Starting phenix.real_space_refine
on Wed Mar 12 12:17:36 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ejc_31158/03_2025/7ejc_31158.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ejc_31158/03_2025/7ejc_31158.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.97
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ejc_31158/03_2025/7ejc_31158.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ejc_31158/03_2025/7ejc_31158.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ejc_31158/03_2025/7ejc_31158.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ejc_31158/03_2025/7ejc_31158.cif"
  }
  resolution = 2.97
  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=   0.012
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: 7
    Type Number    sf(0)   Gaussians
     Br      6      7.06       5
     P      18      5.49       5
     Mg      3      5.21       5
     S      42      5.16       5
     C    4644      2.51       5
     N    1302      2.21       5
     O    1470      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 17 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 7485
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "G"
      Number of atoms: 180
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 180
          Classifications: {'DNA': 9}
          Link IDs: {'rna3p': 8}
    Chain: "A"
      Number of atoms: 2375
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 310, 2375
          Classifications: {'peptide': 310}
          Link IDs: {'CIS': 2, 'PTRANS': 9, 'TRANS': 298}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 2375
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 310, 2375
          Classifications: {'peptide': 310}
          Link IDs: {'CIS': 2, 'PTRANS': 9, 'TRANS': 298}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2375
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 310, 2375
          Classifications: {'peptide': 310}
          Link IDs: {'CIS': 2, 'PTRANS': 9, 'TRANS': 298}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 29
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 29
          Unusual residues: {' MG': 1, 'J46': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "C"
      Number of atoms: 91
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 91
          Unusual residues: {' MG': 1, 'ANP': 2, 'J46': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
    Chain: "B"
      Number of atoms: 60
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 60
          Unusual residues: {' MG': 1, 'ANP': 1, 'J46': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 5.97, per 1000 atoms: 0.80
  Number of scatterers: 7485
  At special positions: 0
  Unit cell: (107.97, 70.8, 110.625, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Br      6     34.99
     S      42     16.00
     P      18     15.00
     Mg      3     11.99
     O    1470      8.00
     N    1302      7.00
     C    4644      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=2, symmetry=0
  Number of additional bonds: simple=2, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.22
  Conformation dependent library (CDL) restraints added in 997.6 milliseconds
  

