8jxj_36703.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jxj_36703/05_2025/8jxj_36703.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jxj_36703/05_2025/8jxj_36703.cif"
  }
  resolution = 3.9
  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=   0.002
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      8      9.91       5
     S      98      5.16       5
     C    5650      2.51       5
     N    1536      2.21       5
     O    1866      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 9158
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 4461
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 570, 4461
          Classifications: {'peptide': 570}
          Link IDs: {'PTRANS': 31, 'TRANS': 538}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 4461
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 570, 4461
          Classifications: {'peptide': 570}
          Link IDs: {'PTRANS': 31, 'TRANS': 538}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 61
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 61
          Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 5
    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: "E"
      Number of atoms: 61
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 61
          Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 5
    Chain: "F"
      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: 18
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 18
          Unusual residues: {' CA': 4, 'NAG': 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
    Chain: "B"
      Number of atoms: 18
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 18
          Unusual residues: {' CA': 4, 'NAG': 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
  Time building chain proxies: 6.01, per 1000 atoms: 0.66
  Number of scatterers: 9158
  At special positions: 0
  Unit cell: (148.155, 152.388, 79.016, 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      8     19.99
     S      98     16.00
     O    1866      8.00
     N    1536      7.00
     C    5650      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=42, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  28 " - pdb=" SG  CYS A  40 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  35 " - pdb=" SG  CYS A  53 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A  47 " - pdb=" SG  CYS A  62 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  67 " - pdb=" SG  CYS A  80 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  74 " - pdb=" SG  CYS A  93 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  87 " - pdb=" SG  CYS A 103 " distance=2.03
    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=2.04
    Simple disulfide: pdb=" SG  CYS B  87 " - pdb=" SG  CYS B 103 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B3930 " - pdb=" SG  CYS B3942 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B3937 " - pdb=" SG  CYS B3955 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B3949 " - pdb=" SG  CYS B3964 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B3972 " - pdb=" SG  CYS B3981 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B3977 " - pdb=" SG  CYS B3991 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B3993 " - pdb=" SG  CYS B4007 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B4013 " - pdb=" SG  CYS B4023 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B4019 " - pdb=" SG  CYS B4032 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B4034 " - pdb=" SG  CYS B4049 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B4336 " - pdb=" SG  CYS B4344 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B4340 " - pdb=" SG  CYS B4353 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B4355 " - pdb=" SG  CYS B4369 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B4383 " - pdb=" SG  CYS B4391 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B4385 " - pdb=" SG  CYS B4401 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B4403 " - pdb=" SG  CYS B4412 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    ALPHA1-3
      " BMA C   3 " - " MAN C   4 "
      " BMA E   3 " - " MAN E   4 "
    ALPHA1-6
      " BMA C   3 " - " MAN C   5 "
      " BMA E   3 " - " MAN E   5 "
    BETA1-3
      " NAG E   1 " - " NAG E   2 "
      " NAG F   2 " - " BMA F   3 "
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
      " NAG C   2 " - " BMA C   3 "
      " NAG D   1 " - " NAG D   2 "
      " NAG D   2 " - " BMA D   3 "
      " NAG E   2 " - " BMA E   3 "
      " NAG F   1 " - " NAG F   2 "
    NAG-ASN
      " NAG A4701 " - " ASN A3980 "
      " NAG B4701 " - " ASN B3980 "
      " NAG C   1 " - " ASN A4070 "
      " NAG D   1 " - " ASN A4329 "
      " NAG E   1 " - " ASN B4070 "
      " NAG F   1 " - " ASN B4329 "
  Time building additional restraints: 2.80
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2100

  Finding SS restraints...
    Secondary structure from input PDB file:
      11 helices and 30 sheets defined
      4.0% alpha, 26.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.11
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 46
      No H-bonds generated for 'chain 'A' and resid 44 through 46'
    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 3971 through 3975
    Processing helix  chain 'A' and resid 4324 through 4328
      removed outlier: 3.657A  pdb=" N   TYR A4328 " --> pdb=" O   GLN A4325 " (cutoff:3.500A)
    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 84 through 86
      No H-bonds generated for 'chain 'B' and resid 84 through 86'
    Processing helix  chain 'B' and resid 96 through 101
    Processing helix  chain 'B' and resid 3946 through 3948
      No H-bonds generated for 'chain 'B' and resid 3946 through 3948'
    Processing helix  chain 'B' and resid 3958 through 3962
      removed outlier: 3.602A  pdb=" N   THR B3962 " --> pdb=" O   SER B3959 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4011 through 4015
      removed outlier: 3.535A  pdb=" N   GLU B4015 " --> pdb=" O   GLU B4012 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4324 through 4328
      removed outlier: 3.653A  pdb=" N   TYR B4328 " --> pdb=" O   GLN B4325 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 34
    Processing sheet with id=AA2, first strand: chain 'A' and resid 71 through 73
    Processing sheet with id=AA3, first strand: chain 'A' and resid 3934 through 3935
      removed outlier: 3.700A  pdb=" N   ILE A3943 " --> pdb=" O   TYR A3935 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 3981 through 3984
    Processing sheet with id=AA5, first strand: chain 'A' and resid 3997 through 3999
    Processing sheet with id=AA6, first strand: chain 'A' and resid 4024 through 4026
    Processing sheet with id=AA7, first strand: chain 'A' and resid 4038 through 4042
    Processing sheet with id=AA8, first strand: chain 'A' and resid 4076 through 4077
    Processing sheet with id=AA9, first strand: chain 'A' and resid 4086 through 4092
      removed outlier: 4.206A  pdb=" N   THR A4088 " --> pdb=" O   THR A4106 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 4148 through 4152
      removed outlier: 4.056A  pdb=" N   GLY A4148 " --> pdb=" O   SER A4161 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   ARG A4167 " --> pdb=" O   ASP A4162 " (cutoff:3.500A)
      removed outlier: 6.554A  pdb=" N   ILE A4168 " --> pdb=" O   LEU A4181 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 4189 through 4195
      removed outlier: 3.956A  pdb=" N   ALA A4191 " --> pdb=" O   THR A4204 " (cutoff:3.500A)
      removed outlier: 6.684A  pdb=" N   ILE A4212 " --> pdb=" O   LEU A4225 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 4235 through 4239
      removed outlier: 3.561A  pdb=" N   GLY A4235 " --> pdb=" O   SER A4249 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   SER A4249 " --> pdb=" O   GLY A4235 " (cutoff:3.500A)
      removed outlier: 6.809A  pdb=" N   ALA A4258 " --> pdb=" O   LEU A4268 " (cutoff:3.500A)
      removed outlier: 5.387A  pdb=" N   LEU A4268 " --> pdb=" O   ALA A4258 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 4276 through 4282
      removed outlier: 4.456A  pdb=" N   SER A4278 " --> pdb=" O   VAL A4289 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   VAL A4289 " --> pdb=" O   SER A4278 " (cutoff:3.500A)
      removed outlier: 6.379A  pdb=" N   ARG A4298 " --> pdb=" O   LYS A4309 " (cutoff:3.500A)
      removed outlier: 5.632A  pdb=" N   LYS A4309 " --> pdb=" O   ARG A4298 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'A' and resid 4343 through 4347
      removed outlier: 3.509A  pdb=" N   LEU A4343 " --> pdb=" O   ALA A4354 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'A' and resid 4390 through 4393
    Processing sheet with id=AB7, first strand: chain 'B' and resid 32 through 34
    Processing sheet with id=AB8, first strand: chain 'B' and resid 71 through 73
    Processing sheet with id=AB9, first strand: chain 'B' and resid 3934 through 3936
    Processing sheet with id=AC1, first strand: chain 'B' and resid 3964 through 3965
      removed outlier: 3.838A  pdb=" N   ASN B3980 " --> pdb=" O   SER B3992 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'B' and resid 3997 through 3999
    Processing sheet with id=AC3, first strand: chain 'B' and resid 4024 through 4026
    Processing sheet with id=AC4, first strand: chain 'B' and resid 4039 through 4043
    Processing sheet with id=AC5, first strand: chain 'B' and resid 4076 through 4077
      removed outlier: 3.509A  pdb=" N   ARG B4321 " --> pdb=" O   LEU B4059 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'B' and resid 4086 through 4092
      removed outlier: 4.627A  pdb=" N   THR B4088 " --> pdb=" O   THR B4106 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'B' and resid 4146 through 4152
      removed outlier: 3.656A  pdb=" N   GLY B4148 " --> pdb=" O   SER B4161 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   ARG B4167 " --> pdb=" O   ASP B4162 " (cutoff:3.500A)
      removed outlier: 6.616A  pdb=" N   ILE B4168 " --> pdb=" O   LEU B4181 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'B' and resid 4189 through 4195
      removed outlier: 4.278A  pdb=" N   ALA B4191 " --> pdb=" O   THR B4204 " (cutoff:3.500A)
      removed outlier: 6.636A  pdb=" N   ILE B4212 " --> pdb=" O   LEU B4225 " (cutoff:3.500A)
    Processing sheet with id=AC9, first strand: chain 'B' and resid 4236 through 4239
      removed outlier: 3.521A  pdb=" N   ARG B4245 " --> pdb=" O   ASP B4239 " (cutoff:3.500A)
      removed outlier: 6.453A  pdb=" N   ALA B4258 " --> pdb=" O   LEU B4268 " (cutoff:3.500A)
      removed outlier: 5.538A  pdb=" N   LEU B4268 " --> pdb=" O   ALA B4258 " (cutoff:3.500A)
    Processing sheet with id=AD1, first strand: chain 'B' and resid 4276 through 4282
      removed outlier: 4.219A  pdb=" N   SER B4278 " --> pdb=" O   VAL B4289 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   GLU B4295 " --> pdb=" O   ALA B4290 " (cutoff:3.500A)
      removed outlier: 6.698A  pdb=" N   VAL B4296 " --> pdb=" O   VAL B4310 " (cutoff:3.500A)
    Processing sheet with id=AD2, first strand: chain 'B' and resid 4343 through 4346
    Processing sheet with id=AD3, first strand: chain 'B' and resid 4392 through 4393

