Starting phenix.real_space_refine
on Fri Jul 25 11:27:47 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7pcq_13325/07_2025/7pcq_13325_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7pcq_13325/07_2025/7pcq_13325.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.62
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7pcq_13325/07_2025/7pcq_13325.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7pcq_13325/07_2025/7pcq_13325.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7pcq_13325/07_2025/7pcq_13325_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7pcq_13325/07_2025/7pcq_13325_neut.cif"
  }
  resolution = 3.62
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.007
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Fe      4      7.16       5
     S      22      5.16       5
     C    4734      2.51       5
     N    1246      2.21       5
     O    1344      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 7350
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "A"
      Number of atoms: 1069
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 141, 1069
          Classifications: {'peptide': 141}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 133}
    Chain: "B"
      Number of atoms: 1134
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 146, 1123
          Classifications: {'peptide': 146}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 138}
      Conformer: "B"
        Number of residues, atoms: 146, 1123
          Classifications: {'peptide': 146}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 138}
          bond proxies already assigned to first conformer: 1141
    Chain: "C"
      Number of atoms: 1078
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 141, 1069
          Classifications: {'peptide': 141}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 133}
      Conformer: "B"
        Number of residues, atoms: 141, 1069
          Classifications: {'peptide': 141}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 133}
          bond proxies already assigned to first conformer: 1087
    Chain: "D"
      Number of atoms: 1111
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 146, 1111
          Classifications: {'peptide': 146}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 7, 'TRANS': 138}
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 13
          Unresolved non-hydrogen dihedrals: 11
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "E"
      Number of atoms: 2786
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 337, 2777
          Classifications: {'peptide': 337}
          Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 324}
      Conformer: "B"
        Number of residues, atoms: 337, 2777
          Classifications: {'peptide': 337}
          Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 324}
          bond proxies already assigned to first conformer: 2823
    Chain: "A"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 43
          Unusual residues: {'HEM': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 43
          Unusual residues: {'HEM': 1}
          Classifications: {'undetermined': 1}
    Chain: "C"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 43
          Unusual residues: {'HEM': 1}
          Classifications: {'undetermined': 1}
    Chain: "D"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 43
          Unusual residues: {'HEM': 1}
          Classifications: {'undetermined': 1}
  Residues with excluded nonbonded symmetry interactions: 3
    residue:
      pdb=" N  AARG B 104 " occ=0.50
      ... (20 atoms not shown)
      pdb=" NH2BARG B 104 " occ=0.50
    residue:
      pdb=" N  ALYS C  56 " occ=0.50
      ... (16 atoms not shown)
      pdb=" NZ BLYS C  56 " occ=0.50
    residue:
      pdb=" N  ALYS E 232 " occ=0.50
      ... (16 atoms not shown)
      pdb=" NZ BLYS E 232 " occ=0.50
  Time building chain proxies: 7.61, per 1000 atoms: 1.04
  Number of scatterers: 7350
  At special positions: 0
  Unit cell: (74.98, 99.104, 97.148, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Fe      4     26.01
     S      22     16.00
     O    1344      8.00
     N    1246      7.00
     C    4734      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=4, symmetry=0
  Number of additional bonds: simple=4, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.98
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1728

  Finding SS restraints...