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1698

  Finding SS restraints...
    Secondary structure from input PDB file:
      42 helices and 3 sheets defined
      49.8% alpha, 13.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.88
  Creating SS restraints...
    Processing helix  chain 'A' and resid 34 through 45
      removed outlier: 3.577A  pdb=" N   VAL A  38 " --> pdb=" O   ASN A  34 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 48 through 54
      removed outlier: 3.824A  pdb=" N   VAL A  52 " --> pdb=" O   THR A  48 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 56 through 62
      removed outlier: 3.718A  pdb=" N   LEU A  60 " --> pdb=" O   PRO A  56 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 68 through 82
      removed outlier: 3.754A  pdb=" N   ASP A  72 " --> pdb=" O   GLU A  68 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 88 through 98
      removed outlier: 3.774A  pdb=" N   PHE A  92 " --> pdb=" O   THR A  88 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   ARG A  95 " --> pdb=" O   GLU A  91 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 106 through 113
    Processing helix  chain 'A' and resid 134 through 144
      removed outlier: 3.720A  pdb=" N   HIS A 138 " --> pdb=" O   THR A 134 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   VAL A 142 " --> pdb=" O   HIS A 138 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 147 through 151
    Processing helix  chain 'A' and resid 167 through 179
      removed outlier: 3.947A  pdb=" N   LEU A 171 " --> pdb=" O   ARG A 167 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 181 through 187
    Processing helix  chain 'A' and resid 196 through 214
      removed outlier: 4.003A  pdb=" N   THR A 201 " --> pdb=" O   THR A 197 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   GLN A 202 " --> pdb=" O   ASP A 198 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 225 through 232
      removed outlier: 3.672A  pdb=" N   ARG A 229 " --> pdb=" O   THR A 225 " (cutoff:3.500A)
      removed outlier: 4.266A  pdb=" N   THR A 230 " --> pdb=" O   ALA A 226 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 237 through 260
    Processing helix  chain 'A' and resid 289 through 296
    Processing helix  chain 'C' and resid 34 through 45
      removed outlier: 3.579A  pdb=" N   VAL C  38 " --> pdb=" O   ASN C  34 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 48 through 54
      removed outlier: 3.823A  pdb=" N   VAL C  52 " --> pdb=" O   THR C  48 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 56 through 62
      removed outlier: 3.717A  pdb=" N   LEU C  60 " --> pdb=" O   PRO C  56 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 68 through 82
      removed outlier: 3.754A  pdb=" N   ASP C  72 " --> pdb=" O   GLU C  68 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 89 through 98
      removed outlier: 3.565A  pdb=" N   ARG C  95 " --> pdb=" O   GLU C  91 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 106 through 113
    Processing helix  chain 'C' and resid 134 through 144
      removed outlier: 3.693A  pdb=" N   HIS C 138 " --> pdb=" O   THR C 134 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   VAL C 142 " --> pdb=" O   HIS C 138 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 147 through 151
    Processing helix  chain 'C' and resid 167 through 179
      removed outlier: 3.947A  pdb=" N   LEU C 171 " --> pdb=" O   ARG C 167 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 181 through 187
    Processing helix  chain 'C' and resid 196 through 214
      removed outlier: 4.003A  pdb=" N   THR C 201 " --> pdb=" O   THR C 197 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   GLN C 202 " --> pdb=" O   ASP C 198 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 225 through 232
      removed outlier: 3.671A  pdb=" N   ARG C 229 " --> pdb=" O   THR C 225 " (cutoff:3.500A)
      removed outlier: 4.267A  pdb=" N   THR C 230 " --> pdb=" O   ALA C 226 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 237 through 260
    Processing helix  chain 'C' and resid 289 through 296
    Processing helix  chain 'B' and resid 34 through 45
      removed outlier: 3.578A  pdb=" N   VAL B  38 " --> pdb=" O   ASN B  34 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 48 through 54
      removed outlier: 3.823A  pdb=" N   VAL B  52 " --> pdb=" O   THR B  48 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 56 through 62
      removed outlier: 3.718A  pdb=" N   LEU B  60 " --> pdb=" O   PRO B  56 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 68 through 82
      removed outlier: 3.754A  pdb=" N   ASP B  72 " --> pdb=" O   GLU B  68 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 89 through 98
      removed outlier: 3.565A  pdb=" N   ARG B  95 " --> pdb=" O   GLU B  91 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 106 through 113
    Processing helix  chain 'B' and resid 134 through 144
      removed outlier: 3.680A  pdb=" N   VAL B 142 " --> pdb=" O   HIS B 138 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 147 through 151
    Processing helix  chain 'B' and resid 167 through 179
      removed outlier: 3.946A  pdb=" N   LEU B 171 " --> pdb=" O   ARG B 167 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 181 through 187
    Processing helix  chain 'B' and resid 196 through 214
      removed outlier: 4.003A  pdb=" N   THR B 201 " --> pdb=" O   THR B 197 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   GLN B 202 " --> pdb=" O   ASP B 198 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 225 through 232
      removed outlier: 3.671A  pdb=" N   ARG B 229 " --> pdb=" O   THR B 225 " (cutoff:3.500A)
      removed outlier: 4.265A  pdb=" N   THR B 230 " --> pdb=" O   ALA B 226 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 237 through 260
    Processing helix  chain 'B' and resid 289 through 296
    Processing sheet with id=AA1, first strand: chain 'A' and resid 333 through 334
      removed outlier: 3.565A  pdb=" N   GLY A 333 " --> pdb=" O   ASN A 330 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   ILE A 311 " --> pdb=" O   ARG A 303 " (cutoff:3.500A)
      removed outlier: 6.645A  pdb=" N   ILE A 122 " --> pdb=" O   THR A 298 " (cutoff:3.500A)
      removed outlier: 8.201A  pdb=" N   LEU A 300 " --> pdb=" O   ILE A 122 " (cutoff:3.500A)
      removed outlier: 6.386A  pdb=" N   GLU A 124 " --> pdb=" O   LEU A 300 " (cutoff:3.500A)
      removed outlier: 7.332A  pdb=" N   LEU A 302 " --> pdb=" O   GLU A 124 " (cutoff:3.500A)
      removed outlier: 6.605A  pdb=" N   PHE A 126 " --> pdb=" O   LEU A 302 " (cutoff:3.500A)
      removed outlier: 8.554A  pdb=" N   LYS A 304 " --> pdb=" O   PHE A 126 " (cutoff:3.500A)
      removed outlier: 5.495A  pdb=" N   LYS A 156 " --> pdb=" O   TYR A 216 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   LEU A 218 " --> pdb=" O   LYS A 156 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 87 through 88
      removed outlier: 5.495A  pdb=" N   LYS B 156 " --> pdb=" O   TYR B 216 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   LEU B 218 " --> pdb=" O   LYS B 156 " (cutoff:3.500A)
      removed outlier: 6.643A  pdb=" N   ILE B 122 " --> pdb=" O   THR B 298 " (cutoff:3.500A)
      removed outlier: 8.201A  pdb=" N   LEU B 300 " --> pdb=" O   ILE B 122 " (cutoff:3.500A)
      removed outlier: 6.386A  pdb=" N   GLU B 124 " --> pdb=" O   LEU B 300 " (cutoff:3.500A)
      removed outlier: 7.333A  pdb=" N   LEU B 302 " --> pdb=" O   GLU B 124 " (cutoff:3.500A)
      removed outlier: 6.606A  pdb=" N   PHE B 126 " --> pdb=" O   LEU B 302 " (cutoff:3.500A)
      removed outlier: 8.554A  pdb=" N   LYS B 304 " --> pdb=" O   PHE B 126 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   ILE B 311 " --> pdb=" O   ARG B 303 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   GLY B 333 " --> pdb=" O   ASN B 330 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 190 through 193
      removed outlier: 5.494A  pdb=" N   LYS C 156 " --> pdb=" O   TYR C 216 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   LEU C 218 " --> pdb=" O   LYS C 156 " (cutoff:3.500A)
      removed outlier: 6.644A  pdb=" N   ILE C 122 " --> pdb=" O   THR C 298 " (cutoff:3.500A)
      removed outlier: 8.200A  pdb=" N   LEU C 300 " --> pdb=" O   ILE C 122 " (cutoff:3.500A)
      removed outlier: 6.386A  pdb=" N   GLU C 124 " --> pdb=" O   LEU C 300 " (cutoff:3.500A)
      removed outlier: 7.332A  pdb=" N   LEU C 302 " --> pdb=" O   GLU C 124 " (cutoff:3.500A)
      removed outlier: 6.606A  pdb=" N   PHE C 126 " --> pdb=" O   LEU C 302 " (cutoff:3.500A)
      removed outlier: 8.554A  pdb=" N   LYS C 304 " --> pdb=" O   PHE C 126 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   ILE C 311 " --> pdb=" O   ARG C 303 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   GLY C 333 " --> pdb=" O   ASN C 330 " (cutoff:3.500A)

    347 hydrogen bonds defined for protein.
    999 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.05