    214 hydrogen bonds defined for protein.
    516 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: 3.11

  Time building geometry restraints manager: 3.22 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: 3029
        1.34 -     1.46: 2002
        1.46 -     1.58: 4217
        1.58 -     1.70: 0
        1.70 -     1.82: 112
  Bond restraints: 9360
  Sorted by residual:
  bond pdb=" N   PHE B4125 "
       pdb=" CA  PHE B4125 "
    ideal  model  delta    sigma   weight residual
    1.454  1.491 -0.036 1.15e-02 7.56e+03 1.00e+01
  bond pdb=" N   LEU B3958 "
       pdb=" CA  LEU B3958 "
    ideal  model  delta    sigma   weight residual
    1.459  1.497 -0.039 1.32e-02 5.74e+03 8.59e+00
  bond pdb=" N   ASP B4284 "
       pdb=" CA  ASP B4284 "
    ideal  model  delta    sigma   weight residual
    1.457  1.494 -0.037 1.29e-02 6.01e+03 8.23e+00
  bond pdb=" N   GLU A4126 "
       pdb=" CA  GLU A4126 "
    ideal  model  delta    sigma   weight residual
    1.456  1.488 -0.032 1.22e-02 6.72e+03 6.80e+00
  bond pdb=" CA  SER A4127 "
       pdb=" CB  SER A4127 "
    ideal  model  delta    sigma   weight residual
    1.533  1.493  0.039 1.65e-02 3.67e+03 5.68e+00
  ... (remaining 9355 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.81: 12133
        1.81 -     3.61: 470
        3.61 -     5.42: 72
        5.42 -     7.23: 10
        7.23 -     9.03: 3
  Bond angle restraints: 12688
  Sorted by residual:
  angle pdb=" N   ASN B4124 "
        pdb=" CA  ASN B4124 "
        pdb=" C   ASN B4124 "
      ideal   model   delta    sigma   weight residual
     113.18  106.83    6.35 1.21e+00 6.83e-01 2.75e+01
  angle pdb=" C   CYS A3937 "
        pdb=" CA  CYS A3937 "
        pdb=" CB  CYS A3937 "
      ideal   model   delta    sigma   weight residual
     117.23  110.18    7.05 1.36e+00 5.41e-01 2.69e+01
  angle pdb=" C   GLU B3978 "
        pdb=" N   GLN B3979 "
        pdb=" CA  GLN B3979 "
      ideal   model   delta    sigma   weight residual
     122.44  116.81    5.63 1.19e+00 7.06e-01 2.24e+01
  angle pdb=" N   ASN A4124 "
        pdb=" CA  ASN A4124 "
        pdb=" C   ASN A4124 "
      ideal   model   delta    sigma   weight residual
     111.28  106.50    4.78 1.09e+00 8.42e-01 1.92e+01
  angle pdb=" N   VAL B4367 "
        pdb=" CA  VAL B4367 "
        pdb=" C   VAL B4367 "
      ideal   model   delta    sigma   weight residual
     113.71  109.55    4.16 9.50e-01 1.11e+00 1.91e+01
  ... (remaining 12683 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.74: 5477
       23.74 -    47.47: 391
       47.47 -    71.21: 51
       71.21 -    94.94: 37
       94.94 -   118.68: 16
  Dihedral angle restraints: 5972
    sinusoidal: 2690
      harmonic: 3282
  Sorted by residual:
  dihedral pdb=" CB  CYS A3972 "
           pdb=" SG  CYS A3972 "
           pdb=" SG  CYS A3981 "
           pdb=" CB  CYS A3981 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -163.37   77.37     1      1.00e+01 1.00e-02 7.50e+01
  dihedral pdb=" CB  CYS B4034 "
           pdb=" SG  CYS B4034 "
           pdb=" SG  CYS B4049 "
           pdb=" CB  CYS B4049 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  161.21  -68.21     1      1.00e+01 1.00e-02 6.04e+01
  dihedral pdb=" CB  CYS A4385 "
           pdb=" SG  CYS A4385 "
           pdb=" SG  CYS A4401 "
           pdb=" CB  CYS A4401 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  161.10  -68.10     1      1.00e+01 1.00e-02 6.02e+01
  ... (remaining 5969 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.056: 1065
       0.056 -    0.112: 263
       0.112 -    0.167: 35
       0.167 -    0.223: 6
       0.223 -    0.279: 5
  Chirality restraints: 1374
  Sorted by residual:
  chirality pdb=" C1  MAN C   4 "
            pdb=" O3  BMA C   3 "
            pdb=" C2  MAN C   4 "
            pdb=" O5  MAN C   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.40    2.13    0.27 2.00e-02 2.50e+03 1.80e+02
  chirality pdb=" C1  NAG E   2 "
            pdb=" O3  NAG E   1 "
            pdb=" C2  NAG E   2 "
            pdb=" O5  NAG E   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.57    0.17 2.00e-02 2.50e+03 7.57e+01
  chirality pdb=" C1  BMA F   3 "
            pdb=" O3  NAG F   2 "
            pdb=" C2  BMA F   3 "
            pdb=" O5  BMA F   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.28   -0.12 2.00e-02 2.50e+03 3.36e+01
  ... (remaining 1371 not shown)

  Planarity restraints: 1670
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG C   1 "   -0.345 2.00e-02 2.50e+03   2.98e-01 1.11e+03
        pdb=" C7  NAG C   1 "    0.082 2.00e-02 2.50e+03
        pdb=" C8  NAG C   1 "   -0.119 2.00e-02 2.50e+03
        pdb=" N2  NAG C   1 "    0.531 2.00e-02 2.50e+03
        pdb=" O7  NAG C   1 "   -0.149 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG E   2 "   -0.331 2.00e-02 2.50e+03   2.85e-01 1.02e+03
        pdb=" C7  NAG E   2 "    0.083 2.00e-02 2.50e+03
        pdb=" C8  NAG E   2 "   -0.156 2.00e-02 2.50e+03
        pdb=" N2  NAG E   2 "    0.505 2.00e-02 2.50e+03
        pdb=" O7  NAG E   2 "   -0.102 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG F   2 "    0.271 2.00e-02 2.50e+03   2.28e-01 6.53e+02
        pdb=" C7  NAG F   2 "   -0.070 2.00e-02 2.50e+03
        pdb=" C8  NAG F   2 "    0.178 2.00e-02 2.50e+03
        pdb=" N2  NAG F   2 "   -0.388 2.00e-02 2.50e+03
        pdb=" O7  NAG F   2 "    0.009 2.00e-02 2.50e+03
  ... (remaining 1667 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.69: 350
        2.69 -     3.25: 9398
        3.25 -     3.80: 14385
        3.80 -     4.35: 18868
        4.35 -     4.90: 30700
  Nonbonded interactions: 73701
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP B3950 "
            pdb="CA    CA B4704 "
     model   vdw
     2.143 2.510
  nonbonded pdb=" OD1 ASP A  48 "
            pdb="CA    CA A4702 "
     model   vdw
     2.172 2.510
  nonbonded pdb=" OD2 ASP B3960 "
            pdb="CA    CA B4704 "
     model   vdw
     2.177 2.510
  nonbonded pdb=" OD2 ASP A  58 "
            pdb="CA    CA A4702 "
     model   vdw
     2.186 2.510
  nonbonded pdb=" O   VAL B3952 "
            pdb="CA    CA B4704 "
     model   vdw
     2.187 2.510
  ... (remaining 73696 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 'B'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'E'
}
ncs_group {
  reference = chain 'D'
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.010
  Normalize map: mean=0, sd=1:             3.250
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.000
  Check model and map are aligned:         0.000
  Set scattering table:                    0.000
  Process input model:                     24.560
  Find NCS groups from input model:        0.280
  Set up NCS constraints:                  0.050
  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:2.470
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.620
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7766
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   0.044   9420  Z= 0.229
  Angle     :  0.818   9.033  12826  Z= 0.443
  Chirality :  0.051   0.279   1374
  Planarity :  0.013   0.298   1664
  Dihedral  : 17.725 118.679   3746
  Min Nonbonded Distance : 2.143

