Starting phenix.real_space_refine
on Tue Jun 10 16:27:55 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9jwg_61852/06_2025/9jwg_61852_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9jwg_61852/06_2025/9jwg_61852.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.47
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9jwg_61852/06_2025/9jwg_61852.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9jwg_61852/06_2025/9jwg_61852.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9jwg_61852/06_2025/9jwg_61852_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9jwg_61852/06_2025/9jwg_61852_neut.cif"
  }
  resolution = 3.47
  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=  -0.001 sd=   0.048
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      64      5.16       5
     C    7421      2.51       5
     N    2024      2.21       5
     O    2138      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 27 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 11647
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "B"
      Number of atoms: 1872
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 235, 1872
          Classifications: {'peptide': 235}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 23, 'TRANS': 211}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 3
    Chain: "A"
      Number of atoms: 9775
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1221, 9775
          Classifications: {'peptide': 1221}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 62, 'TRANS': 1158}
          Chain breaks: 6
          Unresolved non-hydrogen bonds: 11
          Unresolved non-hydrogen angles: 13
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
  Time building chain proxies: 7.76, per 1000 atoms: 0.67
  Number of scatterers: 11647
  At special positions: 0
  Unit cell: (133.985, 124.49, 112.885, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      64     16.00
     O    2138      8.00
     N    2024      7.00
     C    7421      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.76
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  2880 Ramachandran restraints generated.
    1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2802

  Finding SS restraints...
    Secondary structure from input PDB file:
      68 helices and 3 sheets defined
      56.2% alpha, 2.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.34
  Creating SS restraints...
    Processing helix  chain 'B' and resid 38 through 51
    Processing helix  chain 'B' and resid 57 through 72
    Processing helix  chain 'B' and resid 227 through 233
      removed outlier: 3.846A  pdb=" N   LEU B 233 " --> pdb=" O   VAL B 230 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 247 through 259
    Processing helix  chain 'A' and resid 3711 through 3730
      removed outlier: 4.097A  pdb=" N   VAL A3724 " --> pdb=" O   GLU A3720 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   TYR A3728 " --> pdb=" O   VAL A3724 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   THR A3730 " --> pdb=" O   ALA A3726 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3731 through 3733
      No H-bonds generated for 'chain 'A' and resid 3731 through 3733'
    Processing helix  chain 'A' and resid 3734 through 3746
      removed outlier: 4.249A  pdb=" N   VAL A3740 " --> pdb=" O   PRO A3736 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3746 through 3754
    Processing helix  chain 'A' and resid 3758 through 3774
      removed outlier: 4.166A  pdb=" N   LYS A3769 " --> pdb=" O   GLN A3765 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   ILE A3772 " --> pdb=" O   LEU A3768 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3780 through 3801
      removed outlier: 4.082A  pdb=" N   ALA A3801 " --> pdb=" O   LYS A3797 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3810 through 3821
      removed outlier: 4.186A  pdb=" N   VAL A3814 " --> pdb=" O   SER A3810 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   HIS A3815 " --> pdb=" O   LEU A3811 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3821 through 3835
      removed outlier: 3.908A  pdb=" N   LEU A3825 " --> pdb=" O   PHE A3821 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   TYR A3835 " --> pdb=" O   ILE A3831 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3836 through 3844
      removed outlier: 3.659A  pdb=" N   HIS A3840 " --> pdb=" O   PRO A3836 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   GLU A3844 " --> pdb=" O   HIS A3840 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3857 through 3873
    Processing helix  chain 'A' and resid 3879 through 3898
      removed outlier: 4.519A  pdb=" N   MET A3891 " --> pdb=" O   LYS A3887 " (cutoff:3.500A)
      Proline residue:  A3892  - end of helix
    Processing helix  chain 'A' and resid 3899 through 3902
      removed outlier: 3.615A  pdb=" N   MET A3902 " --> pdb=" O   ASP A3899 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 3899 through 3902'
    Processing helix  chain 'A' and resid 3906 through 3926
      removed outlier: 3.873A  pdb=" N   ARG A3922 " --> pdb=" O   ALA A3918 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3926 through 3933
    Processing helix  chain 'A' and resid 3936 through 3941
      removed outlier: 3.716A  pdb=" N   ARG A3940 " --> pdb=" O   GLY A3936 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3943 through 3961
      removed outlier: 4.181A  pdb=" N   LEU A3947 " --> pdb=" O   GLU A3943 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   HIS A3951 " --> pdb=" O   LEU A3947 " (cutoff:3.500A)
      removed outlier: 4.309A  pdb=" N   PHE A3953 " --> pdb=" O   THR A3949 " (cutoff:3.500A)
      removed outlier: 4.059A  pdb=" N   LEU A3954 " --> pdb=" O   GLU A3950 " (cutoff:3.500A)
      removed outlier: 4.152A  pdb=" N   GLU A3961 " --> pdb=" O   LYS A3957 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3967 through 3990
    Processing helix  chain 'A' and resid 4021 through 4027
    Processing helix  chain 'A' and resid 4048 through 4078
      removed outlier: 3.511A  pdb=" N   ALA A4054 " --> pdb=" O   ALA A4050 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 4085 through 4094
    Processing helix  chain 'A' and resid 4095 through 4097
      No H-bonds generated for 'chain 'A' and resid 4095 through 4097'
    Processing helix  chain 'A' and resid 4132 through 4140
      removed outlier: 3.834A  pdb=" N   LEU A4137 " --> pdb=" O   VAL A4133 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 4146 through 4159
      removed outlier: 3.628A  pdb=" N   LYS A4159 " --> pdb=" O   THR A4155 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 4170 through 4186
      removed outlier: 3.595A  pdb=" N   ASN A4176 " --> pdb=" O   MET A4172 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   THR A4186 " --> pdb=" O   ILE A4182 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 4193 through 4204
      removed outlier: 3.967A  pdb=" N   GLU A4199 " --> pdb=" O   LEU A4195 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   GLY A4202 " --> pdb=" O   LEU A4198 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 4222 through 4244
    Processing helix  chain 'A' and resid 4252 through 4271
      removed outlier: 4.020A  pdb=" N   LYS A4256 " --> pdb=" O   MET A4252 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   LEU A4260 " --> pdb=" O   LYS A4256 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   GLU A4271 " --> pdb=" O   CYS A4267 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 4274 through 4287
    Processing helix  chain 'A' and resid 4288 through 4295
      removed outlier: 3.606A  pdb=" N   VAL A4292 " --> pdb=" O   GLY A4288 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 4310 through 4317
    Processing helix  chain 'A' and resid 4325 through 4329
      removed outlier: 4.103A  pdb=" N   VAL A4329 " --> pdb=" O   ARG A4326 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 4331 through 4348
      removed outlier: 3.875A  pdb=" N   LYS A4335 " --> pdb=" O   GLY A4331 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   ASP A4339 " --> pdb=" O   LYS A4335 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 4350 through 4360
      removed outlier: 3.961A  pdb=" N   LYS A4354 " --> pdb=" O   PRO A4350 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   THR A4355 " --> pdb=" O   LEU A4351 " (cutoff:3.500A)
      removed outlier: 4.150A  pdb=" N   LYS A4358 " --> pdb=" O   LYS A4354 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 4363 through 4379
    Processing helix  chain 'A' and resid 4380 through 4383
    Processing helix  chain 'A' and resid 4387 through 4391
    Processing helix  chain 'A' and resid 4393 through 4406
      removed outlier: 3.541A  pdb=" N   CYS A4397 " --> pdb=" O   THR A4393 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   ALA A4399 " --> pdb=" O   GLU A4395 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 4412 through 4424
    Processing helix  chain 'A' and resid 4441 through 4457
    Processing helix  chain 'A' and resid 4459 through 4461
      No H-bonds generated for 'chain 'A' and resid 4459 through 4461'
    Processing helix  chain 'A' and resid 4462 through 4469
    Processing helix  chain 'A' and resid 4575 through 4591
      removed outlier: 3.764A  pdb=" N   LEU A4585 " --> pdb=" O   LEU A4581 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   HIS A4587 " --> pdb=" O   ARG A4583 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 4592 through 4596
      removed outlier: 3.570A  pdb=" N   GLN A4596 " --> pdb=" O   GLY A4593 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 4597 through 4603
      removed outlier: 3.858A  pdb=" N   LEU A4601 " --> pdb=" O   SER A4597 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 4614 through 4632
      removed outlier: 3.600A  pdb=" N   GLN A4618 " --> pdb=" O   GLY A4614 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 4634 through 4651
    Processing helix  chain 'A' and resid 4670 through 4686
      removed outlier: 3.877A  pdb=" N   ALA A4683 " --> pdb=" O   LYS A4679 " (cutoff:3.500A)
      removed outlier: 4.249A  pdb=" N   VAL A4684 " --> pdb=" O   GLU A4680 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 4687 through 4690
      removed outlier: 3.863A  pdb=" N   GLU A4690 " --> pdb=" O   PRO A4687 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 4687 through 4690'
    Processing helix  chain 'A' and resid 4694 through 4704
    Processing helix  chain 'A' and resid 4712 through 4718
    Processing helix  chain 'A' and resid 4733 through 4737
    Processing helix  chain 'A' and resid 4748 through 4759
      removed outlier: 3.540A  pdb=" N   HIS A4754 " --> pdb=" O   GLU A4750 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   GLU A4757 " --> pdb=" O   GLN A4753 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 4765 through 4773
    Processing helix  chain 'A' and resid 4780 through 4782
      No H-bonds generated for 'chain 'A' and resid 4780 through 4782'
    Processing helix  chain 'A' and resid 4783 through 4788
    Processing helix  chain 'A' and resid 4789 through 4798
      removed outlier: 4.203A  pdb=" N   VAL A4795 " --> pdb=" O   GLN A4791 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 4808 through 4816
      removed outlier: 3.640A  pdb=" N   HIS A4816 " --> pdb=" O   PHE A4812 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 4819 through 4838
    Processing helix  chain 'A' and resid 4839 through 4847
      removed outlier: 3.652A  pdb=" N   GLU A4844 " --> pdb=" O   ARG A4840 " (cutoff:3.500A)
      removed outlier: 4.308A  pdb=" N   THR A4845 " --> pdb=" O   ARG A4841 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 4874 through 4876
      No H-bonds generated for 'chain 'A' and resid 4874 through 4876'
    Processing helix  chain 'A' and resid 4877 through 4899
      removed outlier: 3.576A  pdb=" N   THR A4881 " --> pdb=" O   GLY A4877 " (cutoff:3.500A)
      removed outlier: 4.065A  pdb=" N   VAL A4884 " --> pdb=" O   ALA A4880 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 4916 through 4920
      removed outlier: 3.880A  pdb=" N   VAL A4920 " --> pdb=" O   GLU A4917 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 4928 through 4936
    Processing helix  chain 'A' and resid 4952 through 4962
    Processing sheet with id=AA1, first strand: chain 'B' and resid 75 through 77
      removed outlier: 6.423A  pdb=" N   LEU B  76 " --> pdb=" O   GLU B  97 " (cutoff:3.500A)
      removed outlier: 6.995A  pdb=" N   VAL B 239 " --> pdb=" O   PHE B 269 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 4129 through 4130
    Processing sheet with id=AA3, first strand: chain 'A' and resid 4910 through 4911
      removed outlier: 6.591A  pdb=" N   VAL A4910 " --> pdb=" O   LEU A4971 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3