  Time building geometry restraints manager: 2.44 seconds

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

  Histogram of bond lengths:
        1.21 -     1.34: 2496
        1.34 -     1.48: 1724
        1.48 -     1.61: 3312
        1.61 -     1.74: 9
        1.74 -     1.87: 72
  Bond restraints: 7613
  Sorted by residual:
  bond pdb=" O3A ANP B 401 "
       pdb=" PB  ANP B 401 "
    ideal  model  delta    sigma   weight residual
    1.700  1.556  0.144 2.00e-02 2.50e+03 5.17e+01
  bond pdb=" O3A ANP C 401 "
       pdb=" PB  ANP C 401 "
    ideal  model  delta    sigma   weight residual
    1.700  1.557  0.143 2.00e-02 2.50e+03 5.14e+01
  bond pdb=" O3A ANP C 403 "
       pdb=" PB  ANP C 403 "
    ideal  model  delta    sigma   weight residual
    1.700  1.557  0.143 2.00e-02 2.50e+03 5.10e+01
  bond pdb=" C04 J46 C 404 "
       pdb=" C07 J46 C 404 "
    ideal  model  delta    sigma   weight residual
    1.391  1.529 -0.138 2.00e-02 2.50e+03 4.76e+01
  bond pdb=" C04 J46 A 602 "
       pdb=" C07 J46 A 602 "
    ideal  model  delta    sigma   weight residual
    1.391  1.529 -0.138 2.00e-02 2.50e+03 4.73e+01
  ... (remaining 7608 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.94: 10179
        3.94 -     7.88: 122
        7.88 -    11.83: 18
       11.83 -    15.77: 0
       15.77 -    19.71: 6
  Bond angle restraints: 10325
  Sorted by residual:
  angle pdb=" O01 J46 A 602 "
        pdb=" S01 J46 A 602 "
        pdb=" O02 J46 A 602 "
      ideal   model   delta    sigma   weight residual
     119.86  100.15   19.71 3.00e+00 1.11e-01 4.32e+01
  angle pdb=" O01 J46 B 403 "
        pdb=" S01 J46 B 403 "
        pdb=" O02 J46 B 403 "
      ideal   model   delta    sigma   weight residual
     119.86  100.18   19.68 3.00e+00 1.11e-01 4.30e+01
  angle pdb=" O01 J46 C 404 "
        pdb=" S01 J46 C 404 "
        pdb=" O02 J46 C 404 "
      ideal   model   delta    sigma   weight residual
     119.86  100.18   19.68 3.00e+00 1.11e-01 4.30e+01
  angle pdb=" N   GLY C 236 "
        pdb=" CA  GLY C 236 "
        pdb=" C   GLY C 236 "
      ideal   model   delta    sigma   weight residual
     114.69  107.61    7.08 1.19e+00 7.06e-01 3.54e+01
  angle pdb=" N   GLY B 236 "
        pdb=" CA  GLY B 236 "
        pdb=" C   GLY B 236 "
      ideal   model   delta    sigma   weight residual
     114.69  107.67    7.02 1.19e+00 7.06e-01 3.48e+01
  ... (remaining 10320 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.42: 4283
       24.42 -    48.85: 312
       48.85 -    73.27: 34
       73.27 -    97.69: 6
       97.69 -   122.12: 3
  Dihedral angle restraints: 4638
    sinusoidal: 1986
      harmonic: 2652
  Sorted by residual:
  dihedral pdb=" CA  ASN A 188 "
           pdb=" C   ASN A 188 "
           pdb=" N   VAL A 189 "
           pdb=" CA  VAL A 189 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.79  -23.21     0      5.00e+00 4.00e-02 2.16e+01
  dihedral pdb=" CA  ASN C 188 "
           pdb=" C   ASN C 188 "
           pdb=" N   VAL C 189 "
           pdb=" CA  VAL C 189 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -156.81  -23.19     0      5.00e+00 4.00e-02 2.15e+01
  dihedral pdb=" CA  ASN B 188 "
           pdb=" C   ASN B 188 "
           pdb=" N   VAL B 189 "
           pdb=" CA  VAL B 189 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.82  -23.18     0      5.00e+00 4.00e-02 2.15e+01
  ... (remaining 4635 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.059: 950
       0.059 -    0.119: 180
       0.119 -    0.178: 28
       0.178 -    0.238: 3
       0.238 -    0.297: 3
  Chirality restraints: 1164
  Sorted by residual:
  chirality pdb=" C3' ANP C 401 "
            pdb=" C2' ANP C 401 "
            pdb=" C4' ANP C 401 "
            pdb=" O3' ANP C 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.36   -2.65    0.30 2.00e-01 2.50e+01 2.21e+00
  chirality pdb=" C3' ANP B 401 "
            pdb=" C2' ANP B 401 "
            pdb=" C4' ANP B 401 "
            pdb=" O3' ANP B 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.36   -2.65    0.30 2.00e-01 2.50e+01 2.19e+00
  chirality pdb=" C3' ANP C 403 "
            pdb=" C2' ANP C 403 "
            pdb=" C4' ANP C 403 "
            pdb=" O3' ANP C 403 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.36   -2.65    0.29 2.00e-01 2.50e+01 2.16e+00
  ... (remaining 1161 not shown)

  Planarity restraints: 1290
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS B  58 "   -0.012 2.00e-02 2.50e+03   2.62e-02 6.87e+00
        pdb=" C   LYS B  58 "    0.045 2.00e-02 2.50e+03
        pdb=" O   LYS B  58 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   GLU B  59 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS A  58 "    0.012 2.00e-02 2.50e+03   2.50e-02 6.27e+00
        pdb=" C   LYS A  58 "   -0.043 2.00e-02 2.50e+03
        pdb=" O   LYS A  58 "    0.017 2.00e-02 2.50e+03
        pdb=" N   GLU A  59 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS C 285 "    0.034 5.00e-02 4.00e+02   5.14e-02 4.23e+00
        pdb=" N   PRO C 286 "   -0.089 5.00e-02 4.00e+02
        pdb=" CA  PRO C 286 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO C 286 "    0.028 5.00e-02 4.00e+02
  ... (remaining 1287 not shown)

  Histogram of nonbonded interaction distances:
        1.62 -     2.27: 21
        2.27 -     2.93: 3254
        2.93 -     3.59: 10653
        3.59 -     4.24: 17973
        4.24 -     4.90: 30452
  Nonbonded interactions: 62353
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A 134 "
            pdb="MG    MG A 601 "
     model   vdw
     1.616 2.170
  nonbonded pdb=" OG1 THR C 134 "
            pdb="MG    MG C 402 "
     model   vdw
     1.617 2.170
  nonbonded pdb=" OG1 THR B 134 "
            pdb=" OD2 ASP B 222 "
     model   vdw
     1.862 3.040
  nonbonded pdb=" OG1 THR C 134 "
            pdb=" O2B ANP C 401 "
     model   vdw
     1.896 3.040
  nonbonded pdb=" OG1 THR A 134 "
            pdb=" O2B ANP B 401 "
     model   vdw
     1.946 3.040
  ... (remaining 62348 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 22 through 338)
  selection = (chain 'B' and resid 22 through 338)
  selection = (chain 'C' and resid 22 through 338)
}

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:             3.480
  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:          0.270
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     22.300
  Find NCS groups from input model:        0.310
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:11.800
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.310
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7874
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      :  0.011   0.144   7613  Z= 0.724
  Angle     :  1.183  19.709  10325  Z= 0.662
  Chirality :  0.049   0.297   1164
  Planarity :  0.004   0.051   1290
  Dihedral  : 16.421 122.115   2940
  Min Nonbonded Distance : 1.616

Molprobity Statistics.
  All-atom Clashscore : 11.47
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  5.23 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  :  5.38 %
    Favored  : 90.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.67 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.39 (0.22), residues: 918
  helix: -2.04 (0.20), residues: 417
  sheet: -1.38 (0.36), residues: 168
  loop : -2.77 (0.26), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS B 294 
 PHE   0.006   0.001   PHE B 126 
 TYR   0.020   0.002   TYR B 315 
 ARG   0.006   0.001   ARG B 193 