    Secondary structure from input PDB file:
      41 helices and 5 sheets defined
      64.0% alpha, 13.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.74
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 18
    Processing helix  chain 'A' and resid 20 through 36
    Processing helix  chain 'A' and resid 37 through 43
    Processing helix  chain 'A' and resid 52 through 72
    Processing helix  chain 'A' and resid 75 through 80
    Processing helix  chain 'A' and resid 80 through 90
    Processing helix  chain 'A' and resid 94 through 113
      removed outlier: 3.619A  pdb=" N   PHE A  98 " --> pdb=" O   ASP A  94 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   LYS A  99 " --> pdb=" O   PRO A  95 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 118 through 138
    Processing helix  chain 'B' and resid 4 through 18
      removed outlier: 3.806A  pdb=" N   LYS B  17 " --> pdb=" O   ALA B  13 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 19 through 35
      removed outlier: 3.637A  pdb=" N   GLY B  24 " --> pdb=" O   VAL B  20 " (cutoff:3.500A)
      removed outlier: 4.208A  pdb=" N   GLY B  25 " --> pdb=" O   ASP B  21 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   LEU B  28 " --> pdb=" O   GLY B  24 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 36 through 41
    Processing helix  chain 'B' and resid 50 through 57
    Processing helix  chain 'B' and resid 57 through 77
    Processing helix  chain 'B' and resid 85 through 95
    Processing helix  chain 'B' and resid 99 through 119
      removed outlier: 3.773A  pdb=" N   PHE B 103 " --> pdb=" O   ASP B  99 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N  AARG B 104 " --> pdb=" O   PRO B 100 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 120 through 122
      No H-bonds generated for 'chain 'B' and resid 120 through 122'
    Processing helix  chain 'B' and resid 123 through 142
    Processing helix  chain 'C' and resid 3 through 18
    Processing helix  chain 'C' and resid 20 through 36
    Processing helix  chain 'C' and resid 37 through 43
    Processing helix  chain 'C' and resid 52 through 72
    Processing helix  chain 'C' and resid 75 through 90
      removed outlier: 5.372A  pdb=" N   ALA C  82 " --> pdb=" O   ASN C  78 " (cutoff:3.500A)
      removed outlier: 5.709A  pdb=" N   LEU C  83 " --> pdb=" O   ALA C  79 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 94 through 113
    Processing helix  chain 'C' and resid 118 through 137
    Processing helix  chain 'D' and resid 4 through 17
      removed outlier: 3.730A  pdb=" N   LYS D  17 " --> pdb=" O   ALA D  13 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 22 through 35
    Processing helix  chain 'D' and resid 36 through 46
      removed outlier: 3.889A  pdb=" N   GLU D  43 " --> pdb=" O   ARG D  40 " (cutoff:3.500A)
      removed outlier: 5.825A  pdb=" N   SER D  44 " --> pdb=" O   PHE D  41 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   GLY D  46 " --> pdb=" O   GLU D  43 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 50 through 57
    Processing helix  chain 'D' and resid 57 through 77
    Processing helix  chain 'D' and resid 81 through 95
      removed outlier: 5.140A  pdb=" N   THR D  87 " --> pdb=" O   GLY D  83 " (cutoff:3.500A)
      removed outlier: 5.725A  pdb=" N   LEU D  88 " --> pdb=" O   THR D  84 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 99 through 119
      removed outlier: 3.781A  pdb=" N   PHE D 103 " --> pdb=" O   ASP D  99 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   ARG D 104 " --> pdb=" O   PRO D 100 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 120 through 122