    519 hydrogen bonds defined for protein.
    1521 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: 3.46

  Time building geometry restraints manager: 3.29 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 1954
        1.30 -     1.42: 2891
        1.42 -     1.55: 6957
        1.55 -     1.68: 3
        1.68 -     1.81: 89
  Bond restraints: 11894
  Sorted by residual:
  bond pdb=" CA  LEU A3934 "
       pdb=" C   LEU A3934 "
    ideal  model  delta    sigma   weight residual
    1.522  1.361  0.161 1.37e-02 5.33e+03 1.38e+02
  bond pdb=" CA  PHE A3929 "
       pdb=" C   PHE A3929 "
    ideal  model  delta    sigma   weight residual
    1.524  1.372  0.152 1.37e-02 5.33e+03 1.23e+02
  bond pdb=" CA  THR A3926 "
       pdb=" C   THR A3926 "
    ideal  model  delta    sigma   weight residual
    1.522  1.386  0.136 1.40e-02 5.10e+03 9.48e+01
  bond pdb=" CA  GLU A4926 "
       pdb=" C   GLU A4926 "
    ideal  model  delta    sigma   weight residual
    1.523  1.402  0.120 1.35e-02 5.49e+03 7.96e+01
  bond pdb=" CA  LEU A3935 "
       pdb=" C   LEU A3935 "
    ideal  model  delta    sigma   weight residual
    1.522  1.412  0.109 1.40e-02 5.10e+03 6.07e+01
  ... (remaining 11889 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.97: 15783
        2.97 -     5.93: 271
        5.93 -     8.90: 56
        8.90 -    11.87: 11
       11.87 -    14.84: 6
  Bond angle restraints: 16127
  Sorted by residual:
  angle pdb=" N   SER A3939 "
        pdb=" CA  SER A3939 "
        pdb=" C   SER A3939 "
      ideal   model   delta    sigma   weight residual
     111.36   96.52   14.84 1.09e+00 8.42e-01 1.85e+02
  angle pdb=" N   PHE A3929 "
        pdb=" CA  PHE A3929 "
        pdb=" C   PHE A3929 "
      ideal   model   delta    sigma   weight residual
     112.45   99.42   13.03 1.39e+00 5.18e-01 8.79e+01
  angle pdb=" N   LEU A3935 "
        pdb=" CA  LEU A3935 "
        pdb=" C   LEU A3935 "
      ideal   model   delta    sigma   weight residual
     112.90  101.46   11.44 1.31e+00 5.83e-01 7.63e+01
  angle pdb=" N   VAL A4925 "
        pdb=" CA  VAL A4925 "
        pdb=" C   VAL A4925 "
      ideal   model   delta    sigma   weight residual
     110.62  119.22   -8.60 1.02e+00 9.61e-01 7.12e+01
  angle pdb=" N   GLU A3938 "
        pdb=" CA  GLU A3938 "
        pdb=" CB  GLU A3938 "
      ideal   model   delta    sigma   weight residual
     110.73   98.50   12.23 1.55e+00 4.16e-01 6.22e+01
  ... (remaining 16122 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.88: 6336
       17.88 -    35.75: 741
       35.75 -    53.63: 182
       53.63 -    71.51: 32
       71.51 -    89.39: 16
  Dihedral angle restraints: 7307
    sinusoidal: 3025
      harmonic: 4282
  Sorted by residual:
  dihedral pdb=" N   ALA A3985 "
           pdb=" C   ALA A3985 "
           pdb=" CA  ALA A3985 "
           pdb=" CB  ALA A3985 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.90  139.57  -16.67     0      2.50e+00 1.60e-01 4.45e+01
  dihedral pdb=" CA  ILE A4268 "
           pdb=" C   ILE A4268 "
           pdb=" N   ARG A4269 "
           pdb=" CA  ARG A4269 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  148.87   31.13     0      5.00e+00 4.00e-02 3.88e+01
  dihedral pdb=" C   ALA A3985 "
           pdb=" N   ALA A3985 "
           pdb=" CA  ALA A3985 "
           pdb=" CB  ALA A3985 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -137.83   15.23     0      2.50e+00 1.60e-01 3.71e+01
  ... (remaining 7304 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.161: 1801
       0.161 -    0.322: 30
       0.322 -    0.482: 6
       0.482 -    0.643: 1
       0.643 -    0.804: 2
  Chirality restraints: 1840
  Sorted by residual:
  chirality pdb=" CA  ALA A3985 "
            pdb=" N   ALA A3985 "
            pdb=" C   ALA A3985 "
            pdb=" CB  ALA A3985 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    1.68    0.80 2.00e-01 2.50e+01 1.62e+01
  chirality pdb=" CA  ASN A4936 "
            pdb=" N   ASN A4936 "
            pdb=" C   ASN A4936 "
            pdb=" CB  ASN A4936 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.86    0.65 2.00e-01 2.50e+01 1.07e+01
  chirality pdb=" CA  VAL A4925 "
            pdb=" N   VAL A4925 "
            pdb=" C   VAL A4925 "
            pdb=" CB  VAL A4925 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    1.88    0.57 2.00e-01 2.50e+01 7.98e+00
  ... (remaining 1837 not shown)

  Planarity restraints: 2080
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU A3972 "   -0.048 2.00e-02 2.50e+03   9.24e-02 8.54e+01
        pdb=" C   GLU A3972 "    0.160 2.00e-02 2.50e+03
        pdb=" O   GLU A3972 "   -0.059 2.00e-02 2.50e+03
        pdb=" N   ALA A3973 "   -0.053 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A4930 "    0.079 5.00e-02 4.00e+02   1.19e-01 2.26e+01
        pdb=" N   PRO A4931 "   -0.206 5.00e-02 4.00e+02
        pdb=" CA  PRO A4931 "    0.060 5.00e-02 4.00e+02
        pdb=" CD  PRO A4931 "    0.067 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A3988 "    0.023 2.00e-02 2.50e+03   4.52e-02 2.05e+01
        pdb=" C   THR A3988 "   -0.078 2.00e-02 2.50e+03
        pdb=" O   THR A3988 "    0.028 2.00e-02 2.50e+03
        pdb=" N   LEU A3989 "    0.027 2.00e-02 2.50e+03
  ... (remaining 2077 not shown)

  Histogram of nonbonded interaction distances:
        2.01 -     2.59: 131
        2.59 -     3.17: 10068
        3.17 -     3.74: 18276
        3.74 -     4.32: 24553
        4.32 -     4.90: 39582
  Nonbonded interactions: 92610
  Sorted by model distance:
  nonbonded pdb=" N   GLU A3938 "
            pdb=" CG  GLU A3938 "
     model   vdw
     2.010 2.816
  nonbonded pdb=" O   ASP A4440 "
            pdb=" OG1 THR A4444 "
     model   vdw
     2.039 3.040
  nonbonded pdb=" O   ALA A4023 "
            pdb=" OG  SER A4027 "
     model   vdw
     2.136 3.040
  nonbonded pdb=" OG1 THR A4362 "
            pdb=" OE1 GLN A4367 "
     model   vdw
     2.187 3.040
  nonbonded pdb=" OD2 ASP A3964 "
            pdb=" OG1 THR A3967 "
     model   vdw
     2.204 3.040
  ... (remaining 92605 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             7.110
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.460
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     28.690
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.840
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.440
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7601
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      :  0.007   0.161  11894  Z= 0.501
  Angle     :  0.991  14.837  16127  Z= 0.598
  Chirality :  0.063   0.804   1840
  Planarity :  0.007   0.119   2080
  Dihedral  : 16.672  89.386   4505
  Min Nonbonded Distance : 2.010