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

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

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 107
  time to evaluate  : 0.801 
Fit side-chains
REVERT: A   34 ASN cc_start: 0.8335 (t0) cc_final: 0.8001 (t0)
REVERT: A  163 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7677 (mm-30)
REVERT: C   68 GLU cc_start: 0.7765 (tm-30) cc_final: 0.7083 (tm-30)
REVERT: C  210 MET cc_start: 0.8817 (mtp) cc_final: 0.8588 (mtp)
REVERT: B   68 GLU cc_start: 0.7777 (tm-30) cc_final: 0.6987 (tm-30)
REVERT: B  198 ASP cc_start: 0.8725 (m-30) cc_final: 0.8523 (m-30)
  outliers start: 31
  outliers final: 5
  residues processed: 128
  average time/residue: 1.5241
  time to fit residues: 203.9069
Evaluate side-chains
  67 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 62
  time to evaluate  : 0.896 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 ILE
Chi-restraints excluded: chain A residue  143 THR
Chi-restraints excluded: chain C residue   99 ILE
Chi-restraints excluded: chain C residue  143 THR
Chi-restraints excluded: chain B residue  134 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 79 optimal weight:    0.6980
   chunk 71 optimal weight:    9.9990
   chunk 39 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9990
   chunk 48 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9990
   chunk 73 optimal weight:    3.9990
   chunk 28 optimal weight:    4.9990
   chunk 44 optimal weight:   10.0000
   chunk 54 optimal weight:    0.9980
   chunk 85 optimal weight:    0.9990
   overall best weight:    0.9386

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

Flipped N/Q/H residues before XYZ refinement:
A  30 GLN
A  34 ASN
A 138 HIS
** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 242 GLN
A 290 ASN
A 330 ASN
C  30 GLN
C  93 HIS
C 138 HIS
** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 290 ASN
C 330 ASN
B  30 GLN
B  93 HIS
B 138 HIS
** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 242 GLN
B 330 ASN

Total number of N/Q/H flips: 16

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.083189 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2976 r_free = 0.2976 target = 0.068934 restraints weight = 13261.869|
|-----------------------------------------------------------------------------|
r_work (start): 0.2972 rms_B_bonded: 2.11
r_work: 0.2857 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.2731 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.2731
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8956
moved from start:          0.2347

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7613  Z= 0.187
  Angle     :  0.611   7.252  10325  Z= 0.337
  Chirality :  0.041   0.128   1164
  Planarity :  0.004   0.039   1290
  Dihedral  : 12.386  93.214   1252
  Min Nonbonded Distance : 2.127

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.12 %
    Favored  : 94.88 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 14.92 %
    Favored  : 82.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.67 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.65 (0.25), residues: 918
  helix: -0.06 (0.26), residues: 393
  sheet: -0.95 (0.37), residues: 156
  loop : -2.27 (0.26), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS B 294 
 PHE   0.007   0.001   PHE A 248 
 TYR   0.013   0.001   TYR A 315 
 ARG   0.008   0.001   ARG C  27 

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

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

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 80
  time to evaluate  : 0.951 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  326 MET cc_start: 0.8986 (ttm) cc_final: 0.8777 (ttp)
REVERT: B   43 GLU cc_start: 0.8820 (mp0) cc_final: 0.8599 (mt-10)
REVERT: B  159 TYR cc_start: 0.8957 (t80) cc_final: 0.8493 (t80)
  outliers start: 21
  outliers final: 10
  residues processed: 96
  average time/residue: 1.3571
  time to fit residues: 137.4282
Evaluate side-chains
  68 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 58
  time to evaluate  : 0.760 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 LYS
Chi-restraints excluded: chain A residue   97 SER
Chi-restraints excluded: chain A residue  143 THR
Chi-restraints excluded: chain A residue  158 MET
Chi-restraints excluded: chain C residue   99 ILE
Chi-restraints excluded: chain C residue  142 VAL
Chi-restraints excluded: chain B residue   38 VAL
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue   99 ILE
Chi-restraints excluded: chain B residue  189 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 91 optimal weight:   10.0000
   chunk 19 optimal weight:    3.9990
   chunk 22 optimal weight:    0.8980
   chunk 73 optimal weight:    5.9990
   chunk 6 optimal weight:    3.9990
   chunk 61 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9990
   chunk 74 optimal weight:    0.7980
   chunk 84 optimal weight:    3.9990
   chunk 80 optimal weight:    6.9990
   chunk 50 optimal weight:    1.9990
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 290 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.080796 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2913 r_free = 0.2913 target = 0.066012 restraints weight = 13846.582|
|-----------------------------------------------------------------------------|
r_work (start): 0.2907 rms_B_bonded: 2.26
r_work: 0.2787 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.2656 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.2656
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9006
moved from start:          0.2633

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7613  Z= 0.202
  Angle     :  0.592   7.445  10325  Z= 0.326
  Chirality :  0.041   0.132   1164
  Planarity :  0.004   0.038   1290
  Dihedral  : 10.910  57.499   1248
  Min Nonbonded Distance : 1.977

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  4.58 %
    Favored  : 95.21 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 17.07 %
    Favored  : 80.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.67 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.16 (0.27), residues: 918
  helix:  0.43 (0.26), residues: 411
  sheet: -0.94 (0.38), residues: 165
  loop : -2.13 (0.29), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS A 294 
 PHE   0.007   0.001   PHE C 126 
 TYR   0.016   0.001   TYR C 315 
 ARG   0.005   0.000   ARG B 193 

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

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

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 71
  time to evaluate  : 0.792 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   39 LYS cc_start: 0.9008 (OUTLIER) cc_final: 0.8674 (mtmt)
REVERT: A   43 GLU cc_start: 0.8808 (OUTLIER) cc_final: 0.8530 (mt-10)
REVERT: C   39 LYS cc_start: 0.9204 (mppt) cc_final: 0.8827 (mmtm)
REVERT: B   43 GLU cc_start: 0.8850 (OUTLIER) cc_final: 0.8580 (mt-10)
REVERT: B  159 TYR cc_start: 0.9045 (t80) cc_final: 0.8481 (t80)
REVERT: B  184 ASP cc_start: 0.8990 (m-30) cc_final: 0.8768 (m-30)
  outliers start: 21
  outliers final: 10
  residues processed: 84
  average time/residue: 1.2494
  time to fit residues: 111.3376
Evaluate side-chains
  76 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 63
  time to evaluate  : 0.867 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 LYS
Chi-restraints excluded: chain A residue   43 GLU
Chi-restraints excluded: chain A residue   97 SER
Chi-restraints excluded: chain A residue  158 MET
Chi-restraints excluded: chain A residue  218 LEU
Chi-restraints excluded: chain C residue   34 ASN
Chi-restraints excluded: chain C residue   38 VAL
Chi-restraints excluded: chain C residue   43 GLU
Chi-restraints excluded: chain C residue  142 VAL
Chi-restraints excluded: chain B residue   38 VAL
Chi-restraints excluded: chain B residue   43 GLU
Chi-restraints excluded: chain B residue   72 ASP
Chi-restraints excluded: chain B residue   97 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 13 optimal weight:    1.9990
   chunk 55 optimal weight:    0.8980
   chunk 67 optimal weight:    7.9990
   chunk 35 optimal weight:    1.9990
   chunk 59 optimal weight:    8.9990
   chunk 22 optimal weight:    0.9990
   chunk 56 optimal weight:    3.9990
   chunk 31 optimal weight:    9.9990
   chunk 60 optimal weight:    1.9990
   chunk 54 optimal weight:    0.9990
   chunk 51 optimal weight:    0.9980
   overall best weight:    1.1786