Molprobity Statistics.
  All-atom Clashscore : 9.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.13 %
    Favored  : 91.87 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 17.93 %
    Favored  : 80.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.22 (0.25), residues: 1132
  helix: -4.57 (0.61), residues: 25
  sheet: -0.49 (0.34), residues: 247
  loop : -0.82 (0.21), residues: 860

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A4297 
 HIS   0.005   0.001   HIS B4221 
 PHE   0.018   0.001   PHE B  33 
 TYR   0.021   0.001   TYR B4411 
 ARG   0.006   0.000   ARG A  46 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00625 (    6)
  link_NAG-ASN         : angle       3.60778 (   18)
  link_ALPHA1-6        : bond        0.00547 (    2)
  link_ALPHA1-6        : angle       0.58100 (    6)
  link_BETA1-4         : bond        0.00632 (    6)
  link_BETA1-4         : angle       1.74612 (   18)
  link_ALPHA1-3        : bond        0.01092 (    2)
  link_ALPHA1-3        : angle       1.51381 (    6)
  hydrogen bonds       : bond        0.24369 (  214)
  hydrogen bonds       : angle      10.46030 (  516)
  SS BOND              : bond        0.00232 (   42)
  SS BOND              : angle       1.05573 (   84)
  link_BETA1-3         : bond        0.00467 (    2)
  link_BETA1-3         : angle       4.19848 (    6)
  covalent geometry    : bond        0.00424 ( 9360)
  covalent geometry    : angle       0.79827 (12688)

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 60
  time to evaluate  : 1.035 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 4308 GLU cc_start: 0.7719 (tm-30) cc_final: 0.7513 (tm-30)
REVERT: B   39 TYR cc_start: 0.7767 (t80) cc_final: 0.7519 (t80)
REVERT: B 4144 MET cc_start: 0.8222 (mtp) cc_final: 0.7626 (mtt)
  outliers start: 18
  outliers final: 15
  residues processed: 76
  average time/residue: 0.1496
  time to fit residues: 18.5080
Evaluate side-chains
  68 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 53
  time to evaluate  : 1.018 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 THR
Chi-restraints excluded: chain A residue   98 ASP
Chi-restraints excluded: chain A residue 4047 GLU
Chi-restraints excluded: chain A residue 4174 ASP
Chi-restraints excluded: chain A residue 4236 LEU
Chi-restraints excluded: chain A residue 4339 VAL
Chi-restraints excluded: chain A residue 4377 VAL
Chi-restraints excluded: chain A residue 4378 THR
Chi-restraints excluded: chain B residue   58 ASP
Chi-restraints excluded: chain B residue  103 CYS
Chi-restraints excluded: chain B residue 3962 THR
Chi-restraints excluded: chain B residue 3971 THR
Chi-restraints excluded: chain B residue 4130 ASN
Chi-restraints excluded: chain B residue 4154 VAL
Chi-restraints excluded: chain B residue 4339 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 96 optimal weight:    0.4980
   chunk 86 optimal weight:    0.9990
   chunk 47 optimal weight:    1.9990
   chunk 29 optimal weight:    0.0770
   chunk 58 optimal weight:    2.9990
   chunk 46 optimal weight:    0.9980
   chunk 89 optimal weight:    2.9990
   chunk 34 optimal weight:    0.0870
   chunk 54 optimal weight:    0.9980
   chunk 66 optimal weight:    8.9990
   chunk 103 optimal weight:    1.9990
   overall best weight:    0.5316

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

Flipped N/Q/H residues before XYZ refinement:
A 102 ASN
A3941 ASN
A4110 GLN
A4131 ASN
A4206 GLN
A4221 HIS
** A4314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A4342 HIS
B4131 ASN
B4234 ASN
** B4299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.120749 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.085941 restraints weight = 17894.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.087957 restraints weight = 10441.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.089231 restraints weight = 7495.867|
|-----------------------------------------------------------------------------|
r_work (final): 0.3208
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7933
moved from start:          0.0861

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9420  Z= 0.142
  Angle     :  0.714  12.210  12826  Z= 0.355
  Chirality :  0.049   0.338   1374
  Planarity :  0.005   0.047   1664
  Dihedral  : 13.113 103.384   1616
  Min Nonbonded Distance : 2.162

Molprobity Statistics.
  All-atom Clashscore : 5.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.33 %
    Favored  : 92.67 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 16.14 %
    Favored  : 80.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.28 (0.25), residues: 1132
  helix: -4.59 (0.56), residues: 25
  sheet: -0.85 (0.33), residues: 249
  loop : -0.75 (0.21), residues: 858

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A4297 
 HIS   0.004   0.001   HIS B4221 
 PHE   0.011   0.001   PHE A4323 
 TYR   0.016   0.001   TYR B4411 
 ARG   0.004   0.000   ARG A4119 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00823 (    6)
  link_NAG-ASN         : angle       2.62905 (   18)
  link_ALPHA1-6        : bond        0.00845 (    2)
  link_ALPHA1-6        : angle       1.47699 (    6)
  link_BETA1-4         : bond        0.01110 (    6)
  link_BETA1-4         : angle       2.37817 (   18)
  link_ALPHA1-3        : bond        0.02308 (    2)
  link_ALPHA1-3        : angle       1.54627 (    6)
  hydrogen bonds       : bond        0.04394 (  214)
  hydrogen bonds       : angle       8.02140 (  516)
  SS BOND              : bond        0.00316 (   42)
  SS BOND              : angle       0.97113 (   84)
  link_BETA1-3         : bond        0.01347 (    2)
  link_BETA1-3         : angle       5.84189 (    6)
  covalent geometry    : bond        0.00310 ( 9360)
  covalent geometry    : angle       0.68815 (12688)

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 56
  time to evaluate  : 0.947 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 4217 MET cc_start: 0.8621 (mpt) cc_final: 0.7923 (mpt)
REVERT: A 4386 MET cc_start: 0.7958 (pmm) cc_final: 0.7688 (pmm)
REVERT: B   91 LYS cc_start: 0.7016 (OUTLIER) cc_final: 0.6760 (tttp)
REVERT: B 4039 LYS cc_start: 0.8378 (OUTLIER) cc_final: 0.7916 (mtpt)
REVERT: B 4041 MET cc_start: 0.6347 (tpt) cc_final: 0.6089 (tpt)
REVERT: B 4045 TYR cc_start: 0.5778 (OUTLIER) cc_final: 0.5144 (t80)
REVERT: B 4144 MET cc_start: 0.7222 (mtp) cc_final: 0.6991 (mtt)
REVERT: B 4307 LYS cc_start: 0.8620 (OUTLIER) cc_final: 0.8329 (mtpm)
  outliers start: 37
  outliers final: 18
  residues processed: 89
  average time/residue: 0.2092
  time to fit residues: 26.4791
Evaluate side-chains
  73 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 51
  time to evaluate  : 1.012 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 THR
Chi-restraints excluded: chain A residue 4047 GLU
Chi-restraints excluded: chain A residue 4174 ASP
Chi-restraints excluded: chain A residue 4236 LEU
Chi-restraints excluded: chain A residue 4353 CYS
Chi-restraints excluded: chain A residue 4377 VAL
Chi-restraints excluded: chain A residue 4401 CYS
Chi-restraints excluded: chain B residue   58 ASP
Chi-restraints excluded: chain B residue   91 LYS
Chi-restraints excluded: chain B residue  103 CYS
Chi-restraints excluded: chain B residue 3962 THR
Chi-restraints excluded: chain B residue 3965 ASN
Chi-restraints excluded: chain B residue 3971 THR
Chi-restraints excluded: chain B residue 4039 LYS
Chi-restraints excluded: chain B residue 4043 THR
Chi-restraints excluded: chain B residue 4045 TYR
Chi-restraints excluded: chain B residue 4086 ILE
Chi-restraints excluded: chain B residue 4147 ASP
Chi-restraints excluded: chain B residue 4154 VAL
Chi-restraints excluded: chain B residue 4201 MET
Chi-restraints excluded: chain B residue 4307 LYS
Chi-restraints excluded: chain B residue 4339 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 70 optimal weight:    5.9990
   chunk 78 optimal weight:    0.9990
   chunk 75 optimal weight:    0.1980
   chunk 110 optimal weight:    8.9990
   chunk 37 optimal weight:    0.0980
   chunk 40 optimal weight:    1.9990
   chunk 26 optimal weight:    0.8980
   chunk 19 optimal weight:    0.0870
   chunk 103 optimal weight:    0.7980
   chunk 94 optimal weight:    0.9980
   chunk 69 optimal weight:    0.0370
   overall best weight:    0.2436