Molprobity Statistics.
  All-atom Clashscore : 14.53
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  :  8.96 %
    Favored  : 90.62 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 16.53 %
    Favored  : 81.79 %
  Cbeta Deviations :  0.57 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.15 %

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: -1.58 (0.22), residues: 1440
  helix: -0.18 (0.20), residues: 741
  sheet: -2.17 (0.75), residues: 52
  loop : -1.98 (0.24), residues: 647

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A3723 
 HIS   0.008   0.001   HIS A3932 
 PHE   0.022   0.002   PHE A4951 
 TYR   0.019   0.002   TYR A4923 
 ARG   0.006   0.000   ARG A4970 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17466 (  519)
  hydrogen bonds       : angle       6.91848 ( 1521)
  covalent geometry    : bond        0.00744 (11894)
  covalent geometry    : angle       0.99146 (16127)

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

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

  2880 Ramachandran restraints generated.
    1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2880 Ramachandran restraints generated.
    1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 147
  time to evaluate  : 1.435 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  172 GLU cc_start: 0.4859 (tm-30) cc_final: 0.3656 (tt0)
REVERT: A 3940 ARG cc_start: 0.8808 (OUTLIER) cc_final: 0.7446 (tmt170)
REVERT: A 4866 PHE cc_start: 0.8840 (t80) cc_final: 0.8582 (t80)
REVERT: A 4926 GLU cc_start: 0.7875 (tt0) cc_final: 0.7655 (tt0)
REVERT: A 4952 ASP cc_start: 0.7562 (t0) cc_final: 0.7183 (t70)
REVERT: A 4974 LYS cc_start: 0.6007 (mtmm) cc_final: 0.5756 (mttt)
  outliers start: 22
  outliers final: 9
  residues processed: 164
  average time/residue: 0.2485
  time to fit residues: 59.2942
Evaluate side-chains
  139 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 129
  time to evaluate  : 1.465 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  219 MET
Chi-restraints excluded: chain A residue 3933 VAL
Chi-restraints excluded: chain A residue 3935 LEU
Chi-restraints excluded: chain A residue 3938 GLU
Chi-restraints excluded: chain A residue 3940 ARG
Chi-restraints excluded: chain A residue 3981 CYS
Chi-restraints excluded: chain A residue 4061 PHE
Chi-restraints excluded: chain A residue 4284 SER
Chi-restraints excluded: chain A residue 4800 ASN
Chi-restraints excluded: chain A residue 4924 GLU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 122 optimal weight:    0.7980
   chunk 109 optimal weight:    0.8980
   chunk 60 optimal weight:    0.6980
   chunk 37 optimal weight:    3.9990
   chunk 74 optimal weight:    0.5980
   chunk 58 optimal weight:    1.9990
   chunk 113 optimal weight:    5.9990
   chunk 43 optimal weight:    0.8980
   chunk 69 optimal weight:    0.5980
   chunk 84 optimal weight:    1.9990
   chunk 131 optimal weight:    1.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A3727 GLN
A4016 HIS
A4063 GLN
A4121 ASN
** A4587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A4654 HIS
** A4936 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A4959 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4264 r_free = 0.4264 target = 0.165158 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.115371 restraints weight = 22000.598|
|-----------------------------------------------------------------------------|
r_work (start): 0.3638 rms_B_bonded: 3.83
r_work: 0.3470 rms_B_bonded: 4.77 restraints_weight: 0.5000
r_work (final): 0.3470
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7854
moved from start:          0.0940

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058  11894  Z= 0.158
  Angle     :  0.704  10.028  16127  Z= 0.352
  Chirality :  0.043   0.315   1840
  Planarity :  0.006   0.056   2080
  Dihedral  :  6.300  56.951   1582
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 10.90
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  8.89 %
    Favored  : 90.97 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 15.99 %
    Favored  : 81.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.15 %

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 (0.22), residues: 1440
  helix: -0.04 (0.19), residues: 764
  sheet: -1.96 (0.79), residues: 48
  loop : -1.93 (0.24), residues: 628

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A3723 
 HIS   0.008   0.001   HIS A4113 
 PHE   0.019   0.002   PHE A4812 
 TYR   0.013   0.001   TYR A3818 
 ARG   0.006   0.000   ARG A4970 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05283 (  519)
  hydrogen bonds       : angle       5.02308 ( 1521)
  covalent geometry    : bond        0.00365 (11894)
  covalent geometry    : angle       0.70380 (16127)

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

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

  2880 Ramachandran restraints generated.
    1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2880 Ramachandran restraints generated.
    1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 146
  time to evaluate  : 1.278 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  172 GLU cc_start: 0.5404 (tm-30) cc_final: 0.4377 (mt-10)
REVERT: A 3919 GLN cc_start: 0.8930 (mt0) cc_final: 0.8698 (mp10)
REVERT: A 3940 ARG cc_start: 0.8859 (OUTLIER) cc_final: 0.7855 (tmt170)
REVERT: A 3964 ASP cc_start: 0.8363 (t70) cc_final: 0.8070 (t0)
REVERT: A 4327 TYR cc_start: 0.8728 (m-80) cc_final: 0.8411 (m-80)
REVERT: A 4673 MET cc_start: 0.8127 (mmt) cc_final: 0.7921 (mmt)
REVERT: A 4866 PHE cc_start: 0.8941 (t80) cc_final: 0.8540 (t80)
  outliers start: 33
  outliers final: 12
  residues processed: 168
  average time/residue: 0.2244
  time to fit residues: 55.3575
Evaluate side-chains
  142 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 129
  time to evaluate  : 1.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  219 MET
Chi-restraints excluded: chain A residue 3774 LEU
Chi-restraints excluded: chain A residue 3898 SER
Chi-restraints excluded: chain A residue 3933 VAL
Chi-restraints excluded: chain A residue 3940 ARG
Chi-restraints excluded: chain A residue 3983 GLU
Chi-restraints excluded: chain A residue 4021 LEU
Chi-restraints excluded: chain A residue 4058 HIS
Chi-restraints excluded: chain A residue 4073 VAL
Chi-restraints excluded: chain A residue 4164 THR
Chi-restraints excluded: chain A residue 4468 LEU
Chi-restraints excluded: chain A residue 4609 VAL
Chi-restraints excluded: chain A residue 4843 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 35 optimal weight:    1.9990
   chunk 137 optimal weight:    2.9990
   chunk 123 optimal weight:    0.9980
   chunk 98 optimal weight:    1.9990
   chunk 107 optimal weight:    0.8980
   chunk 129 optimal weight:    0.9990
   chunk 54 optimal weight:    0.0570
   chunk 75 optimal weight:    6.9990
   chunk 33 optimal weight:    6.9990
   chunk 63 optimal weight:    1.9990
   chunk 71 optimal weight:    0.8980
   overall best weight:    0.7700

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

Flipped N/Q/H residues before XYZ refinement:
A3727 GLN
** A4587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A4654 HIS
** A4936 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A4959 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4253 r_free = 0.4253 target = 0.164291 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.115386 restraints weight = 22359.870|
|-----------------------------------------------------------------------------|
r_work (start): 0.3627 rms_B_bonded: 3.74
r_work: 0.3457 rms_B_bonded: 4.67 restraints_weight: 0.5000
r_work (final): 0.3457
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7848
moved from start:          0.1380

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  11894  Z= 0.147
  Angle     :  0.664   9.646  16127  Z= 0.333
  Chirality :  0.043   0.203   1840
  Planarity :  0.005   0.051   2080
  Dihedral  :  5.662  56.002   1568
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 11.24
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  8.40 %
    Favored  : 91.46 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 16.68 %
    Favored  : 80.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.15 %

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: -1.10 (0.22), residues: 1440
  helix:  0.28 (0.19), residues: 755
  sheet: -1.93 (0.80), residues: 48
  loop : -1.89 (0.24), residues: 637

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A3792 
 HIS   0.008   0.001   HIS A4113 
 PHE   0.022   0.002   PHE A3751 
 TYR   0.013   0.001   TYR A3818 
 ARG   0.005   0.000   ARG A4970 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04317 (  519)
  hydrogen bonds       : angle       4.60233 ( 1521)
  covalent geometry    : bond        0.00348 (11894)
  covalent geometry    : angle       0.66378 (16127)