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

Flipped N/Q/H residues before XYZ refinement:
** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 114 GLN
** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.081235 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2924 r_free = 0.2924 target = 0.066525 restraints weight = 13567.086|
|-----------------------------------------------------------------------------|
r_work (start): 0.2918 rms_B_bonded: 2.22
r_work: 0.2799 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.2669 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.2669
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8995
moved from start:          0.2913

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7613  Z= 0.186
  Angle     :  0.573   7.538  10325  Z= 0.316
  Chirality :  0.041   0.164   1164
  Planarity :  0.003   0.035   1290
  Dihedral  : 10.719  59.227   1245
  Min Nonbonded Distance : 2.008

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  4.47 %
    Favored  : 95.42 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 18.28 %
    Favored  : 79.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.67 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.78 (0.27), residues: 918
  helix:  0.72 (0.26), residues: 411
  sheet: -0.71 (0.39), residues: 165
  loop : -1.92 (0.30), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS A 294 
 PHE   0.006   0.001   PHE C 126 
 TYR   0.013   0.001   TYR C 315 
 ARG   0.004   0.000   ARG B  27 

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

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

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 70
  time to evaluate  : 0.984 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   39 LYS cc_start: 0.9000 (OUTLIER) cc_final: 0.8666 (mtmt)
REVERT: A   43 GLU cc_start: 0.8822 (mp0) cc_final: 0.8530 (mt-10)
REVERT: C   43 GLU cc_start: 0.8825 (OUTLIER) cc_final: 0.8558 (mt-10)
REVERT: B   43 GLU cc_start: 0.8856 (OUTLIER) cc_final: 0.8577 (mt-10)
REVERT: B  159 TYR cc_start: 0.9061 (t80) cc_final: 0.8467 (t80)
  outliers start: 16
  outliers final: 8
  residues processed: 81
  average time/residue: 1.2426
  time to fit residues: 106.9771
Evaluate side-chains
  74 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 63
  time to evaluate  : 0.789 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 LYS
Chi-restraints excluded: chain A residue  158 MET
Chi-restraints excluded: chain A residue  189 VAL
Chi-restraints excluded: chain C residue   34 ASN
Chi-restraints excluded: chain C residue   38 VAL
Chi-restraints excluded: chain C residue   43 GLU
Chi-restraints excluded: chain C residue  142 VAL
Chi-restraints excluded: chain C residue  218 LEU
Chi-restraints excluded: chain B residue   38 VAL
Chi-restraints excluded: chain B residue   43 GLU
Chi-restraints excluded: chain B residue   97 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 37 optimal weight:    2.9990
   chunk 67 optimal weight:    9.9990
   chunk 36 optimal weight:    1.9990
   chunk 88 optimal weight:    0.9980
   chunk 16 optimal weight:    2.9990
   chunk 35 optimal weight:    2.9990
   chunk 68 optimal weight:    1.9990
   chunk 22 optimal weight:    0.6980
   chunk 50 optimal weight:    1.9990
   chunk 91 optimal weight:    9.9990
   chunk 76 optimal weight:   10.0000
   overall best weight:    1.5386

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

Flipped N/Q/H residues before XYZ refinement:
** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.079814 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2891 r_free = 0.2891 target = 0.065040 restraints weight = 13276.338|
|-----------------------------------------------------------------------------|
r_work (start): 0.2887 rms_B_bonded: 2.19
r_work: 0.2768 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.2638 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.2638
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9023
moved from start:          0.3072

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7613  Z= 0.211
  Angle     :  0.575   7.596  10325  Z= 0.318
  Chirality :  0.041   0.139   1164
  Planarity :  0.003   0.032   1290
  Dihedral  : 10.781  63.889   1245
  Min Nonbonded Distance : 1.986

Molprobity Statistics.
  All-atom Clashscore : 7.42
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  4.58 %
    Favored  : 95.21 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 19.89 %
    Favored  : 78.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.67 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.52 (0.28), residues: 918
  helix:  0.91 (0.27), residues: 408
  sheet: -0.50 (0.41), residues: 165
  loop : -1.78 (0.30), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS A 294 
 PHE   0.007   0.001   PHE C 126 
 TYR   0.015   0.001   TYR A 315 
 ARG   0.003   0.000   ARG B  27 

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

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

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 72
  time to evaluate  : 0.955 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 GLU cc_start: 0.8794 (mp0) cc_final: 0.8490 (mt-10)
REVERT: A   68 GLU cc_start: 0.7891 (tm-30) cc_final: 0.7462 (tp30)
REVERT: C   39 LYS cc_start: 0.9237 (mppt) cc_final: 0.8796 (mmtm)
REVERT: C   43 GLU cc_start: 0.8816 (OUTLIER) cc_final: 0.8545 (mt-10)
REVERT: C  196 ASN cc_start: 0.8470 (m110) cc_final: 0.8208 (m-40)
REVERT: B   43 GLU cc_start: 0.8849 (mp0) cc_final: 0.8589 (mt-10)
REVERT: B  159 TYR cc_start: 0.9143 (t80) cc_final: 0.8566 (t80)
  outliers start: 13
  outliers final: 9
  residues processed: 79
  average time/residue: 1.7505
  time to fit residues: 145.8392
Evaluate side-chains
  73 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 63
  time to evaluate  : 0.920 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 LYS
Chi-restraints excluded: chain A residue   72 ASP
Chi-restraints excluded: chain A residue  158 MET
Chi-restraints excluded: chain A residue  189 VAL
Chi-restraints excluded: chain A residue  218 LEU
Chi-restraints excluded: chain C residue   38 VAL
Chi-restraints excluded: chain C residue   43 GLU
Chi-restraints excluded: chain C residue  142 VAL
Chi-restraints excluded: chain C residue  218 LEU
Chi-restraints excluded: chain B residue   38 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 30 optimal weight:    0.8980
   chunk 68 optimal weight:    2.9990
   chunk 54 optimal weight:    3.9990
   chunk 14 optimal weight:    8.9990
   chunk 2 optimal weight:    0.0470
   chunk 77 optimal weight:    5.9990
   chunk 34 optimal weight:    1.9990
   chunk 92 optimal weight:    4.9990
   chunk 49 optimal weight:    5.9990
   chunk 86 optimal weight:    0.8980
   chunk 4 optimal weight:    3.9990
   overall best weight:    1.3682