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

Flipped N/Q/H residues before XYZ refinement:
** A4314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B4008 GLN
** B4299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.122448 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.087503 restraints weight = 18024.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.089542 restraints weight = 10466.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.090851 restraints weight = 7498.146|
|-----------------------------------------------------------------------------|
r_work (final): 0.3238
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7905
moved from start:          0.1301

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   9420  Z= 0.114
  Angle     :  0.662  10.423  12826  Z= 0.329
  Chirality :  0.048   0.301   1374
  Planarity :  0.004   0.046   1664
  Dihedral  : 10.629  93.907   1610
  Min Nonbonded Distance : 2.183

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.24 %
    Favored  : 92.76 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 16.93 %
    Favored  : 79.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.19 (0.25), residues: 1132
  helix: -4.54 (0.58), residues: 25
  sheet: -0.80 (0.33), residues: 257
  loop : -0.67 (0.22), residues: 850

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A4297 
 HIS   0.003   0.001   HIS B4221 
 PHE   0.008   0.001   PHE A4323 
 TYR   0.015   0.001   TYR A4079 
 ARG   0.009   0.000   ARG B4067 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00796 (    6)
  link_NAG-ASN         : angle       2.37116 (   18)
  link_ALPHA1-6        : bond        0.01091 (    2)
  link_ALPHA1-6        : angle       1.87534 (    6)
  link_BETA1-4         : bond        0.00914 (    6)
  link_BETA1-4         : angle       2.35006 (   18)
  link_ALPHA1-3        : bond        0.02000 (    2)
  link_ALPHA1-3        : angle       1.90513 (    6)
  hydrogen bonds       : bond        0.03502 (  214)
  hydrogen bonds       : angle       7.29532 (  516)
  SS BOND              : bond        0.00258 (   42)
  SS BOND              : angle       0.82600 (   84)
  link_BETA1-3         : bond        0.00946 (    2)
  link_BETA1-3         : angle       4.94906 (    6)
  covalent geometry    : bond        0.00245 ( 9360)
  covalent geometry    : angle       0.63902 (12688)

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 65
  time to evaluate  : 1.132 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   88 ASP cc_start: 0.7177 (t70) cc_final: 0.6948 (t0)
REVERT: A 4217 MET cc_start: 0.8630 (OUTLIER) cc_final: 0.7941 (mpt)
REVERT: A 4308 GLU cc_start: 0.7484 (tm-30) cc_final: 0.7281 (tm-30)
REVERT: B   91 LYS cc_start: 0.7210 (OUTLIER) cc_final: 0.6876 (tttp)
REVERT: B 4039 LYS cc_start: 0.8391 (OUTLIER) cc_final: 0.7943 (mtpt)
REVERT: B 4045 TYR cc_start: 0.5715 (OUTLIER) cc_final: 0.5217 (t80)
REVERT: B 4144 MET cc_start: 0.7037 (mtp) cc_final: 0.6817 (mtt)
  outliers start: 33
  outliers final: 16
  residues processed: 95
  average time/residue: 0.1845
  time to fit residues: 26.1264
Evaluate side-chains
  76 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 56
  time to evaluate  : 1.078 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 THR
Chi-restraints excluded: chain A residue   98 ASP
Chi-restraints excluded: chain A residue 4047 GLU
Chi-restraints excluded: chain A residue 4174 ASP
Chi-restraints excluded: chain A residue 4217 MET
Chi-restraints excluded: chain A residue 4236 LEU
Chi-restraints excluded: chain A residue 4339 VAL
Chi-restraints excluded: chain A residue 4353 CYS
Chi-restraints excluded: chain B residue   58 ASP
Chi-restraints excluded: chain B residue   91 LYS
Chi-restraints excluded: chain B residue  103 CYS
Chi-restraints excluded: chain B residue 3960 ASP
Chi-restraints excluded: chain B residue 3962 THR
Chi-restraints excluded: chain B residue 3965 ASN
Chi-restraints excluded: chain B residue 4039 LYS
Chi-restraints excluded: chain B residue 4045 TYR
Chi-restraints excluded: chain B residue 4147 ASP
Chi-restraints excluded: chain B residue 4154 VAL
Chi-restraints excluded: chain B residue 4255 VAL
Chi-restraints excluded: chain B residue 4339 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 68 optimal weight:    0.8980
   chunk 4 optimal weight:    6.9990
   chunk 10 optimal weight:    0.0030
   chunk 77 optimal weight:    5.9990
   chunk 13 optimal weight:    2.9990
   chunk 37 optimal weight:    0.6980
   chunk 80 optimal weight:    0.5980
   chunk 36 optimal weight:    0.4980
   chunk 87 optimal weight:    1.9990
   chunk 60 optimal weight:    0.9980
   chunk 67 optimal weight:    0.6980
   overall best weight:    0.4990

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

Flipped N/Q/H residues before XYZ refinement:
** A4314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B4008 GLN
B4299 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.121568 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.086412 restraints weight = 17869.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.088450 restraints weight = 10504.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.089728 restraints weight = 7562.306|
|-----------------------------------------------------------------------------|
r_work (final): 0.3218
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7929
moved from start:          0.1511

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9420  Z= 0.126
  Angle     :  0.649  10.709  12826  Z= 0.321
  Chirality :  0.047   0.279   1374
  Planarity :  0.004   0.044   1664
  Dihedral  :  9.229  76.311   1608
  Min Nonbonded Distance : 2.160

Molprobity Statistics.
  All-atom Clashscore : 5.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.24 %
    Favored  : 92.76 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 17.23 %
    Favored  : 79.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.23 (0.25), residues: 1132
  helix: -4.41 (0.63), residues: 25
  sheet: -0.97 (0.32), residues: 269
  loop : -0.64 (0.22), residues: 838

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A4297 
 HIS   0.003   0.001   HIS B4221 
 PHE   0.008   0.001   PHE A4323 
 TYR   0.012   0.001   TYR A4079 
 ARG   0.004   0.000   ARG B4067 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00727 (    6)
  link_NAG-ASN         : angle       2.25982 (   18)
  link_ALPHA1-6        : bond        0.00747 (    2)
  link_ALPHA1-6        : angle       2.22690 (    6)
  link_BETA1-4         : bond        0.00884 (    6)
  link_BETA1-4         : angle       2.08792 (   18)
  link_ALPHA1-3        : bond        0.01875 (    2)
  link_ALPHA1-3        : angle       2.03886 (    6)
  hydrogen bonds       : bond        0.03212 (  214)
  hydrogen bonds       : angle       7.01061 (  516)
  SS BOND              : bond        0.00313 (   42)
  SS BOND              : angle       0.80638 (   84)
  link_BETA1-3         : bond        0.01163 (    2)
  link_BETA1-3         : angle       5.15495 (    6)
  covalent geometry    : bond        0.00278 ( 9360)
  covalent geometry    : angle       0.62556 (12688)

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 62
  time to evaluate  : 1.093 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 4217 MET cc_start: 0.8617 (OUTLIER) cc_final: 0.7917 (mpt)
REVERT: B   91 LYS cc_start: 0.7216 (OUTLIER) cc_final: 0.6900 (tttp)
REVERT: B 4008 GLN cc_start: 0.4961 (OUTLIER) cc_final: 0.4436 (pm20)
REVERT: B 4039 LYS cc_start: 0.8378 (OUTLIER) cc_final: 0.7852 (mtpt)
REVERT: B 4045 TYR cc_start: 0.5701 (OUTLIER) cc_final: 0.5231 (t80)
  outliers start: 35
  outliers final: 22
  residues processed: 89
  average time/residue: 0.1832
  time to fit residues: 24.6927
Evaluate side-chains
  80 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 53
  time to evaluate  : 1.087 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 THR
Chi-restraints excluded: chain A residue 4047 GLU
Chi-restraints excluded: chain A residue 4174 ASP
Chi-restraints excluded: chain A residue 4201 MET
Chi-restraints excluded: chain A residue 4217 MET
Chi-restraints excluded: chain A residue 4236 LEU
Chi-restraints excluded: chain A residue 4339 VAL
Chi-restraints excluded: chain A residue 4353 CYS
Chi-restraints excluded: chain B residue   58 ASP
Chi-restraints excluded: chain B residue   91 LYS
Chi-restraints excluded: chain B residue  103 CYS
Chi-restraints excluded: chain B residue 3960 ASP
Chi-restraints excluded: chain B residue 3962 THR
Chi-restraints excluded: chain B residue 3965 ASN
Chi-restraints excluded: chain B residue 4008 GLN
Chi-restraints excluded: chain B residue 4039 LYS
Chi-restraints excluded: chain B residue 4043 THR
Chi-restraints excluded: chain B residue 4045 TYR
Chi-restraints excluded: chain B residue 4086 ILE
Chi-restraints excluded: chain B residue 4147 ASP
Chi-restraints excluded: chain B residue 4154 VAL
Chi-restraints excluded: chain B residue 4158 ILE
Chi-restraints excluded: chain B residue 4201 MET
Chi-restraints excluded: chain B residue 4255 VAL
Chi-restraints excluded: chain B residue 4274 MET
Chi-restraints excluded: chain B residue 4339 VAL
Chi-restraints excluded: chain B residue 4385 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 36 optimal weight:    0.9980
   chunk 27 optimal weight:    3.9990
   chunk 61 optimal weight:    7.9990
   chunk 76 optimal weight:    2.9990
   chunk 85 optimal weight:    0.8980
   chunk 70 optimal weight:    3.9990
   chunk 71 optimal weight:    5.9990
   chunk 92 optimal weight:    0.6980
   chunk 105 optimal weight:    3.9990
   chunk 98 optimal weight:    2.9990
   chunk 79 optimal weight:    0.9980
   overall best weight:    1.3182