      No H-bonds generated for 'chain 'D' and resid 120 through 122'
    Processing helix  chain 'D' and resid 123 through 142
    Processing helix  chain 'E' and resid 128 through 135
      removed outlier: 4.049A  pdb=" N   LYS E 134 " --> pdb=" O   ARG E 130 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   ASN E 135 " --> pdb=" O   GLU E 131 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 163 through 169
    Processing helix  chain 'E' and resid 263 through 267
    Processing helix  chain 'E' and resid 269 through 285
      Proline residue:  E 281  - end of helix
    Processing helix  chain 'E' and resid 287 through 302
      removed outlier: 3.516A  pdb=" N   LYS E 297 " --> pdb=" O   TYR E 293 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   ASP E 300 " --> pdb=" O   ASN E 296 " (cutoff:3.500A)
      removed outlier: 3.993A  pdb=" N   LYS E 301 " --> pdb=" O   LYS E 297 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 303 through 332
      removed outlier: 4.407A  pdb=" N   ALA E 308 " --> pdb=" O   GLU E 304 " (cutoff:3.500A)
      removed outlier: 4.764A  pdb=" N   GLU E 309 " --> pdb=" O   LYS E 305 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 361 through 365
    Processing helix  chain 'E' and resid 451 through 460
      removed outlier: 3.747A  pdb=" N   LYS E 456 " --> pdb=" O   GLU E 452 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'E' and resid 148 through 151
      removed outlier: 5.814A  pdb=" N   GLY E 188 " --> pdb=" O   PRO E 173 " (cutoff:3.500A)
      removed outlier: 6.882A  pdb=" N   ARG E 224 " --> pdb=" O   LEU E 211 " (cutoff:3.500A)
      removed outlier: 5.823A  pdb=" N   LEU E 211 " --> pdb=" O   ARG E 224 " (cutoff:3.500A)
      removed outlier: 8.071A  pdb=" N   SER E 226 " --> pdb=" O   ILE E 209 " (cutoff:3.500A)
      removed outlier: 7.512A  pdb=" N   ILE E 209 " --> pdb=" O   SER E 226 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'E' and resid 153 through 156
      removed outlier: 6.057A  pdb=" N   HIS E 241 " --> pdb=" O   TRP E 195 " (cutoff:3.500A)
      removed outlier: 7.080A  pdb=" N   TRP E 195 " --> pdb=" O   HIS E 241 " (cutoff:3.500A)
      removed outlier: 4.843A  pdb=" N   VAL E 200 " --> pdb=" O   LEU E 207 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'E' and resid 153 through 156
    Processing sheet with id=AA4, first strand: chain 'E' and resid 346 through 348
      removed outlier: 4.126A  pdb=" N   ILE E 371 " --> pdb=" O   THR E 348 " (cutoff:3.500A)
      removed outlier: 6.544A  pdb=" N   LYS E 368 " --> pdb=" O   THR E 387 " (cutoff:3.500A)
      removed outlier: 7.023A  pdb=" N   THR E 387 " --> pdb=" O   LYS E 368 " (cutoff:3.500A)
      removed outlier: 5.988A  pdb=" N   GLU E 385 " --> pdb=" O   PRO E 370 " (cutoff:3.500A)
      removed outlier: 4.340A  pdb=" N   SER E 406 " --> pdb=" O   THR E 415 " (cutoff:3.500A)
      removed outlier: 6.986A  pdb=" N   ILE E 417 " --> pdb=" O   THR E 404 " (cutoff:3.500A)
      removed outlier: 6.027A  pdb=" N   THR E 404 " --> pdb=" O   ILE E 417 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'E' and resid 350 through 353
      removed outlier: 7.274A  pdb=" N   ASP E 428 " --> pdb=" O   VAL E 397 " (cutoff:3.500A)
      removed outlier: 4.931A  pdb=" N   VAL E 397 " --> pdb=" O   ASP E 428 " (cutoff:3.500A)
      removed outlier: 6.715A  pdb=" N   ILE E 430 " --> pdb=" O   PHE E 395 " (cutoff:3.500A)
      removed outlier: 4.355A  pdb=" N   PHE E 395 " --> pdb=" O   ILE E 430 " (cutoff:3.500A)
      removed outlier: 6.450A  pdb=" N   LYS E 432 " --> pdb=" O   LYS E 393 " (cutoff:3.500A)

    477 hydrogen bonds defined for protein.