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

Flipped N/Q/H residues before XYZ refinement:
** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.079729 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2890 r_free = 0.2890 target = 0.065004 restraints weight = 13249.262|
|-----------------------------------------------------------------------------|
r_work (start): 0.2893 rms_B_bonded: 2.20
r_work: 0.2773 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.2644 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.2644
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9018
moved from start:          0.3214

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7613  Z= 0.198
  Angle     :  0.574   7.594  10325  Z= 0.317
  Chirality :  0.041   0.127   1164
  Planarity :  0.003   0.043   1290
  Dihedral  : 10.758  65.071   1245
  Min Nonbonded Distance : 1.997

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  4.79 %
    Favored  : 94.99 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 21.10 %
    Favored  : 76.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.67 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.37 (0.28), residues: 918
  helix:  1.00 (0.27), residues: 408
  sheet: -0.42 (0.41), residues: 165
  loop : -1.65 (0.30), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS A 294 
 PHE   0.006   0.001   PHE C 126 
 TYR   0.014   0.001   TYR C 315 
 ARG   0.011   0.000   ARG B  27 

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

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

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 66
  time to evaluate  : 0.879 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   39 LYS cc_start: 0.9047 (OUTLIER) cc_final: 0.8767 (mppt)
REVERT: A   43 GLU cc_start: 0.8815 (mt-10) cc_final: 0.8499 (mt-10)
REVERT: A   68 GLU cc_start: 0.7818 (tm-30) cc_final: 0.7385 (tp30)
REVERT: A   72 ASP cc_start: 0.8721 (p0) cc_final: 0.8519 (OUTLIER)
REVERT: C   39 LYS cc_start: 0.9243 (mppt) cc_final: 0.8793 (mmtm)
REVERT: C   43 GLU cc_start: 0.8826 (OUTLIER) cc_final: 0.8532 (mt-10)
REVERT: B   43 GLU cc_start: 0.8837 (mp0) cc_final: 0.8562 (mt-10)
REVERT: B  159 TYR cc_start: 0.9139 (t80) cc_final: 0.8581 (t80)
REVERT: B  223 SER cc_start: 0.8646 (m) cc_final: 0.8271 (p)
REVERT: B  306 ARG cc_start: 0.8257 (mmp-170) cc_final: 0.8039 (mmp-170)
  outliers start: 15
  outliers final: 10
  residues processed: 75
  average time/residue: 1.3257
  time to fit residues: 105.2181
Evaluate side-chains
  75 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 64
  time to evaluate  : 0.781 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 LYS
Chi-restraints excluded: chain A residue   97 SER
Chi-restraints excluded: chain A residue  158 MET
Chi-restraints excluded: chain A residue  189 VAL
Chi-restraints excluded: chain A residue  218 LEU
Chi-restraints excluded: chain C residue   38 VAL
Chi-restraints excluded: chain C residue   43 GLU
Chi-restraints excluded: chain C residue  142 VAL
Chi-restraints excluded: chain C residue  218 LEU
Chi-restraints excluded: chain B residue   38 VAL
Chi-restraints excluded: chain B residue   72 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 24 optimal weight:    3.9990
   chunk 7 optimal weight:    4.9990
   chunk 64 optimal weight:    3.9990
   chunk 62 optimal weight:    5.9990
   chunk 35 optimal weight:    3.9990
   chunk 22 optimal weight:    1.9990
   chunk 77 optimal weight:    5.9990
   chunk 90 optimal weight:    4.9990
   chunk 81 optimal weight:    4.9990
   chunk 46 optimal weight:    8.9990
   chunk 19 optimal weight:    0.7980
   overall best weight:    2.9588

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

Flipped N/Q/H residues before XYZ refinement:
** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 196 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.076521 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2821 r_free = 0.2821 target = 0.061840 restraints weight = 13209.968|
|-----------------------------------------------------------------------------|
r_work (start): 0.2819 rms_B_bonded: 2.14
r_work: 0.2698 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.2570 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.2570
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9096
moved from start:          0.3214

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   7613  Z= 0.342
  Angle     :  0.647   7.646  10325  Z= 0.355
  Chirality :  0.043   0.142   1164
  Planarity :  0.004   0.044   1290
  Dihedral  : 11.248  73.262   1245
  Min Nonbonded Distance : 1.953

Molprobity Statistics.
  All-atom Clashscore : 7.35
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  5.01 %
    Favored  : 94.66 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 21.51 %
    Favored  : 76.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.67 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.41 (0.28), residues: 918
  helix:  0.87 (0.27), residues: 408
  sheet: -0.30 (0.42), residues: 165
  loop : -1.62 (0.31), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS A 294 
 PHE   0.007   0.001   PHE A 327 
 TYR   0.021   0.001   TYR A 315 
 ARG   0.008   0.001   ARG B  27 