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

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

  2880 Ramachandran restraints generated.
    1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2880 Ramachandran restraints generated.
    1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 153
  time to evaluate  : 1.450 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  172 GLU cc_start: 0.5417 (tm-30) cc_final: 0.4403 (mt-10)
REVERT: A 3964 ASP cc_start: 0.8375 (t70) cc_final: 0.8030 (t0)
REVERT: A 4327 TYR cc_start: 0.8766 (m-80) cc_final: 0.8426 (m-80)
REVERT: A 4673 MET cc_start: 0.8136 (mmt) cc_final: 0.7680 (mmt)
REVERT: A 4808 SER cc_start: 0.8889 (t) cc_final: 0.8682 (t)
REVERT: A 4855 TYR cc_start: 0.7534 (m-80) cc_final: 0.6762 (m-80)
REVERT: A 4927 ARG cc_start: 0.8073 (ttp80) cc_final: 0.7736 (ttp80)
REVERT: A 4945 ARG cc_start: 0.6816 (OUTLIER) cc_final: 0.5773 (mpp80)
  outliers start: 36
  outliers final: 22
  residues processed: 177
  average time/residue: 0.2517
  time to fit residues: 64.3166
Evaluate side-chains
  156 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 133
  time to evaluate  : 1.476 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  219 MET
Chi-restraints excluded: chain A residue 3768 LEU
Chi-restraints excluded: chain A residue 3774 LEU
Chi-restraints excluded: chain A residue 3869 MET
Chi-restraints excluded: chain A residue 3935 LEU
Chi-restraints excluded: chain A residue 3940 ARG
Chi-restraints excluded: chain A residue 3967 THR
Chi-restraints excluded: chain A residue 4021 LEU
Chi-restraints excluded: chain A residue 4058 HIS
Chi-restraints excluded: chain A residue 4073 VAL
Chi-restraints excluded: chain A residue 4164 THR
Chi-restraints excluded: chain A residue 4195 LEU
Chi-restraints excluded: chain A residue 4324 MET
Chi-restraints excluded: chain A residue 4609 VAL
Chi-restraints excluded: chain A residue 4619 HIS
Chi-restraints excluded: chain A residue 4778 LEU
Chi-restraints excluded: chain A residue 4790 LEU
Chi-restraints excluded: chain A residue 4800 ASN
Chi-restraints excluded: chain A residue 4838 LYS
Chi-restraints excluded: chain A residue 4843 LEU
Chi-restraints excluded: chain A residue 4894 ILE
Chi-restraints excluded: chain A residue 4941 VAL
Chi-restraints excluded: chain A residue 4945 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 71 optimal weight:    2.9990
   chunk 16 optimal weight:    9.9990
   chunk 10 optimal weight:   30.0000
   chunk 92 optimal weight:    0.1980
   chunk 123 optimal weight:    1.9990
   chunk 1 optimal weight:   10.0000
   chunk 141 optimal weight:    0.8980
   chunk 61 optimal weight:    0.0030
   chunk 58 optimal weight:    4.9990
   chunk 18 optimal weight:    6.9990
   chunk 124 optimal weight:    0.7980
   overall best weight:    0.7792

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

Flipped N/Q/H residues before XYZ refinement:
A3727 GLN
A3919 GLN
A3945 GLN
** A4587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A4654 HIS
** A4936 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A4959 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4251 r_free = 0.4251 target = 0.164198 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.114858 restraints weight = 22160.992|
|-----------------------------------------------------------------------------|
r_work (start): 0.3619 rms_B_bonded: 3.82
r_work: 0.3451 rms_B_bonded: 4.71 restraints_weight: 0.5000
r_work (final): 0.3451
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7862
moved from start:          0.1653

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053  11894  Z= 0.147
  Angle     :  0.661  11.213  16127  Z= 0.326
  Chirality :  0.043   0.284   1840
  Planarity :  0.005   0.054   2080
  Dihedral  :  5.547  55.078   1567
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 10.94
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  8.47 %
    Favored  : 91.39 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 18.52 %
    Favored  : 78.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.15 %

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: -1.00 (0.22), residues: 1440
  helix:  0.36 (0.19), residues: 761
  sheet: -1.87 (0.82), residues: 48
  loop : -1.85 (0.24), residues: 631

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A3792 
 HIS   0.006   0.001   HIS A4113 
 PHE   0.031   0.002   PHE A4306 
 TYR   0.012   0.001   TYR A3818 
 ARG   0.004   0.000   ARG A4970 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04025 (  519)
  hydrogen bonds       : angle       4.45007 ( 1521)
  covalent geometry    : bond        0.00349 (11894)
  covalent geometry    : angle       0.66103 (16127)

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

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

  2880 Ramachandran restraints generated.
    1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2880 Ramachandran restraints generated.
    1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 141
  time to evaluate  : 1.259 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  172 GLU cc_start: 0.5518 (tm-30) cc_final: 0.4635 (mt-10)
REVERT: A 3964 ASP cc_start: 0.8341 (t70) cc_final: 0.7951 (t0)
REVERT: A 3972 GLU cc_start: 0.8250 (mp0) cc_final: 0.7995 (tp30)
REVERT: A 4064 MET cc_start: 0.7954 (mpp) cc_final: 0.7707 (mpp)
REVERT: A 4189 TYR cc_start: 0.6898 (OUTLIER) cc_final: 0.6486 (m-10)
REVERT: A 4327 TYR cc_start: 0.8762 (m-80) cc_final: 0.8446 (m-80)
REVERT: A 4644 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8582 (mt)
REVERT: A 4673 MET cc_start: 0.8218 (mmt) cc_final: 0.7622 (mmt)
REVERT: A 4808 SER cc_start: 0.8907 (t) cc_final: 0.8650 (t)
REVERT: A 4855 TYR cc_start: 0.7509 (m-80) cc_final: 0.7171 (m-80)
REVERT: A 4945 ARG cc_start: 0.6876 (OUTLIER) cc_final: 0.5818 (mpp80)
REVERT: A 4952 ASP cc_start: 0.7746 (t0) cc_final: 0.7141 (t0)
  outliers start: 41
  outliers final: 24
  residues processed: 169
  average time/residue: 0.2712
  time to fit residues: 66.2660
Evaluate side-chains
  158 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 131
  time to evaluate  : 1.611 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  182 ARG
Chi-restraints excluded: chain B residue  219 MET
Chi-restraints excluded: chain A residue 3774 LEU
Chi-restraints excluded: chain A residue 3869 MET
Chi-restraints excluded: chain A residue 3899 ASP
Chi-restraints excluded: chain A residue 3940 ARG
Chi-restraints excluded: chain A residue 3967 THR
Chi-restraints excluded: chain A residue 4021 LEU
Chi-restraints excluded: chain A residue 4057 LYS
Chi-restraints excluded: chain A residue 4058 HIS
Chi-restraints excluded: chain A residue 4073 VAL
Chi-restraints excluded: chain A residue 4138 LEU
Chi-restraints excluded: chain A residue 4164 THR
Chi-restraints excluded: chain A residue 4189 TYR
Chi-restraints excluded: chain A residue 4195 LEU
Chi-restraints excluded: chain A residue 4609 VAL
Chi-restraints excluded: chain A residue 4619 HIS
Chi-restraints excluded: chain A residue 4644 LEU
Chi-restraints excluded: chain A residue 4778 LEU
Chi-restraints excluded: chain A residue 4790 LEU
Chi-restraints excluded: chain A residue 4800 ASN
Chi-restraints excluded: chain A residue 4801 VAL
Chi-restraints excluded: chain A residue 4838 LYS
Chi-restraints excluded: chain A residue 4894 ILE
Chi-restraints excluded: chain A residue 4916 THR
Chi-restraints excluded: chain A residue 4941 VAL
Chi-restraints excluded: chain A residue 4945 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 21 optimal weight:    4.9990
   chunk 32 optimal weight:    2.9990
   chunk 110 optimal weight:    0.6980
   chunk 142 optimal weight:    0.9980
   chunk 34 optimal weight:    0.8980
   chunk 40 optimal weight:    0.9980
   chunk 24 optimal weight:    0.6980
   chunk 81 optimal weight:    0.0050
   chunk 53 optimal weight:   10.0000
   chunk 19 optimal weight:   20.0000
   chunk 113 optimal weight:    4.9990
   overall best weight:    0.6594

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

Flipped N/Q/H residues before XYZ refinement:
A3727 GLN
** A3827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A4587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A4654 HIS
** A4936 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A4959 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4258 r_free = 0.4258 target = 0.164852 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.115499 restraints weight = 22070.206|
|-----------------------------------------------------------------------------|
r_work (start): 0.3631 rms_B_bonded: 3.70
r_work: 0.3463 rms_B_bonded: 4.65 restraints_weight: 0.5000
r_work (final): 0.3463
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7856
moved from start:          0.1845

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053  11894  Z= 0.135
  Angle     :  0.646  13.549  16127  Z= 0.319
  Chirality :  0.043   0.413   1840
  Planarity :  0.005   0.052   2080
  Dihedral  :  5.425  51.398   1567
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 10.90
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  8.47 %
    Favored  : 91.39 %
  Rotamer:
    Outliers :  4.21 %
    Allowed  : 18.52 %
    Favored  : 77.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.15 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.95 (0.22), residues: 1440
  helix:  0.38 (0.19), residues: 769
  sheet: -1.95 (0.81), residues: 49
  loop : -1.82 (0.24), residues: 622

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A3792 
 HIS   0.005   0.001   HIS A4113 
 PHE   0.026   0.002   PHE A4812 
 TYR   0.012   0.001   TYR A4896 
 ARG   0.004   0.000   ARG A4970 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03826 (  519)
  hydrogen bonds       : angle       4.34829 ( 1521)
  covalent geometry    : bond        0.00322 (11894)
  covalent geometry    : angle       0.64590 (16127)