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

Flipped N/Q/H residues before XYZ refinement:
** A4314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.118692 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.085513 restraints weight = 18006.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.086160 restraints weight = 11114.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.087021 restraints weight = 9022.472|
|-----------------------------------------------------------------------------|
r_work (final): 0.3151
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8006
moved from start:          0.1617

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   9420  Z= 0.221
  Angle     :  0.691  10.227  12826  Z= 0.347
  Chirality :  0.048   0.253   1374
  Planarity :  0.005   0.044   1664
  Dihedral  :  7.918  48.932   1608
  Min Nonbonded Distance : 2.120

Molprobity Statistics.
  All-atom Clashscore : 6.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.04 %
    Favored  : 91.96 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 17.33 %
    Favored  : 78.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.44 (0.25), residues: 1132
  helix: -4.47 (0.75), residues: 19
  sheet: -1.10 (0.30), residues: 299
  loop : -0.81 (0.22), residues: 814

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A4297 
 HIS   0.006   0.001   HIS B4221 
 PHE   0.010   0.002   PHE A4361 
 TYR   0.013   0.002   TYR A4079 
 ARG   0.005   0.001   ARG B4067 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00667 (    6)
  link_NAG-ASN         : angle       2.45493 (   18)
  link_ALPHA1-6        : bond        0.00615 (    2)
  link_ALPHA1-6        : angle       2.14415 (    6)
  link_BETA1-4         : bond        0.00774 (    6)
  link_BETA1-4         : angle       2.17158 (   18)
  link_ALPHA1-3        : bond        0.01900 (    2)
  link_ALPHA1-3        : angle       1.93396 (    6)
  hydrogen bonds       : bond        0.03620 (  214)
  hydrogen bonds       : angle       7.03011 (  516)
  SS BOND              : bond        0.00341 (   42)
  SS BOND              : angle       0.88366 (   84)
  link_BETA1-3         : bond        0.01313 (    2)
  link_BETA1-3         : angle       4.73852 (    6)
  covalent geometry    : bond        0.00506 ( 9360)
  covalent geometry    : angle       0.66948 (12688)

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 54
  time to evaluate  : 1.094 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   51 ARG cc_start: 0.7131 (OUTLIER) cc_final: 0.6781 (mtm-85)
REVERT: A   88 ASP cc_start: 0.6377 (t0) cc_final: 0.6058 (t0)
REVERT: A 4217 MET cc_start: 0.8623 (OUTLIER) cc_final: 0.7909 (mpt)
REVERT: B   91 LYS cc_start: 0.7245 (OUTLIER) cc_final: 0.6949 (tttp)
REVERT: B 4039 LYS cc_start: 0.8266 (OUTLIER) cc_final: 0.7766 (mtpt)
REVERT: B 4045 TYR cc_start: 0.5798 (OUTLIER) cc_final: 0.5306 (t80)
  outliers start: 41
  outliers final: 26
  residues processed: 86
  average time/residue: 0.1799
  time to fit residues: 23.5986
Evaluate side-chains
  84 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 53
  time to evaluate  : 0.951 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 THR
Chi-restraints excluded: chain A residue   51 ARG
Chi-restraints excluded: chain A residue   54 LEU
Chi-restraints excluded: chain A residue   74 CYS
Chi-restraints excluded: chain A residue 4047 GLU
Chi-restraints excluded: chain A residue 4122 ILE
Chi-restraints excluded: chain A residue 4174 ASP
Chi-restraints excluded: chain A residue 4201 MET
Chi-restraints excluded: chain A residue 4217 MET
Chi-restraints excluded: chain A residue 4236 LEU
Chi-restraints excluded: chain A residue 4339 VAL
Chi-restraints excluded: chain A residue 4353 CYS
Chi-restraints excluded: chain A residue 4366 THR
Chi-restraints excluded: chain A residue 4377 VAL
Chi-restraints excluded: chain B residue   58 ASP
Chi-restraints excluded: chain B residue   91 LYS
Chi-restraints excluded: chain B residue  103 CYS
Chi-restraints excluded: chain B residue 3960 ASP
Chi-restraints excluded: chain B residue 3962 THR
Chi-restraints excluded: chain B residue 3965 ASN
Chi-restraints excluded: chain B residue 4039 LYS
Chi-restraints excluded: chain B residue 4043 THR
Chi-restraints excluded: chain B residue 4045 TYR
Chi-restraints excluded: chain B residue 4147 ASP
Chi-restraints excluded: chain B residue 4154 VAL
Chi-restraints excluded: chain B residue 4158 ILE
Chi-restraints excluded: chain B residue 4201 MET
Chi-restraints excluded: chain B residue 4255 VAL
Chi-restraints excluded: chain B residue 4274 MET
Chi-restraints excluded: chain B residue 4339 VAL
Chi-restraints excluded: chain B residue 4385 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 26 optimal weight:    0.6980
   chunk 72 optimal weight:    3.9990
   chunk 21 optimal weight:    0.8980
   chunk 36 optimal weight:    0.8980
   chunk 37 optimal weight:    0.7980
   chunk 24 optimal weight:    0.8980
   chunk 73 optimal weight:    0.8980
   chunk 108 optimal weight:    0.0030
   chunk 94 optimal weight:    0.7980
   chunk 18 optimal weight:    0.5980
   chunk 88 optimal weight:    0.6980
   overall best weight:    0.5590

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

Flipped N/Q/H residues before XYZ refinement:
** A4314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B4008 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.120360 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.086775 restraints weight = 17918.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.087462 restraints weight = 10888.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.088424 restraints weight = 8864.773|
|-----------------------------------------------------------------------------|
r_work (final): 0.3183
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7971
moved from start:          0.1721

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9420  Z= 0.128
  Angle     :  0.644  13.943  12826  Z= 0.319
  Chirality :  0.047   0.271   1374
  Planarity :  0.004   0.044   1664
  Dihedral  :  7.312  48.664   1608
  Min Nonbonded Distance : 2.171

Molprobity Statistics.
  All-atom Clashscore : 5.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.33 %
    Favored  : 92.67 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 17.03 %
    Favored  : 78.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.39 (0.25), residues: 1132
  helix: -4.54 (0.56), residues: 25
  sheet: -0.96 (0.31), residues: 279
  loop : -0.80 (0.22), residues: 828

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A4297 
 HIS   0.004   0.001   HIS B4221 
 PHE   0.009   0.001   PHE A4323 
 TYR   0.017   0.001   TYR A4079 
 ARG   0.005   0.000   ARG B4067 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00680 (    6)
  link_NAG-ASN         : angle       2.38353 (   18)
  link_ALPHA1-6        : bond        0.00341 (    2)
  link_ALPHA1-6        : angle       1.83215 (    6)
  link_BETA1-4         : bond        0.00705 (    6)
  link_BETA1-4         : angle       1.91040 (   18)
  link_ALPHA1-3        : bond        0.01736 (    2)
  link_ALPHA1-3        : angle       2.15808 (    6)
  hydrogen bonds       : bond        0.03080 (  214)
  hydrogen bonds       : angle       6.77266 (  516)
  SS BOND              : bond        0.00266 (   42)
  SS BOND              : angle       0.77347 (   84)
  link_BETA1-3         : bond        0.01164 (    2)
  link_BETA1-3         : angle       4.29613 (    6)
  covalent geometry    : bond        0.00287 ( 9360)
  covalent geometry    : angle       0.62446 (12688)