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

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

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 63
  time to evaluate  : 0.773 
Fit side-chains
   revert: symmetry clash
REVERT: A   39 LYS cc_start: 0.9094 (OUTLIER) cc_final: 0.8803 (mppt)
REVERT: A   43 GLU cc_start: 0.8812 (mt-10) cc_final: 0.8534 (mt-10)
REVERT: A   68 GLU cc_start: 0.7986 (tm-30) cc_final: 0.7555 (tp30)
REVERT: A   72 ASP cc_start: 0.8767 (p0) cc_final: 0.8555 (OUTLIER)
REVERT: C   43 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.8504 (mt-10)
REVERT: C  184 ASP cc_start: 0.9004 (m-30) cc_final: 0.8788 (m-30)
REVERT: B   43 GLU cc_start: 0.8802 (mt-10) cc_final: 0.8543 (mt-10)
REVERT: B  184 ASP cc_start: 0.9013 (m-30) cc_final: 0.8756 (m-30)
  outliers start: 16
  outliers final: 11
  residues processed: 72
  average time/residue: 1.3246
  time to fit residues: 100.9029
Evaluate side-chains
  74 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 62
  time to evaluate  : 0.772 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 LYS
Chi-restraints excluded: chain A residue   97 SER
Chi-restraints excluded: chain A residue  158 MET
Chi-restraints excluded: chain A residue  189 VAL
Chi-restraints excluded: chain A residue  218 LEU
Chi-restraints excluded: chain C residue   38 VAL
Chi-restraints excluded: chain C residue   43 GLU
Chi-restraints excluded: chain C residue  142 VAL
Chi-restraints excluded: chain C residue  218 LEU
Chi-restraints excluded: chain B residue   38 VAL
Chi-restraints excluded: chain B residue   72 ASP
Chi-restraints excluded: chain B residue  189 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 15 optimal weight:    0.5980
   chunk 18 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9990
   chunk 93 optimal weight:   10.0000
   chunk 31 optimal weight:    7.9990
   chunk 67 optimal weight:    3.9990
   chunk 33 optimal weight:    8.9990
   chunk 57 optimal weight:    1.9990
   chunk 47 optimal weight:    0.5980
   chunk 78 optimal weight:    1.9990
   chunk 87 optimal weight:    3.9990
   overall best weight:    1.2386

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

Flipped N/Q/H residues before XYZ refinement:
A 145 GLN
** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.079340 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2887 r_free = 0.2887 target = 0.064797 restraints weight = 13260.394|
|-----------------------------------------------------------------------------|
r_work (start): 0.2884 rms_B_bonded: 2.16
r_work: 0.2764 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.2636 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.2636
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9039
moved from start:          0.3366

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7613  Z= 0.193
  Angle     :  0.581   7.529  10325  Z= 0.321
  Chirality :  0.041   0.125   1164
  Planarity :  0.003   0.033   1290
  Dihedral  : 10.879  68.182   1245
  Min Nonbonded Distance : 1.996

Molprobity Statistics.
  All-atom Clashscore : 7.42
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  5.01 %
    Favored  : 94.88 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 21.51 %
    Favored  : 76.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.67 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

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: -0.28 (0.28), residues: 918
  helix:  0.96 (0.27), residues: 414
  sheet: -0.39 (0.42), residues: 165
  loop : -1.47 (0.32), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS A 294 
 PHE   0.007   0.001   PHE C 126 
 TYR   0.011   0.001   TYR C 315 
 ARG   0.008   0.000   ARG B  27 

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

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

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 66
  time to evaluate  : 0.788 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   39 LYS cc_start: 0.9069 (OUTLIER) cc_final: 0.8772 (mppt)
REVERT: A   43 GLU cc_start: 0.8787 (mt-10) cc_final: 0.8506 (mt-10)
REVERT: A   68 GLU cc_start: 0.7838 (tm-30) cc_final: 0.7389 (tp30)
REVERT: A   72 ASP cc_start: 0.8743 (p0) cc_final: 0.8486 (OUTLIER)
REVERT: C   43 GLU cc_start: 0.8767 (mp0) cc_final: 0.8498 (mt-10)
REVERT: C  184 ASP cc_start: 0.8959 (m-30) cc_final: 0.8733 (m-30)
REVERT: B   43 GLU cc_start: 0.8767 (mt-10) cc_final: 0.8507 (mt-10)
REVERT: B   68 GLU cc_start: 0.8241 (tm-30) cc_final: 0.8012 (tp30)
REVERT: B  223 SER cc_start: 0.8666 (m) cc_final: 0.8296 (p)
  outliers start: 16
  outliers final: 12
  residues processed: 76
  average time/residue: 1.3391
  time to fit residues: 107.5286
Evaluate side-chains
  73 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 61
  time to evaluate  : 0.775 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 LYS
Chi-restraints excluded: chain A residue   97 SER
Chi-restraints excluded: chain A residue  158 MET
Chi-restraints excluded: chain A residue  189 VAL
Chi-restraints excluded: chain A residue  218 LEU
Chi-restraints excluded: chain C residue   38 VAL
Chi-restraints excluded: chain C residue   77 GLU
Chi-restraints excluded: chain C residue  142 VAL
Chi-restraints excluded: chain C residue  218 LEU
Chi-restraints excluded: chain B residue   38 VAL
Chi-restraints excluded: chain B residue   72 ASP
Chi-restraints excluded: chain B residue   97 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 80 optimal weight:    7.9990
   chunk 21 optimal weight:    3.9990
   chunk 76 optimal weight:   10.0000
   chunk 92 optimal weight:    2.9990
   chunk 32 optimal weight:    6.9990
   chunk 4 optimal weight:    3.9990
   chunk 84 optimal weight:    2.9990
   chunk 57 optimal weight:    5.9990
   chunk 69 optimal weight:    0.5980
   chunk 20 optimal weight:    1.9990
   chunk 11 optimal weight:    7.9990
   overall best weight:    2.5188

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

Flipped N/Q/H residues before XYZ refinement:
** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 196 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.076933 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2831 r_free = 0.2831 target = 0.062285 restraints weight = 13283.879|
|-----------------------------------------------------------------------------|
r_work (start): 0.2826 rms_B_bonded: 2.15
r_work: 0.2704 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.2575 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.2575
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9087
moved from start:          0.3349

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   7613  Z= 0.302
  Angle     :  0.637   7.615  10325  Z= 0.349
  Chirality :  0.043   0.137   1164
  Planarity :  0.004   0.037   1290
  Dihedral  : 11.172  72.036   1245
  Min Nonbonded Distance : 1.967

Molprobity Statistics.
  All-atom Clashscore : 7.22
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  5.12 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 22.72 %
    Favored  : 75.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.67 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

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: -0.28 (0.28), residues: 918
  helix:  0.88 (0.26), residues: 414
  sheet: -0.31 (0.42), residues: 165
  loop : -1.41 (0.33), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS C 294 
 PHE   0.007   0.001   PHE C 126 
 TYR   0.019   0.001   TYR A 315 
 ARG   0.008   0.001   ARG C  27 