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

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

  2880 Ramachandran restraints generated.
    1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2880 Ramachandran restraints generated.
    1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 136
  time to evaluate  : 1.600 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  112 MET cc_start: 0.2193 (OUTLIER) cc_final: 0.1734 (mpt)
REVERT: B  172 GLU cc_start: 0.5544 (tm-30) cc_final: 0.4661 (mt-10)
REVERT: A 3919 GLN cc_start: 0.8890 (OUTLIER) cc_final: 0.8550 (mp10)
REVERT: A 3964 ASP cc_start: 0.8307 (t70) cc_final: 0.7932 (t0)
REVERT: A 3972 GLU cc_start: 0.8221 (mp0) cc_final: 0.7977 (tp30)
REVERT: A 4064 MET cc_start: 0.7999 (mpp) cc_final: 0.6891 (mpp)
REVERT: A 4068 PHE cc_start: 0.8146 (m-10) cc_final: 0.7741 (m-10)
REVERT: A 4189 TYR cc_start: 0.6761 (OUTLIER) cc_final: 0.6424 (m-10)
REVERT: A 4256 LYS cc_start: 0.8034 (OUTLIER) cc_final: 0.7800 (tttp)
REVERT: A 4327 TYR cc_start: 0.8751 (m-80) cc_final: 0.8447 (m-80)
REVERT: A 4644 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8576 (mt)
REVERT: A 4673 MET cc_start: 0.8247 (mmt) cc_final: 0.7563 (mmt)
REVERT: A 4802 GLN cc_start: 0.8037 (OUTLIER) cc_final: 0.6736 (tp40)
REVERT: A 4855 TYR cc_start: 0.7493 (m-80) cc_final: 0.6611 (m-80)
REVERT: A 4927 ARG cc_start: 0.8130 (ttp80) cc_final: 0.7614 (ttp80)
REVERT: A 4945 ARG cc_start: 0.6933 (OUTLIER) cc_final: 0.5974 (mpp80)
REVERT: A 4952 ASP cc_start: 0.7655 (t0) cc_final: 0.7021 (t0)
  outliers start: 55
  outliers final: 33
  residues processed: 173
  average time/residue: 0.2970
  time to fit residues: 74.5449
Evaluate side-chains
  169 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 129
  time to evaluate  : 1.424 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  112 MET
Chi-restraints excluded: chain B residue  143 ILE
Chi-restraints excluded: chain B residue  182 ARG
Chi-restraints excluded: chain B residue  219 MET
Chi-restraints excluded: chain A residue 3768 LEU
Chi-restraints excluded: chain A residue 3774 LEU
Chi-restraints excluded: chain A residue 3869 MET
Chi-restraints excluded: chain A residue 3891 MET
Chi-restraints excluded: chain A residue 3899 ASP
Chi-restraints excluded: chain A residue 3919 GLN
Chi-restraints excluded: chain A residue 3933 VAL
Chi-restraints excluded: chain A residue 3940 ARG
Chi-restraints excluded: chain A residue 3967 THR
Chi-restraints excluded: chain A residue 4021 LEU
Chi-restraints excluded: chain A residue 4051 HIS
Chi-restraints excluded: chain A residue 4057 LYS
Chi-restraints excluded: chain A residue 4058 HIS
Chi-restraints excluded: chain A residue 4061 PHE
Chi-restraints excluded: chain A residue 4073 VAL
Chi-restraints excluded: chain A residue 4138 LEU
Chi-restraints excluded: chain A residue 4164 THR
Chi-restraints excluded: chain A residue 4189 TYR
Chi-restraints excluded: chain A residue 4195 LEU
Chi-restraints excluded: chain A residue 4256 LYS
Chi-restraints excluded: chain A residue 4324 MET
Chi-restraints excluded: chain A residue 4362 THR
Chi-restraints excluded: chain A residue 4609 VAL
Chi-restraints excluded: chain A residue 4619 HIS
Chi-restraints excluded: chain A residue 4644 LEU
Chi-restraints excluded: chain A residue 4778 LEU
Chi-restraints excluded: chain A residue 4790 LEU
Chi-restraints excluded: chain A residue 4800 ASN
Chi-restraints excluded: chain A residue 4801 VAL
Chi-restraints excluded: chain A residue 4802 GLN
Chi-restraints excluded: chain A residue 4838 LYS
Chi-restraints excluded: chain A residue 4843 LEU
Chi-restraints excluded: chain A residue 4894 ILE
Chi-restraints excluded: chain A residue 4916 THR
Chi-restraints excluded: chain A residue 4941 VAL
Chi-restraints excluded: chain A residue 4945 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 107 optimal weight:    0.3980
   chunk 33 optimal weight:    5.9990
   chunk 7 optimal weight:    0.5980
   chunk 60 optimal weight:    2.9990
   chunk 92 optimal weight:    0.1980
   chunk 130 optimal weight:    2.9990
   chunk 75 optimal weight:    0.2980
   chunk 24 optimal weight:    0.1980
   chunk 84 optimal weight:    0.6980
   chunk 117 optimal weight:    0.9990
   chunk 43 optimal weight:    7.9990
   overall best weight:    0.3380

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

Flipped N/Q/H residues before XYZ refinement:
A3727 GLN
** A3827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A3945 GLN
** A4587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A4654 HIS
** A4936 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A4959 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4204 r_free = 0.4204 target = 0.163833 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.114706 restraints weight = 21728.475|
|-----------------------------------------------------------------------------|
r_work (start): 0.3575 rms_B_bonded: 3.82
r_work: 0.3405 rms_B_bonded: 4.73 restraints_weight: 0.5000
r_work (final): 0.3405
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7746
moved from start:          0.2063

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055  11894  Z= 0.112
  Angle     :  0.624  11.123  16127  Z= 0.308
  Chirality :  0.042   0.380   1840
  Planarity :  0.005   0.055   2080
  Dihedral  :  5.237  44.902   1567
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 10.17
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  8.40 %
    Favored  : 91.53 %
  Rotamer:
    Outliers :  4.21 %
    Allowed  : 18.90 %
    Favored  : 76.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.15 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.80 (0.22), residues: 1440
  helix:  0.55 (0.19), residues: 768
  sheet: -2.02 (0.80), residues: 51
  loop : -1.80 (0.24), residues: 621

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A3792 
 HIS   0.004   0.001   HIS A4113 
 PHE   0.024   0.001   PHE A4812 
 TYR   0.011   0.001   TYR A4896 
 ARG   0.003   0.000   ARG A4970 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03567 (  519)
  hydrogen bonds       : angle       4.17897 ( 1521)
  covalent geometry    : bond        0.00262 (11894)
  covalent geometry    : angle       0.62426 (16127)

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

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

  2880 Ramachandran restraints generated.
    1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2880 Ramachandran restraints generated.
    1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 147
  time to evaluate  : 1.554 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  172 GLU cc_start: 0.5580 (tm-30) cc_final: 0.4752 (mt-10)
REVERT: B  175 LEU cc_start: 0.2633 (tp) cc_final: 0.1979 (mp)
REVERT: A 3915 GLU cc_start: 0.8772 (tp30) cc_final: 0.8375 (tp30)
REVERT: A 3919 GLN cc_start: 0.8848 (OUTLIER) cc_final: 0.8123 (mp-120)
REVERT: A 3964 ASP cc_start: 0.8221 (t70) cc_final: 0.7773 (t0)
REVERT: A 3972 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7989 (tp30)
REVERT: A 4064 MET cc_start: 0.7936 (mpp) cc_final: 0.6836 (mpp)
REVERT: A 4068 PHE cc_start: 0.8266 (m-10) cc_final: 0.7841 (m-10)
REVERT: A 4256 LYS cc_start: 0.7950 (OUTLIER) cc_final: 0.7697 (tttp)
REVERT: A 4327 TYR cc_start: 0.8691 (m-80) cc_final: 0.8383 (m-80)
REVERT: A 4644 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8461 (mt)
REVERT: A 4673 MET cc_start: 0.8153 (mmt) cc_final: 0.7473 (mmt)
REVERT: A 4802 GLN cc_start: 0.8012 (OUTLIER) cc_final: 0.6718 (tp40)
REVERT: A 4855 TYR cc_start: 0.7407 (m-80) cc_final: 0.6407 (m-80)
REVERT: A 4927 ARG cc_start: 0.8143 (ttp80) cc_final: 0.7623 (ttp80)
REVERT: A 4945 ARG cc_start: 0.6714 (OUTLIER) cc_final: 0.5799 (mpp80)
REVERT: A 4952 ASP cc_start: 0.7611 (t0) cc_final: 0.6822 (t0)
  outliers start: 55
  outliers final: 33
  residues processed: 182
  average time/residue: 0.3553
  time to fit residues: 95.9070
Evaluate side-chains
  168 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 129
  time to evaluate  : 1.454 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  112 MET
Chi-restraints excluded: chain B residue  143 ILE
Chi-restraints excluded: chain B residue  182 ARG
Chi-restraints excluded: chain B residue  219 MET
Chi-restraints excluded: chain A residue 3728 TYR
Chi-restraints excluded: chain A residue 3730 THR
Chi-restraints excluded: chain A residue 3774 LEU
Chi-restraints excluded: chain A residue 3839 LEU
Chi-restraints excluded: chain A residue 3869 MET
Chi-restraints excluded: chain A residue 3891 MET
Chi-restraints excluded: chain A residue 3899 ASP
Chi-restraints excluded: chain A residue 3919 GLN
Chi-restraints excluded: chain A residue 3933 VAL
Chi-restraints excluded: chain A residue 3940 ARG
Chi-restraints excluded: chain A residue 3967 THR
Chi-restraints excluded: chain A residue 3972 GLU
Chi-restraints excluded: chain A residue 4021 LEU
Chi-restraints excluded: chain A residue 4051 HIS
Chi-restraints excluded: chain A residue 4057 LYS
Chi-restraints excluded: chain A residue 4058 HIS
Chi-restraints excluded: chain A residue 4061 PHE
Chi-restraints excluded: chain A residue 4089 ILE
Chi-restraints excluded: chain A residue 4138 LEU
Chi-restraints excluded: chain A residue 4164 THR
Chi-restraints excluded: chain A residue 4195 LEU
Chi-restraints excluded: chain A residue 4256 LYS
Chi-restraints excluded: chain A residue 4324 MET
Chi-restraints excluded: chain A residue 4351 LEU
Chi-restraints excluded: chain A residue 4609 VAL
Chi-restraints excluded: chain A residue 4619 HIS
Chi-restraints excluded: chain A residue 4644 LEU
Chi-restraints excluded: chain A residue 4790 LEU
Chi-restraints excluded: chain A residue 4800 ASN
Chi-restraints excluded: chain A residue 4801 VAL
Chi-restraints excluded: chain A residue 4802 GLN
Chi-restraints excluded: chain A residue 4838 LYS
Chi-restraints excluded: chain A residue 4843 LEU
Chi-restraints excluded: chain A residue 4941 VAL
Chi-restraints excluded: chain A residue 4945 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 41 optimal weight:    0.7980
   chunk 20 optimal weight:    0.9990
   chunk 52 optimal weight:    0.9990
   chunk 17 optimal weight:    6.9990
   chunk 57 optimal weight:    0.7980
   chunk 92 optimal weight:    0.9980
   chunk 32 optimal weight:    0.8980
   chunk 1 optimal weight:    0.9990
   chunk 79 optimal weight:    0.5980
   chunk 48 optimal weight:    0.7980
   chunk 40 optimal weight:    0.2980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A3727 GLN
** A3827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A4293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A4587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A4654 HIS
** A4936 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A4959 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4189 r_free = 0.4189 target = 0.162466 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.112869 restraints weight = 21844.129|
|-----------------------------------------------------------------------------|
r_work (start): 0.3551 rms_B_bonded: 3.91
r_work: 0.3380 rms_B_bonded: 4.77 restraints_weight: 0.5000
r_work (final): 0.3380
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7780
moved from start:          0.2236