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 66
  time to evaluate  : 1.098 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   51 ARG cc_start: 0.7051 (OUTLIER) cc_final: 0.6635 (mtm-85)
REVERT: A   88 ASP cc_start: 0.6966 (t0) cc_final: 0.6593 (t0)
REVERT: A 4217 MET cc_start: 0.8559 (OUTLIER) cc_final: 0.7930 (mpt)
REVERT: B   91 LYS cc_start: 0.7259 (OUTLIER) cc_final: 0.6925 (tttp)
REVERT: B 4039 LYS cc_start: 0.8186 (OUTLIER) cc_final: 0.7768 (mtpt)
REVERT: B 4187 ASP cc_start: 0.6771 (OUTLIER) cc_final: 0.6536 (m-30)
REVERT: B 4384 ARG cc_start: 0.7635 (OUTLIER) cc_final: 0.6865 (ttp80)
  outliers start: 41
  outliers final: 24
  residues processed: 96
  average time/residue: 0.1806
  time to fit residues: 25.7954
Evaluate side-chains
  88 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 58
  time to evaluate  : 1.050 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 THR
Chi-restraints excluded: chain A residue   51 ARG
Chi-restraints excluded: chain A residue   54 LEU
Chi-restraints excluded: chain A residue   74 CYS
Chi-restraints excluded: chain A residue 4047 GLU
Chi-restraints excluded: chain A residue 4122 ILE
Chi-restraints excluded: chain A residue 4174 ASP
Chi-restraints excluded: chain A residue 4201 MET
Chi-restraints excluded: chain A residue 4217 MET
Chi-restraints excluded: chain A residue 4236 LEU
Chi-restraints excluded: chain A residue 4339 VAL
Chi-restraints excluded: chain A residue 4353 CYS
Chi-restraints excluded: chain B residue   91 LYS
Chi-restraints excluded: chain B residue  103 CYS
Chi-restraints excluded: chain B residue 3960 ASP
Chi-restraints excluded: chain B residue 3962 THR
Chi-restraints excluded: chain B residue 3965 ASN
Chi-restraints excluded: chain B residue 4039 LYS
Chi-restraints excluded: chain B residue 4043 THR
Chi-restraints excluded: chain B residue 4086 ILE
Chi-restraints excluded: chain B residue 4147 ASP
Chi-restraints excluded: chain B residue 4154 VAL
Chi-restraints excluded: chain B residue 4158 ILE
Chi-restraints excluded: chain B residue 4187 ASP
Chi-restraints excluded: chain B residue 4201 MET
Chi-restraints excluded: chain B residue 4255 VAL
Chi-restraints excluded: chain B residue 4274 MET
Chi-restraints excluded: chain B residue 4339 VAL
Chi-restraints excluded: chain B residue 4384 ARG
Chi-restraints excluded: chain B residue 4385 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 25 optimal weight:    0.5980
   chunk 80 optimal weight:    0.7980
   chunk 19 optimal weight:    0.9990
   chunk 83 optimal weight:    1.9990
   chunk 58 optimal weight:    3.9990
   chunk 13 optimal weight:    2.9990
   chunk 5 optimal weight:    3.9990
   chunk 65 optimal weight:    0.0000
   chunk 100 optimal weight:    2.9990
   chunk 24 optimal weight:    0.5980
   chunk 18 optimal weight:    0.7980
   overall best weight:    0.5584

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

Flipped N/Q/H residues before XYZ refinement:
B4008 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.120661 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.087300 restraints weight = 18133.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.087980 restraints weight = 11554.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.088707 restraints weight = 9796.884|
|-----------------------------------------------------------------------------|
r_work (final): 0.3187
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7976
moved from start:          0.1900

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9420  Z= 0.130
  Angle     :  0.645  11.701  12826  Z= 0.321
  Chirality :  0.046   0.264   1374
  Planarity :  0.004   0.044   1664
  Dihedral  :  6.996  49.690   1606
  Min Nonbonded Distance : 2.171

Molprobity Statistics.
  All-atom Clashscore : 6.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.13 %
    Favored  : 91.87 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 18.33 %
    Favored  : 78.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.37 (0.25), residues: 1132
  helix: -4.49 (0.58), residues: 25
  sheet: -1.09 (0.31), residues: 291
  loop : -0.71 (0.22), residues: 816

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A4297 
 HIS   0.004   0.001   HIS B4221 
 PHE   0.010   0.001   PHE A3989 
 TYR   0.017   0.001   TYR A4079 
 ARG   0.005   0.000   ARG B4067 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00618 (    6)
  link_NAG-ASN         : angle       2.20246 (   18)
  link_ALPHA1-6        : bond        0.00348 (    2)
  link_ALPHA1-6        : angle       1.76462 (    6)
  link_BETA1-4         : bond        0.00686 (    6)
  link_BETA1-4         : angle       1.81682 (   18)
  link_ALPHA1-3        : bond        0.01748 (    2)
  link_ALPHA1-3        : angle       2.17983 (    6)
  hydrogen bonds       : bond        0.03047 (  214)
  hydrogen bonds       : angle       6.67769 (  516)
  SS BOND              : bond        0.00252 (   42)
  SS BOND              : angle       0.88863 (   84)
  link_BETA1-3         : bond        0.01103 (    2)
  link_BETA1-3         : angle       4.08262 (    6)
  covalent geometry    : bond        0.00294 ( 9360)
  covalent geometry    : angle       0.62618 (12688)

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 65
  time to evaluate  : 1.143 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   51 ARG cc_start: 0.7040 (OUTLIER) cc_final: 0.6619 (mtm-85)
REVERT: A   88 ASP cc_start: 0.6901 (t0) cc_final: 0.6505 (t0)
REVERT: A 4217 MET cc_start: 0.8609 (OUTLIER) cc_final: 0.7935 (mpt)
REVERT: B   91 LYS cc_start: 0.7338 (OUTLIER) cc_final: 0.7016 (tttp)
REVERT: B 4008 GLN cc_start: 0.4158 (OUTLIER) cc_final: 0.3795 (pm20)
REVERT: B 4039 LYS cc_start: 0.8197 (OUTLIER) cc_final: 0.7794 (mtpt)
REVERT: B 4174 ASP cc_start: 0.8118 (OUTLIER) cc_final: 0.7589 (p0)
REVERT: B 4384 ARG cc_start: 0.7628 (OUTLIER) cc_final: 0.6883 (ttp80)
  outliers start: 35
  outliers final: 23
  residues processed: 92
  average time/residue: 0.1902
  time to fit residues: 25.6776
Evaluate side-chains
  89 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 59
  time to evaluate  : 0.996 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 THR
Chi-restraints excluded: chain A residue   51 ARG
Chi-restraints excluded: chain A residue   54 LEU
Chi-restraints excluded: chain A residue   74 CYS
Chi-restraints excluded: chain A residue 4047 GLU
Chi-restraints excluded: chain A residue 4174 ASP
Chi-restraints excluded: chain A residue 4201 MET
Chi-restraints excluded: chain A residue 4217 MET
Chi-restraints excluded: chain A residue 4236 LEU
Chi-restraints excluded: chain A residue 4339 VAL
Chi-restraints excluded: chain A residue 4353 CYS
Chi-restraints excluded: chain B residue   91 LYS
Chi-restraints excluded: chain B residue  103 CYS
Chi-restraints excluded: chain B residue 3960 ASP
Chi-restraints excluded: chain B residue 3971 THR
Chi-restraints excluded: chain B residue 4008 GLN
Chi-restraints excluded: chain B residue 4039 LYS
Chi-restraints excluded: chain B residue 4043 THR
Chi-restraints excluded: chain B residue 4086 ILE
Chi-restraints excluded: chain B residue 4147 ASP
Chi-restraints excluded: chain B residue 4154 VAL
Chi-restraints excluded: chain B residue 4158 ILE
Chi-restraints excluded: chain B residue 4174 ASP
Chi-restraints excluded: chain B residue 4201 MET
Chi-restraints excluded: chain B residue 4255 VAL
Chi-restraints excluded: chain B residue 4274 MET
Chi-restraints excluded: chain B residue 4339 VAL
Chi-restraints excluded: chain B residue 4384 ARG
Chi-restraints excluded: chain B residue 4385 CYS
Chi-restraints excluded: chain B residue 4402 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 65 optimal weight:    0.0030
   chunk 4 optimal weight:    2.9990
   chunk 38 optimal weight:    0.4980
   chunk 33 optimal weight:    1.9990
   chunk 11 optimal weight:    4.9990
   chunk 63 optimal weight:    0.9980
   chunk 5 optimal weight:    4.9990
   chunk 45 optimal weight:    0.6980
   chunk 98 optimal weight:    0.7980
   chunk 12 optimal weight:    0.4980
   chunk 104 optimal weight:    0.7980
   overall best weight:    0.4990

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

Flipped N/Q/H residues before XYZ refinement:
B4008 GLN
** B4314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.120837 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.087053 restraints weight = 18432.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.088608 restraints weight = 10698.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.089211 restraints weight = 8492.143|
|-----------------------------------------------------------------------------|
r_work (final): 0.3198
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7959
moved from start:          0.1948

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9420  Z= 0.123
  Angle     :  0.635  11.232  12826  Z= 0.317
  Chirality :  0.046   0.261   1374
  Planarity :  0.004   0.044   1664
  Dihedral  :  6.853  49.677   1605
  Min Nonbonded Distance : 2.178