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

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

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 62
  time to evaluate  : 0.798 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   39 LYS cc_start: 0.9084 (OUTLIER) cc_final: 0.8782 (mppt)
REVERT: A   43 GLU cc_start: 0.8787 (mt-10) cc_final: 0.8509 (mt-10)
REVERT: A   68 GLU cc_start: 0.7977 (tm-30) cc_final: 0.7523 (tp30)
REVERT: A   72 ASP cc_start: 0.8772 (p0) cc_final: 0.8518 (OUTLIER)
REVERT: C   43 GLU cc_start: 0.8807 (mp0) cc_final: 0.8527 (mt-10)
REVERT: C  184 ASP cc_start: 0.8990 (m-30) cc_final: 0.8776 (m-30)
REVERT: B   43 GLU cc_start: 0.8767 (mt-10) cc_final: 0.8511 (mt-10)
REVERT: B   68 GLU cc_start: 0.8293 (tm-30) cc_final: 0.8037 (tp30)
  outliers start: 14
  outliers final: 13
  residues processed: 72
  average time/residue: 1.4018
  time to fit residues: 106.5576
Evaluate side-chains
  75 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 62
  time to evaluate  : 0.837 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 LYS
Chi-restraints excluded: chain A residue   77 GLU
Chi-restraints excluded: chain A residue   97 SER
Chi-restraints excluded: chain A residue  158 MET
Chi-restraints excluded: chain A residue  189 VAL
Chi-restraints excluded: chain A residue  218 LEU
Chi-restraints excluded: chain C residue   38 VAL
Chi-restraints excluded: chain C residue   77 GLU
Chi-restraints excluded: chain C residue  142 VAL
Chi-restraints excluded: chain C residue  218 LEU
Chi-restraints excluded: chain B residue   38 VAL
Chi-restraints excluded: chain B residue   72 ASP
Chi-restraints excluded: chain B residue   97 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 78 optimal weight:    6.9990
   chunk 27 optimal weight:    2.9990
   chunk 23 optimal weight:    0.6980
   chunk 28 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 61 optimal weight:    3.9990
   chunk 91 optimal weight:    5.9990
   chunk 62 optimal weight:    7.9990
   chunk 10 optimal weight:    0.4980
   chunk 66 optimal weight:    1.9990
   overall best weight:    1.4386

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

Flipped N/Q/H residues before XYZ refinement:
** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.078892 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2877 r_free = 0.2877 target = 0.064352 restraints weight = 13269.109|
|-----------------------------------------------------------------------------|
r_work (start): 0.2873 rms_B_bonded: 2.16
r_work: 0.2753 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.2624 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.2624
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9047
moved from start:          0.3443

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7613  Z= 0.208
  Angle     :  0.595   7.560  10325  Z= 0.327
  Chirality :  0.041   0.124   1164
  Planarity :  0.003   0.034   1290
  Dihedral  : 10.896  68.647   1245
  Min Nonbonded Distance : 1.990

Molprobity Statistics.
  All-atom Clashscore : 7.56
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  5.34 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 22.85 %
    Favored  : 75.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.67 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.16 (0.28), residues: 918
  helix:  1.01 (0.26), residues: 414
  sheet: -0.34 (0.42), residues: 165
  loop : -1.33 (0.33), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS A 294 
 PHE   0.007   0.001   PHE C 126 
 TYR   0.012   0.001   TYR A 315 
 ARG   0.008   0.000   ARG C  27 

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

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

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 62
  time to evaluate  : 0.774 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   39 LYS cc_start: 0.9095 (OUTLIER) cc_final: 0.8784 (mppt)
REVERT: A   43 GLU cc_start: 0.8770 (mt-10) cc_final: 0.8492 (mt-10)
REVERT: A   68 GLU cc_start: 0.7872 (tm-30) cc_final: 0.7409 (tp30)
REVERT: A   72 ASP cc_start: 0.8739 (p0) cc_final: 0.8419 (p0)
REVERT: C   43 GLU cc_start: 0.8798 (mp0) cc_final: 0.8514 (mt-10)
REVERT: C  184 ASP cc_start: 0.8956 (m-30) cc_final: 0.8737 (m-30)
REVERT: B   43 GLU cc_start: 0.8758 (mt-10) cc_final: 0.8500 (mt-10)
REVERT: B   68 GLU cc_start: 0.8214 (tm-30) cc_final: 0.7990 (tp30)
REVERT: B  223 SER cc_start: 0.8677 (m) cc_final: 0.8297 (p)
  outliers start: 14
  outliers final: 13
  residues processed: 73
  average time/residue: 1.2966
  time to fit residues: 100.0345
Evaluate side-chains
  73 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 59
  time to evaluate  : 0.748 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 LYS
Chi-restraints excluded: chain A residue   77 GLU
Chi-restraints excluded: chain A residue   97 SER
Chi-restraints excluded: chain A residue  158 MET
Chi-restraints excluded: chain A residue  189 VAL
Chi-restraints excluded: chain A residue  218 LEU
Chi-restraints excluded: chain C residue   38 VAL
Chi-restraints excluded: chain C residue   77 GLU
Chi-restraints excluded: chain C residue  142 VAL
Chi-restraints excluded: chain C residue  218 LEU
Chi-restraints excluded: chain B residue   38 VAL
Chi-restraints excluded: chain B residue   72 ASP
Chi-restraints excluded: chain B residue   77 GLU
Chi-restraints excluded: chain B residue  158 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 50 optimal weight:    1.9990
   chunk 66 optimal weight:    2.9990
   chunk 72 optimal weight:    3.9990
   chunk 48 optimal weight:    3.9990
   chunk 9 optimal weight:    0.5980
   chunk 13 optimal weight:    0.1980
   chunk 25 optimal weight:    6.9990
   chunk 20 optimal weight:    0.7980
   chunk 24 optimal weight:    0.7980
   chunk 89 optimal weight:    0.6980
   chunk 0 optimal weight:    1.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 196 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.082483 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2953 r_free = 0.2953 target = 0.067946 restraints weight = 13222.887|
|-----------------------------------------------------------------------------|
r_work (start): 0.2952 rms_B_bonded: 2.22
r_work: 0.2835 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.2706 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.2706
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8964
moved from start:          0.3682

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   7613  Z= 0.150
  Angle     :  0.551   7.679  10325  Z= 0.302
  Chirality :  0.040   0.124   1164
  Planarity :  0.003   0.032   1290
  Dihedral  : 10.465  61.671   1245
  Min Nonbonded Distance : 2.047

Molprobity Statistics.
  All-atom Clashscore : 7.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.01 %
    Favored  : 94.99 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 23.12 %
    Favored  : 75.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.67 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.02 (0.29), residues: 918
  helix:  1.13 (0.26), residues: 423
  sheet: -0.31 (0.42), residues: 162
  loop : -1.23 (0.34), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS A 294 
 PHE   0.006   0.001   PHE C 126 
 TYR   0.008   0.001   TYR C 315 
 ARG   0.007   0.000   ARG C  27 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4972.59 seconds
wall clock time: 86 minutes 41.93 seconds (5201.93 seconds total)