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054  11894  Z= 0.136
  Angle     :  0.646  10.870  16127  Z= 0.320
  Chirality :  0.042   0.215   1840
  Planarity :  0.005   0.054   2080
  Dihedral  :  5.219  45.136   1567
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 10.85
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  7.64 %
    Favored  : 92.22 %
  Rotamer:
    Outliers :  3.98 %
    Allowed  : 19.97 %
    Favored  : 76.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.15 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.71 (0.23), residues: 1440
  helix:  0.60 (0.19), residues: 769
  sheet: -1.88 (0.82), residues: 49
  loop : -1.74 (0.25), residues: 622

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A3792 
 HIS   0.003   0.001   HIS A4113 
 PHE   0.027   0.002   PHE A4306 
 TYR   0.015   0.001   TYR A4189 
 ARG   0.004   0.000   ARG A4970 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03604 (  519)
  hydrogen bonds       : angle       4.17985 ( 1521)
  covalent geometry    : bond        0.00327 (11894)
  covalent geometry    : angle       0.64641 (16127)

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

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

  2880 Ramachandran restraints generated.
    1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2880 Ramachandran restraints generated.
    1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 137
  time to evaluate  : 1.245 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  172 GLU cc_start: 0.5563 (tm-30) cc_final: 0.4776 (mt-10)
REVERT: A 3915 GLU cc_start: 0.8777 (tp30) cc_final: 0.8375 (tp30)
REVERT: A 3919 GLN cc_start: 0.8854 (OUTLIER) cc_final: 0.8139 (mp-120)
REVERT: A 3940 ARG cc_start: 0.8752 (OUTLIER) cc_final: 0.7639 (tmm160)
REVERT: A 3964 ASP cc_start: 0.8223 (t70) cc_final: 0.7768 (t0)
REVERT: A 3972 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.8011 (tp30)
REVERT: A 4064 MET cc_start: 0.8021 (mpp) cc_final: 0.6790 (mpp)
REVERT: A 4068 PHE cc_start: 0.8225 (m-10) cc_final: 0.7770 (m-10)
REVERT: A 4327 TYR cc_start: 0.8740 (m-80) cc_final: 0.8437 (m-80)
REVERT: A 4621 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8702 (mp)
REVERT: A 4644 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8542 (mp)
REVERT: A 4673 MET cc_start: 0.8133 (mmt) cc_final: 0.7444 (mmt)
REVERT: A 4802 GLN cc_start: 0.7989 (OUTLIER) cc_final: 0.6694 (tp40)
REVERT: A 4927 ARG cc_start: 0.8168 (ttp80) cc_final: 0.7641 (ttp80)
REVERT: A 4945 ARG cc_start: 0.6758 (OUTLIER) cc_final: 0.5845 (mpp80)
REVERT: A 4952 ASP cc_start: 0.7588 (t0) cc_final: 0.6803 (t0)
  outliers start: 52
  outliers final: 34
  residues processed: 171
  average time/residue: 0.3046
  time to fit residues: 75.2694
Evaluate side-chains
  169 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 128
  time to evaluate  : 1.692 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  112 MET
Chi-restraints excluded: chain B residue  143 ILE
Chi-restraints excluded: chain B residue  182 ARG
Chi-restraints excluded: chain B residue  219 MET
Chi-restraints excluded: chain A residue 3728 TYR
Chi-restraints excluded: chain A residue 3730 THR
Chi-restraints excluded: chain A residue 3774 LEU
Chi-restraints excluded: chain A residue 3869 MET
Chi-restraints excluded: chain A residue 3891 MET
Chi-restraints excluded: chain A residue 3899 ASP
Chi-restraints excluded: chain A residue 3919 GLN
Chi-restraints excluded: chain A residue 3933 VAL
Chi-restraints excluded: chain A residue 3940 ARG
Chi-restraints excluded: chain A residue 3967 THR
Chi-restraints excluded: chain A residue 3972 GLU
Chi-restraints excluded: chain A residue 4021 LEU
Chi-restraints excluded: chain A residue 4051 HIS
Chi-restraints excluded: chain A residue 4057 LYS
Chi-restraints excluded: chain A residue 4058 HIS
Chi-restraints excluded: chain A residue 4061 PHE
Chi-restraints excluded: chain A residue 4138 LEU
Chi-restraints excluded: chain A residue 4164 THR
Chi-restraints excluded: chain A residue 4195 LEU
Chi-restraints excluded: chain A residue 4324 MET
Chi-restraints excluded: chain A residue 4351 LEU
Chi-restraints excluded: chain A residue 4362 THR
Chi-restraints excluded: chain A residue 4440 ASP
Chi-restraints excluded: chain A residue 4609 VAL
Chi-restraints excluded: chain A residue 4619 HIS
Chi-restraints excluded: chain A residue 4621 LEU
Chi-restraints excluded: chain A residue 4644 LEU
Chi-restraints excluded: chain A residue 4790 LEU
Chi-restraints excluded: chain A residue 4800 ASN
Chi-restraints excluded: chain A residue 4801 VAL
Chi-restraints excluded: chain A residue 4802 GLN
Chi-restraints excluded: chain A residue 4838 LYS
Chi-restraints excluded: chain A residue 4843 LEU
Chi-restraints excluded: chain A residue 4894 ILE
Chi-restraints excluded: chain A residue 4916 THR
Chi-restraints excluded: chain A residue 4941 VAL
Chi-restraints excluded: chain A residue 4945 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 128 optimal weight:    0.9990
   chunk 37 optimal weight:    1.9990
   chunk 106 optimal weight:    0.9980
   chunk 74 optimal weight:    0.9990
   chunk 71 optimal weight:    1.9990
   chunk 73 optimal weight:    0.9990
   chunk 100 optimal weight:    0.6980
   chunk 85 optimal weight:    0.0980
   chunk 72 optimal weight:    1.9990
   chunk 109 optimal weight:    0.1980
   chunk 132 optimal weight:    0.7980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
A3708 ASN
A3727 GLN
** A3827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A4293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A4587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A4654 HIS
** A4936 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A4959 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4192 r_free = 0.4192 target = 0.162571 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.113864 restraints weight = 21649.778|
|-----------------------------------------------------------------------------|
r_work (start): 0.3565 rms_B_bonded: 3.73
r_work: 0.3400 rms_B_bonded: 4.61 restraints_weight: 0.5000
r_work (final): 0.3400
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7746
moved from start:          0.2365

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056  11894  Z= 0.127
  Angle     :  0.650  14.585  16127  Z= 0.319
  Chirality :  0.042   0.267   1840
  Planarity :  0.005   0.056   2080
  Dihedral  :  5.228  50.906   1567
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 10.34
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  8.12 %
    Favored  : 91.74 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 20.20 %
    Favored  : 75.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.15 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.62 (0.23), residues: 1440
  helix:  0.71 (0.19), residues: 767
  sheet: -1.93 (0.81), residues: 50
  loop : -1.73 (0.25), residues: 623