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.69 %
    Favored  : 92.31 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 17.73 %
    Favored  : 78.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.38 (0.25), residues: 1132
  helix: -4.47 (0.59), residues: 25
  sheet: -1.17 (0.31), residues: 281
  loop : -0.70 (0.22), residues: 826

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A4297 
 HIS   0.004   0.001   HIS B4221 
 PHE   0.008   0.001   PHE A4323 
 TYR   0.022   0.001   TYR A4079 
 ARG   0.005   0.000   ARG B4067 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00617 (    6)
  link_NAG-ASN         : angle       2.19206 (   18)
  link_ALPHA1-6        : bond        0.00328 (    2)
  link_ALPHA1-6        : angle       1.72469 (    6)
  link_BETA1-4         : bond        0.00668 (    6)
  link_BETA1-4         : angle       1.73915 (   18)
  link_ALPHA1-3        : bond        0.01690 (    2)
  link_ALPHA1-3        : angle       2.19490 (    6)
  hydrogen bonds       : bond        0.02943 (  214)
  hydrogen bonds       : angle       6.61324 (  516)
  SS BOND              : bond        0.00245 (   42)
  SS BOND              : angle       0.86528 (   84)
  link_BETA1-3         : bond        0.01061 (    2)
  link_BETA1-3         : angle       3.99110 (    6)
  covalent geometry    : bond        0.00279 ( 9360)
  covalent geometry    : angle       0.61623 (12688)

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 63
  time to evaluate  : 0.964 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   41 ILE cc_start: 0.8850 (OUTLIER) cc_final: 0.8644 (pt)
REVERT: A   51 ARG cc_start: 0.7115 (OUTLIER) cc_final: 0.6635 (mtm-85)
REVERT: A   88 ASP cc_start: 0.6961 (t0) cc_final: 0.6638 (t0)
REVERT: A 4217 MET cc_start: 0.8596 (OUTLIER) cc_final: 0.7963 (mpt)
REVERT: B   91 LYS cc_start: 0.7292 (OUTLIER) cc_final: 0.6961 (tttp)
REVERT: B 4174 ASP cc_start: 0.8110 (OUTLIER) cc_final: 0.7579 (p0)
REVERT: B 4187 ASP cc_start: 0.7090 (OUTLIER) cc_final: 0.6862 (m-30)
REVERT: B 4384 ARG cc_start: 0.7633 (OUTLIER) cc_final: 0.6903 (ttp80)
  outliers start: 34
  outliers final: 22
  residues processed: 90
  average time/residue: 0.1907
  time to fit residues: 25.3158
Evaluate side-chains
  89 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 60
  time to evaluate  : 0.953 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 ILE
Chi-restraints excluded: chain A residue   50 THR
Chi-restraints excluded: chain A residue   51 ARG
Chi-restraints excluded: chain A residue   74 CYS
Chi-restraints excluded: chain A residue 4047 GLU
Chi-restraints excluded: chain A residue 4174 ASP
Chi-restraints excluded: chain A residue 4201 MET
Chi-restraints excluded: chain A residue 4217 MET
Chi-restraints excluded: chain A residue 4236 LEU
Chi-restraints excluded: chain A residue 4339 VAL
Chi-restraints excluded: chain A residue 4353 CYS
Chi-restraints excluded: chain B residue   91 LYS
Chi-restraints excluded: chain B residue  103 CYS
Chi-restraints excluded: chain B residue 3960 ASP
Chi-restraints excluded: chain B residue 3971 THR
Chi-restraints excluded: chain B residue 4008 GLN
Chi-restraints excluded: chain B residue 4043 THR
Chi-restraints excluded: chain B residue 4086 ILE
Chi-restraints excluded: chain B residue 4147 ASP
Chi-restraints excluded: chain B residue 4154 VAL
Chi-restraints excluded: chain B residue 4158 ILE
Chi-restraints excluded: chain B residue 4174 ASP
Chi-restraints excluded: chain B residue 4187 ASP
Chi-restraints excluded: chain B residue 4201 MET
Chi-restraints excluded: chain B residue 4255 VAL
Chi-restraints excluded: chain B residue 4274 MET
Chi-restraints excluded: chain B residue 4384 ARG
Chi-restraints excluded: chain B residue 4385 CYS
Chi-restraints excluded: chain B residue 4402 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 72 optimal weight:    1.9990
   chunk 18 optimal weight:    3.9990
   chunk 93 optimal weight:    2.9990
   chunk 13 optimal weight:    2.9990
   chunk 89 optimal weight:    0.9980
   chunk 33 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9980
   chunk 36 optimal weight:    0.9990
   chunk 103 optimal weight:    0.8980
   chunk 23 optimal weight:    1.9990
   chunk 45 optimal weight:    1.9990
   overall best weight:    1.1784

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

Flipped N/Q/H residues before XYZ refinement:
B4008 GLN
** B4314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.119204 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.086382 restraints weight = 18137.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.086626 restraints weight = 11184.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.087428 restraints weight = 8860.680|
|-----------------------------------------------------------------------------|
r_work (final): 0.3166
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7990
moved from start:          0.2003

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   9420  Z= 0.205
  Angle     :  0.682  10.842  12826  Z= 0.343
  Chirality :  0.047   0.227   1374
  Planarity :  0.004   0.043   1664
  Dihedral  :  7.051  52.092   1604
  Min Nonbonded Distance : 2.125

Molprobity Statistics.
  All-atom Clashscore : 7.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.30 %
    Favored  : 91.70 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 17.83 %
    Favored  : 78.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.43 (0.25), residues: 1132
  helix: -4.49 (0.59), residues: 25
  sheet: -1.13 (0.31), residues: 285
  loop : -0.76 (0.22), residues: 822

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B4248 
 HIS   0.005   0.001   HIS B4221 
 PHE   0.010   0.001   PHE A4361 
 TYR   0.019   0.002   TYR A4079 
 ARG   0.005   0.000   ARG B4067 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00625 (    6)
  link_NAG-ASN         : angle       2.33568 (   18)
  link_ALPHA1-6        : bond        0.00255 (    2)
  link_ALPHA1-6        : angle       1.83480 (    6)
  link_BETA1-4         : bond        0.00662 (    6)
  link_BETA1-4         : angle       1.86136 (   18)
  link_ALPHA1-3        : bond        0.01782 (    2)
  link_ALPHA1-3        : angle       2.07560 (    6)
  hydrogen bonds       : bond        0.03243 (  214)
  hydrogen bonds       : angle       6.66449 (  516)
  SS BOND              : bond        0.00322 (   42)
  SS BOND              : angle       0.95197 (   84)
  link_BETA1-3         : bond        0.01053 (    2)
  link_BETA1-3         : angle       3.88343 (    6)
  covalent geometry    : bond        0.00471 ( 9360)
  covalent geometry    : angle       0.66376 (12688)

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 59
  time to evaluate  : 0.966 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   41 ILE cc_start: 0.8809 (OUTLIER) cc_final: 0.8595 (pt)
REVERT: A   51 ARG cc_start: 0.7136 (OUTLIER) cc_final: 0.6802 (mtm-85)
REVERT: A   88 ASP cc_start: 0.6992 (t0) cc_final: 0.6729 (t0)
REVERT: A 4217 MET cc_start: 0.8634 (OUTLIER) cc_final: 0.7999 (mpt)
REVERT: B   91 LYS cc_start: 0.7353 (OUTLIER) cc_final: 0.7020 (tttp)
REVERT: B 4008 GLN cc_start: 0.5129 (OUTLIER) cc_final: 0.3998 (pm20)
REVERT: B 4174 ASP cc_start: 0.8145 (OUTLIER) cc_final: 0.7602 (p0)
REVERT: B 4187 ASP cc_start: 0.6766 (OUTLIER) cc_final: 0.6517 (m-30)
REVERT: B 4384 ARG cc_start: 0.7999 (OUTLIER) cc_final: 0.7139 (ttp80)
  outliers start: 35
  outliers final: 23
  residues processed: 86
  average time/residue: 0.1755
  time to fit residues: 22.7691
Evaluate side-chains
  88 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 57
  time to evaluate  : 0.916 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 ILE
Chi-restraints excluded: chain A residue   50 THR
Chi-restraints excluded: chain A residue   51 ARG
Chi-restraints excluded: chain A residue   54 LEU
Chi-restraints excluded: chain A residue   74 CYS
Chi-restraints excluded: chain A residue 3931 THR
Chi-restraints excluded: chain A residue 4047 GLU
Chi-restraints excluded: chain A residue 4174 ASP
Chi-restraints excluded: chain A residue 4201 MET
Chi-restraints excluded: chain A residue 4217 MET
Chi-restraints excluded: chain A residue 4236 LEU
Chi-restraints excluded: chain A residue 4339 VAL
Chi-restraints excluded: chain A residue 4353 CYS
Chi-restraints excluded: chain B residue   91 LYS
Chi-restraints excluded: chain B residue  103 CYS
Chi-restraints excluded: chain B residue 3960 ASP
Chi-restraints excluded: chain B residue 3971 THR
Chi-restraints excluded: chain B residue 3992 SER
Chi-restraints excluded: chain B residue 4008 GLN
Chi-restraints excluded: chain B residue 4043 THR
Chi-restraints excluded: chain B residue 4086 ILE
Chi-restraints excluded: chain B residue 4147 ASP
Chi-restraints excluded: chain B residue 4154 VAL
Chi-restraints excluded: chain B residue 4158 ILE
Chi-restraints excluded: chain B residue 4174 ASP
Chi-restraints excluded: chain B residue 4187 ASP
Chi-restraints excluded: chain B residue 4201 MET
Chi-restraints excluded: chain B residue 4255 VAL
Chi-restraints excluded: chain B residue 4274 MET
Chi-restraints excluded: chain B residue 4384 ARG
Chi-restraints excluded: chain B residue 4385 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 100 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   chunk 50 optimal weight:    0.6980
   chunk 78 optimal weight:    0.6980
   chunk 47 optimal weight:    0.9990
   chunk 111 optimal weight:    0.9990
   chunk 68 optimal weight:    0.8980
   chunk 13 optimal weight:    3.9990
   chunk 90 optimal weight:    0.6980
   chunk 10 optimal weight:    2.9990
   chunk 6 optimal weight:    0.6980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** B4008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B4314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.119915 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.086032 restraints weight = 18265.921|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.087698 restraints weight = 10592.777|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.088350 restraints weight = 8290.108|
|-----------------------------------------------------------------------------|
r_work (final): 0.3180
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7954
moved from start:          0.2045