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A3792 
 HIS   0.003   0.001   HIS A4113 
 PHE   0.044   0.002   PHE A4812 
 TYR   0.012   0.001   TYR A4189 
 ARG   0.003   0.000   ARG A4970 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03557 (  519)
  hydrogen bonds       : angle       4.17704 ( 1521)
  covalent geometry    : bond        0.00303 (11894)
  covalent geometry    : angle       0.64956 (16127)

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

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

  2880 Ramachandran restraints generated.
    1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2880 Ramachandran restraints generated.
    1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 137
  time to evaluate  : 1.573 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  172 GLU cc_start: 0.5538 (tm-30) cc_final: 0.4765 (mt-10)
REVERT: A 3915 GLU cc_start: 0.8736 (tp30) cc_final: 0.8345 (tp30)
REVERT: A 3919 GLN cc_start: 0.8835 (OUTLIER) cc_final: 0.8081 (mp-120)
REVERT: A 3964 ASP cc_start: 0.8208 (t70) cc_final: 0.7771 (t0)
REVERT: A 3972 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7970 (tp30)
REVERT: A 4068 PHE cc_start: 0.8226 (m-10) cc_final: 0.7889 (m-10)
REVERT: A 4327 TYR cc_start: 0.8715 (m-80) cc_final: 0.8409 (m-80)
REVERT: A 4621 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8684 (mp)
REVERT: A 4644 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8528 (mp)
REVERT: A 4673 MET cc_start: 0.8126 (mmt) cc_final: 0.7431 (mmt)
REVERT: A 4802 GLN cc_start: 0.7966 (OUTLIER) cc_final: 0.6694 (tp40)
REVERT: A 4927 ARG cc_start: 0.8159 (ttp80) cc_final: 0.7616 (ttp80)
REVERT: A 4945 ARG cc_start: 0.6761 (OUTLIER) cc_final: 0.5848 (mpp80)
REVERT: A 4952 ASP cc_start: 0.7591 (t0) cc_final: 0.6793 (t0)
  outliers start: 50
  outliers final: 34
  residues processed: 170
  average time/residue: 0.3652
  time to fit residues: 91.0822
Evaluate side-chains
  168 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 128
  time to evaluate  : 1.633 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  112 MET
Chi-restraints excluded: chain B residue  143 ILE
Chi-restraints excluded: chain B residue  182 ARG
Chi-restraints excluded: chain B residue  219 MET
Chi-restraints excluded: chain A residue 3728 TYR
Chi-restraints excluded: chain A residue 3730 THR
Chi-restraints excluded: chain A residue 3774 LEU
Chi-restraints excluded: chain A residue 3839 LEU
Chi-restraints excluded: chain A residue 3869 MET
Chi-restraints excluded: chain A residue 3891 MET
Chi-restraints excluded: chain A residue 3899 ASP
Chi-restraints excluded: chain A residue 3919 GLN
Chi-restraints excluded: chain A residue 3940 ARG
Chi-restraints excluded: chain A residue 3967 THR
Chi-restraints excluded: chain A residue 3972 GLU
Chi-restraints excluded: chain A residue 4021 LEU
Chi-restraints excluded: chain A residue 4051 HIS
Chi-restraints excluded: chain A residue 4057 LYS
Chi-restraints excluded: chain A residue 4058 HIS
Chi-restraints excluded: chain A residue 4061 PHE
Chi-restraints excluded: chain A residue 4138 LEU
Chi-restraints excluded: chain A residue 4164 THR
Chi-restraints excluded: chain A residue 4195 LEU
Chi-restraints excluded: chain A residue 4324 MET
Chi-restraints excluded: chain A residue 4351 LEU
Chi-restraints excluded: chain A residue 4362 THR
Chi-restraints excluded: chain A residue 4609 VAL
Chi-restraints excluded: chain A residue 4619 HIS
Chi-restraints excluded: chain A residue 4621 LEU
Chi-restraints excluded: chain A residue 4644 LEU
Chi-restraints excluded: chain A residue 4790 LEU
Chi-restraints excluded: chain A residue 4800 ASN
Chi-restraints excluded: chain A residue 4801 VAL
Chi-restraints excluded: chain A residue 4802 GLN
Chi-restraints excluded: chain A residue 4838 LYS
Chi-restraints excluded: chain A residue 4843 LEU
Chi-restraints excluded: chain A residue 4903 LYS
Chi-restraints excluded: chain A residue 4916 THR
Chi-restraints excluded: chain A residue 4941 VAL
Chi-restraints excluded: chain A residue 4945 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 137 optimal weight:    0.5980
   chunk 113 optimal weight:    1.9990
   chunk 89 optimal weight:    0.2980
   chunk 2 optimal weight:    4.9990
   chunk 51 optimal weight:    0.9990
   chunk 117 optimal weight:    0.8980
   chunk 8 optimal weight:    8.9990
   chunk 21 optimal weight:    9.9990
   chunk 127 optimal weight:    2.9990
   chunk 60 optimal weight:    0.7980
   chunk 53 optimal weight:    0.0070
   overall best weight:    0.5198

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

Flipped N/Q/H residues before XYZ refinement:
A3727 GLN
** A3827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A4293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A4587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A4654 HIS
** A4936 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A4959 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4196 r_free = 0.4196 target = 0.163099 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.113875 restraints weight = 21705.522|
|-----------------------------------------------------------------------------|
r_work (start): 0.3557 rms_B_bonded: 3.88
r_work: 0.3401 rms_B_bonded: 4.71 restraints_weight: 0.5000
r_work (final): 0.3401
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7755
moved from start:          0.2477

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057  11894  Z= 0.125
  Angle     :  0.662  16.141  16127  Z= 0.321
  Chirality :  0.042   0.283   1840
  Planarity :  0.005   0.057   2080
  Dihedral  :  5.232  51.124   1567
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 10.21
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  7.85 %
    Favored  : 92.01 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 20.35 %
    Favored  : 76.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.15 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.59 (0.23), residues: 1440
  helix:  0.75 (0.19), residues: 767
  sheet: -1.95 (0.81), residues: 50
  loop : -1.74 (0.25), residues: 623

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A3792 
 HIS   0.003   0.001   HIS A4113 
 PHE   0.037   0.001   PHE A4812 
 TYR   0.010   0.001   TYR A3818 
 ARG   0.004   0.000   ARG A3777 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03559 (  519)
  hydrogen bonds       : angle       4.15922 ( 1521)
  covalent geometry    : bond        0.00301 (11894)
  covalent geometry    : angle       0.66151 (16127)

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

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

  2880 Ramachandran restraints generated.
    1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2880 Ramachandran restraints generated.
    1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 133
  time to evaluate  : 1.375 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  172 GLU cc_start: 0.5541 (tm-30) cc_final: 0.4792 (mt-10)
REVERT: A 3915 GLU cc_start: 0.8738 (tp30) cc_final: 0.8360 (tp30)
REVERT: A 3919 GLN cc_start: 0.8835 (OUTLIER) cc_final: 0.8110 (mp-120)
REVERT: A 3964 ASP cc_start: 0.8192 (t70) cc_final: 0.7766 (t0)
REVERT: A 3972 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.7970 (tp30)
REVERT: A 4068 PHE cc_start: 0.8335 (m-10) cc_final: 0.7889 (m-10)
REVERT: A 4327 TYR cc_start: 0.8720 (m-80) cc_final: 0.8410 (m-80)
REVERT: A 4371 PHE cc_start: 0.8154 (t80) cc_final: 0.7601 (t80)
REVERT: A 4621 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8685 (mp)
REVERT: A 4644 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8530 (mp)
REVERT: A 4652 GLU cc_start: 0.7498 (tp30) cc_final: 0.7150 (tp30)
REVERT: A 4673 MET cc_start: 0.8129 (mmt) cc_final: 0.7430 (mmt)
REVERT: A 4802 GLN cc_start: 0.7927 (OUTLIER) cc_final: 0.6731 (tp40)
REVERT: A 4927 ARG cc_start: 0.8106 (ttp80) cc_final: 0.7552 (ttp80)
REVERT: A 4945 ARG cc_start: 0.6737 (OUTLIER) cc_final: 0.5845 (mpp80)
REVERT: A 4952 ASP cc_start: 0.7551 (t0) cc_final: 0.6829 (t0)
  outliers start: 46
  outliers final: 33
  residues processed: 162
  average time/residue: 0.2421
  time to fit residues: 57.3988
Evaluate side-chains
  172 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 133
  time to evaluate  : 1.459 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  112 MET
Chi-restraints excluded: chain B residue  143 ILE
Chi-restraints excluded: chain B residue  182 ARG
Chi-restraints excluded: chain B residue  219 MET
Chi-restraints excluded: chain A residue 3728 TYR
Chi-restraints excluded: chain A residue 3730 THR
Chi-restraints excluded: chain A residue 3774 LEU
Chi-restraints excluded: chain A residue 3839 LEU
Chi-restraints excluded: chain A residue 3869 MET
Chi-restraints excluded: chain A residue 3891 MET
Chi-restraints excluded: chain A residue 3899 ASP
Chi-restraints excluded: chain A residue 3919 GLN
Chi-restraints excluded: chain A residue 3967 THR
Chi-restraints excluded: chain A residue 3972 GLU
Chi-restraints excluded: chain A residue 4021 LEU
Chi-restraints excluded: chain A residue 4057 LYS
Chi-restraints excluded: chain A residue 4058 HIS
Chi-restraints excluded: chain A residue 4061 PHE
Chi-restraints excluded: chain A residue 4138 LEU
Chi-restraints excluded: chain A residue 4164 THR
Chi-restraints excluded: chain A residue 4195 LEU
Chi-restraints excluded: chain A residue 4324 MET
Chi-restraints excluded: chain A residue 4351 LEU
Chi-restraints excluded: chain A residue 4362 THR
Chi-restraints excluded: chain A residue 4609 VAL
Chi-restraints excluded: chain A residue 4619 HIS
Chi-restraints excluded: chain A residue 4621 LEU
Chi-restraints excluded: chain A residue 4644 LEU
Chi-restraints excluded: chain A residue 4790 LEU
Chi-restraints excluded: chain A residue 4800 ASN
Chi-restraints excluded: chain A residue 4801 VAL
Chi-restraints excluded: chain A residue 4802 GLN
Chi-restraints excluded: chain A residue 4838 LYS
Chi-restraints excluded: chain A residue 4843 LEU
Chi-restraints excluded: chain A residue 4894 ILE
Chi-restraints excluded: chain A residue 4907 SER
Chi-restraints excluded: chain A residue 4916 THR
Chi-restraints excluded: chain A residue 4941 VAL
Chi-restraints excluded: chain A residue 4945 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 26 optimal weight:    0.8980
   chunk 22 optimal weight:    6.9990
   chunk 36 optimal weight:    0.5980
   chunk 53 optimal weight:    0.9980
   chunk 43 optimal weight:    0.0770
   chunk 144 optimal weight:    0.4980
   chunk 75 optimal weight:    0.0030
   chunk 89 optimal weight:    2.9990
   chunk 42 optimal weight:    0.0570
   chunk 37 optimal weight:    0.6980
   chunk 40 optimal weight:    0.0370
   overall best weight:    0.1344