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   9420  Z= 0.153
  Angle     :  0.665  11.128  12826  Z= 0.334
  Chirality :  0.047   0.224   1374
  Planarity :  0.004   0.044   1664
  Dihedral  :  7.086  58.593   1604
  Min Nonbonded Distance : 2.143

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.95 %
    Favored  : 92.05 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 18.03 %
    Favored  : 78.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.40 (0.25), residues: 1132
  helix: -4.48 (0.59), residues: 25
  sheet: -1.12 (0.31), residues: 285
  loop : -0.73 (0.22), residues: 822

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B4248 
 HIS   0.005   0.001   HIS B4221 
 PHE   0.008   0.001   PHE B4038 
 TYR   0.019   0.001   TYR A4079 
 ARG   0.005   0.000   ARG B4067 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00611 (    6)
  link_NAG-ASN         : angle       2.28794 (   18)
  link_ALPHA1-6        : bond        0.00263 (    2)
  link_ALPHA1-6        : angle       1.77268 (    6)
  link_BETA1-4         : bond        0.00653 (    6)
  link_BETA1-4         : angle       1.82250 (   18)
  link_ALPHA1-3        : bond        0.01690 (    2)
  link_ALPHA1-3        : angle       2.13016 (    6)
  hydrogen bonds       : bond        0.03041 (  214)
  hydrogen bonds       : angle       6.63297 (  516)
  SS BOND              : bond        0.00272 (   42)
  SS BOND              : angle       0.91431 (   84)
  link_BETA1-3         : bond        0.01043 (    2)
  link_BETA1-3         : angle       3.84578 (    6)
  covalent geometry    : bond        0.00350 ( 9360)
  covalent geometry    : angle       0.64693 (12688)

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 59
  time to evaluate  : 1.088 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   41 ILE cc_start: 0.8790 (OUTLIER) cc_final: 0.8582 (pt)
REVERT: A   51 ARG cc_start: 0.7071 (OUTLIER) cc_final: 0.6666 (mtm-85)
REVERT: A   88 ASP cc_start: 0.6968 (t0) cc_final: 0.6682 (t0)
REVERT: A 4217 MET cc_start: 0.8627 (OUTLIER) cc_final: 0.7968 (mpt)
REVERT: B   91 LYS cc_start: 0.7295 (OUTLIER) cc_final: 0.6971 (tttp)
REVERT: B 4174 ASP cc_start: 0.8098 (OUTLIER) cc_final: 0.7534 (p0)
REVERT: B 4187 ASP cc_start: 0.6892 (OUTLIER) cc_final: 0.6661 (m-30)
REVERT: B 4384 ARG cc_start: 0.7980 (OUTLIER) cc_final: 0.7088 (ttp80)
  outliers start: 31
  outliers final: 23
  residues processed: 81
  average time/residue: 0.1883
  time to fit residues: 22.9749
Evaluate side-chains
  87 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 57
  time to evaluate  : 1.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 ILE
Chi-restraints excluded: chain A residue   50 THR
Chi-restraints excluded: chain A residue   51 ARG
Chi-restraints excluded: chain A residue   54 LEU
Chi-restraints excluded: chain A residue   74 CYS
Chi-restraints excluded: chain A residue 3931 THR
Chi-restraints excluded: chain A residue 4047 GLU
Chi-restraints excluded: chain A residue 4174 ASP
Chi-restraints excluded: chain A residue 4201 MET
Chi-restraints excluded: chain A residue 4217 MET
Chi-restraints excluded: chain A residue 4236 LEU
Chi-restraints excluded: chain A residue 4339 VAL
Chi-restraints excluded: chain A residue 4353 CYS
Chi-restraints excluded: chain A residue 4377 VAL
Chi-restraints excluded: chain B residue   58 ASP
Chi-restraints excluded: chain B residue   91 LYS
Chi-restraints excluded: chain B residue  103 CYS
Chi-restraints excluded: chain B residue 3971 THR
Chi-restraints excluded: chain B residue 4043 THR
Chi-restraints excluded: chain B residue 4086 ILE
Chi-restraints excluded: chain B residue 4147 ASP
Chi-restraints excluded: chain B residue 4154 VAL
Chi-restraints excluded: chain B residue 4158 ILE
Chi-restraints excluded: chain B residue 4174 ASP
Chi-restraints excluded: chain B residue 4187 ASP
Chi-restraints excluded: chain B residue 4201 MET
Chi-restraints excluded: chain B residue 4255 VAL
Chi-restraints excluded: chain B residue 4274 MET
Chi-restraints excluded: chain B residue 4384 ARG
Chi-restraints excluded: chain B residue 4385 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 82 optimal weight:    1.9990
   chunk 86 optimal weight:    2.9990
   chunk 19 optimal weight:    0.8980
   chunk 33 optimal weight:    1.9990
   chunk 77 optimal weight:    4.9990
   chunk 97 optimal weight:    2.9990
   chunk 35 optimal weight:    0.7980
   chunk 32 optimal weight:    0.5980
   chunk 37 optimal weight:    0.6980
   chunk 3 optimal weight:    0.3980
   chunk 102 optimal weight:    0.8980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
B4008 GLN
** B4314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.120196 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.086341 restraints weight = 18097.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.087686 restraints weight = 10299.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.088558 restraints weight = 8028.373|
|-----------------------------------------------------------------------------|
r_work (final): 0.3185
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7953
moved from start:          0.2165

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   9420  Z= 0.143
  Angle     :  0.651  11.039  12826  Z= 0.328
  Chirality :  0.046   0.225   1374
  Planarity :  0.004   0.044   1664
  Dihedral  :  6.961  58.814   1604
  Min Nonbonded Distance : 2.185

Molprobity Statistics.
  All-atom Clashscore : 7.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.30 %
    Favored  : 91.70 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 18.03 %
    Favored  : 78.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.40 (0.25), residues: 1132
  helix: -4.47 (0.59), residues: 25
  sheet: -1.07 (0.32), residues: 265
  loop : -0.77 (0.22), residues: 842

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A4297 
 HIS   0.004   0.001   HIS B4221 
 PHE   0.009   0.001   PHE A4323 
 TYR   0.018   0.001   TYR A4079 
 ARG   0.005   0.000   ARG B4067 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00585 (    6)
  link_NAG-ASN         : angle       2.21746 (   18)
  link_ALPHA1-6        : bond        0.00288 (    2)
  link_ALPHA1-6        : angle       1.72690 (    6)
  link_BETA1-4         : bond        0.00629 (    6)
  link_BETA1-4         : angle       1.66955 (   18)
  link_ALPHA1-3        : bond        0.01681 (    2)
  link_ALPHA1-3        : angle       2.11292 (    6)
  hydrogen bonds       : bond        0.02985 (  214)
  hydrogen bonds       : angle       6.58384 (  516)
  SS BOND              : bond        0.00264 (   42)
  SS BOND              : angle       0.90292 (   84)
  link_BETA1-3         : bond        0.00954 (    2)
  link_BETA1-3         : angle       3.68396 (    6)
  covalent geometry    : bond        0.00327 ( 9360)
  covalent geometry    : angle       0.63461 (12688)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2760.87 seconds
wall clock time: 49 minutes 12.58 seconds (2952.58 seconds total)