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

Flipped N/Q/H residues before XYZ refinement:
A3727 GLN
** A3827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A4016 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A4293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A4587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A4654 HIS
** A4959 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4234 r_free = 0.4234 target = 0.166439 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.118104 restraints weight = 21587.635|
|-----------------------------------------------------------------------------|
r_work (start): 0.3620 rms_B_bonded: 3.79
r_work: 0.3464 rms_B_bonded: 4.61 restraints_weight: 0.5000
r_work (final): 0.3464
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7672
moved from start:          0.2741

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060  11894  Z= 0.109
  Angle     :  0.650  16.526  16127  Z= 0.314
  Chirality :  0.042   0.349   1840
  Planarity :  0.005   0.060   2080
  Dihedral  :  4.850  34.648   1563
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 9.10
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  7.78 %
    Favored  : 92.15 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 20.89 %
    Favored  : 76.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.15 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.44 (0.23), residues: 1440
  helix:  0.89 (0.19), residues: 765
  sheet: -1.93 (0.82), residues: 50
  loop : -1.68 (0.25), residues: 625

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A3792 
 HIS   0.005   0.001   HIS A4816 
 PHE   0.014   0.001   PHE A4866 
 TYR   0.014   0.001   TYR A4259 
 ARG   0.009   0.000   ARG A3940 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03371 (  519)
  hydrogen bonds       : angle       4.07026 ( 1521)
  covalent geometry    : bond        0.00253 (11894)
  covalent geometry    : angle       0.64952 (16127)

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

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

  2880 Ramachandran restraints generated.
    1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2880 Ramachandran restraints generated.
    1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 152
  time to evaluate  : 1.371 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 3919 GLN cc_start: 0.8826 (OUTLIER) cc_final: 0.8440 (mp10)
REVERT: A 3964 ASP cc_start: 0.8166 (t70) cc_final: 0.7874 (t0)
REVERT: A 3972 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7975 (tp30)
REVERT: A 4057 LYS cc_start: 0.8100 (OUTLIER) cc_final: 0.6890 (pttt)
REVERT: A 4066 ASN cc_start: 0.7509 (m-40) cc_final: 0.7055 (t0)
REVERT: A 4068 PHE cc_start: 0.8273 (m-10) cc_final: 0.7833 (m-10)
REVERT: A 4086 LYS cc_start: 0.9098 (tppt) cc_final: 0.8805 (tptp)
REVERT: A 4151 GLN cc_start: 0.8846 (tp-100) cc_final: 0.8181 (tt0)
REVERT: A 4327 TYR cc_start: 0.8632 (m-80) cc_final: 0.8312 (m-80)
REVERT: A 4371 PHE cc_start: 0.7921 (t80) cc_final: 0.7597 (t80)
REVERT: A 4621 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8627 (mp)
REVERT: A 4644 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8489 (mp)
REVERT: A 4673 MET cc_start: 0.7954 (mmt) cc_final: 0.7260 (mmt)
REVERT: A 4802 GLN cc_start: 0.7897 (OUTLIER) cc_final: 0.6812 (tp40)
REVERT: A 4927 ARG cc_start: 0.8145 (ttp80) cc_final: 0.7630 (ttp80)
REVERT: A 4945 ARG cc_start: 0.6684 (OUTLIER) cc_final: 0.5837 (mpp80)
REVERT: A 4952 ASP cc_start: 0.7464 (t0) cc_final: 0.6751 (t0)
  outliers start: 39
  outliers final: 23
  residues processed: 177
  average time/residue: 0.2533
  time to fit residues: 66.0212
Evaluate side-chains
  167 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 137
  time to evaluate  : 1.429 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  112 MET
Chi-restraints excluded: chain B residue  143 ILE
Chi-restraints excluded: chain B residue  182 ARG
Chi-restraints excluded: chain B residue  219 MET
Chi-restraints excluded: chain A residue 3728 TYR
Chi-restraints excluded: chain A residue 3730 THR
Chi-restraints excluded: chain A residue 3869 MET
Chi-restraints excluded: chain A residue 3891 MET
Chi-restraints excluded: chain A residue 3899 ASP
Chi-restraints excluded: chain A residue 3919 GLN
Chi-restraints excluded: chain A residue 3972 GLU
Chi-restraints excluded: chain A residue 4051 HIS
Chi-restraints excluded: chain A residue 4057 LYS
Chi-restraints excluded: chain A residue 4058 HIS
Chi-restraints excluded: chain A residue 4061 PHE
Chi-restraints excluded: chain A residue 4138 LEU
Chi-restraints excluded: chain A residue 4195 LEU
Chi-restraints excluded: chain A residue 4324 MET
Chi-restraints excluded: chain A residue 4362 THR
Chi-restraints excluded: chain A residue 4440 ASP
Chi-restraints excluded: chain A residue 4619 HIS
Chi-restraints excluded: chain A residue 4621 LEU
Chi-restraints excluded: chain A residue 4644 LEU
Chi-restraints excluded: chain A residue 4790 LEU
Chi-restraints excluded: chain A residue 4800 ASN
Chi-restraints excluded: chain A residue 4802 GLN
Chi-restraints excluded: chain A residue 4843 LEU
Chi-restraints excluded: chain A residue 4907 SER
Chi-restraints excluded: chain A residue 4916 THR
Chi-restraints excluded: chain A residue 4945 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 134 optimal weight:    1.9990
   chunk 136 optimal weight:    1.9990
   chunk 82 optimal weight:    2.9990
   chunk 85 optimal weight:    0.6980
   chunk 37 optimal weight:    5.9990
   chunk 62 optimal weight:    0.9990
   chunk 132 optimal weight:    0.0980
   chunk 71 optimal weight:    0.5980
   chunk 49 optimal weight:    4.9990
   chunk 101 optimal weight:    0.5980
   chunk 61 optimal weight:    2.9990
   overall best weight:    0.5982

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

Flipped N/Q/H residues before XYZ refinement:
A3727 GLN
** A3827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A4016 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A4293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A4587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A4654 HIS
** A4936 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A4959 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4207 r_free = 0.4207 target = 0.164145 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.114996 restraints weight = 21504.554|
|-----------------------------------------------------------------------------|
r_work (start): 0.3580 rms_B_bonded: 3.86
r_work: 0.3413 rms_B_bonded: 4.77 restraints_weight: 0.5000
r_work (final): 0.3413
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7755
moved from start:          0.2802

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057  11894  Z= 0.130
  Angle     :  0.670  15.231  16127  Z= 0.324
  Chirality :  0.043   0.388   1840
  Planarity :  0.005   0.058   2080
  Dihedral  :  4.837  34.404   1563
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 10.21
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  7.29 %
    Favored  : 92.64 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 20.81 %
    Favored  : 76.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.15 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.45 (0.23), residues: 1440
  helix:  0.88 (0.19), residues: 775
  sheet: -1.92 (0.82), residues: 50
  loop : -1.73 (0.25), residues: 615

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A3792 
 HIS   0.003   0.001   HIS A4113 
 PHE   0.030   0.002   PHE A4306 
 TYR   0.011   0.001   TYR A3818 
 ARG   0.005   0.000   ARG A3796 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03433 (  519)
  hydrogen bonds       : angle       4.12728 ( 1521)
  covalent geometry    : bond        0.00315 (11894)
  covalent geometry    : angle       0.67013 (16127)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7667.69 seconds
wall clock time: 137 minutes 21.56 seconds (8241.56 seconds total)