    1340 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: 2.09

  Time building geometry restraints manager: 2.32 seconds

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

  Histogram of bond lengths:
        1.19 -     1.37: 2475
        1.37 -     1.55: 5010
        1.55 -     1.72: 14
        1.72 -     1.90: 38
        1.90 -     2.08: 16
  Bond restraints: 7553
  Sorted by residual:
  bond pdb=" CA  SER E 169 "
       pdb=" CB  SER E 169 "
    ideal  model  delta    sigma   weight residual
    1.527  1.465  0.062 1.36e-02 5.41e+03 2.07e+01
  bond pdb=" C   VAL D 109 "
       pdb=" O   VAL D 109 "
    ideal  model  delta    sigma   weight residual
    1.237  1.187  0.050 1.19e-02 7.06e+03 1.74e+01
  bond pdb=" N   VAL E 356 "
       pdb=" CA  VAL E 356 "
    ideal  model  delta    sigma   weight residual
    1.459  1.495 -0.037 9.10e-03 1.21e+04 1.62e+01
  bond pdb=" N   VAL E 234 "
       pdb=" CA  VAL E 234 "
    ideal  model  delta    sigma   weight residual
    1.456  1.496 -0.041 1.11e-02 8.12e+03 1.34e+01
  bond pdb=" C3D HEM A 201 "
       pdb=" CAD HEM A 201 "
    ideal  model  delta    sigma   weight residual
    1.544  1.472  0.072 2.00e-02 2.50e+03 1.30e+01
  ... (remaining 7548 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.27: 8730
        2.27 -     4.53: 1486
        4.53 -     6.80: 61
        6.80 -     9.06: 5
        9.06 -    11.33: 11
  Bond angle restraints: 10293
  Sorted by residual:
  angle pdb=" CA  GLN D 127 "
        pdb=" C   GLN D 127 "
        pdb=" O   GLN D 127 "
      ideal   model   delta    sigma   weight residual
     120.55  115.25    5.30 1.06e+00 8.90e-01 2.50e+01
  angle pdb=" CA  GLN B 127 "
        pdb=" C   GLN B 127 "
        pdb=" O   GLN B 127 "
      ideal   model   delta    sigma   weight residual
     120.55  115.29    5.26 1.06e+00 8.90e-01 2.46e+01
  angle pdb=" N   ASP E 364 "
        pdb=" CA  ASP E 364 "
        pdb=" C   ASP E 364 "
      ideal   model   delta    sigma   weight residual
     111.28  105.97    5.31 1.09e+00 8.42e-01 2.37e+01
  angle pdb=" CA  PHE C  43 "
        pdb=" C   PHE C  43 "
        pdb=" N   PRO C  44 "
      ideal   model   delta    sigma   weight residual
     117.78  122.72   -4.94 1.06e+00 8.90e-01 2.17e+01
  angle pdb=" CA  PHE A  43 "
        pdb=" C   PHE A  43 "
        pdb=" N   PRO A  44 "
      ideal   model   delta    sigma   weight residual
     117.78  122.69   -4.91 1.06e+00 8.90e-01 2.14e+01
  ... (remaining 10288 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.93: 4092
       17.93 -    35.85: 263
       35.85 -    53.78: 57
       53.78 -    71.71: 10
       71.71 -    89.63: 13
  Dihedral angle restraints: 4435
    sinusoidal: 1762
      harmonic: 2673
  Sorted by residual:
  dihedral pdb=" C2C HEM A 201 "
           pdb=" C3C HEM A 201 "
           pdb=" CAC HEM A 201 "
           pdb=" CBC HEM A 201 "
      ideal   model   delta sinusoidal    sigma   weight residual
      -0.00  -85.15   85.15     2      1.00e+01 1.00e-02 4.77e+01
  dihedral pdb=" C2C HEM C 201 "
           pdb=" C3C HEM C 201 "
           pdb=" CAC HEM C 201 "
           pdb=" CBC HEM C 201 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -72.45   72.45     2      1.00e+01 1.00e-02 4.36e+01
  dihedral pdb=" C2B HEM C 201 "
           pdb=" C3B HEM C 201 "
           pdb=" CAB HEM C 201 "
           pdb=" CBB HEM C 201 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  109.92   70.08     2      1.00e+01 1.00e-02 4.24e+01
  ... (remaining 4432 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.062: 505
       0.062 -    0.123: 342
       0.123 -    0.185: 219
       0.185 -    0.246: 40
       0.246 -    0.307: 8
  Chirality restraints: 1114
  Sorted by residual:
  chirality pdb=" CA  VAL E 176 "
            pdb=" N   VAL E 176 "
            pdb=" C   VAL E 176 "
            pdb=" CB  VAL E 176 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.75   -0.31 2.00e-01 2.50e+01 2.36e+00
  chirality pdb=" CA  ARG E 130 "
            pdb=" N   ARG E 130 "
            pdb=" C   ARG E 130 "
            pdb=" CB  ARG E 130 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.81   -0.30 2.00e-01 2.50e+01 2.28e+00
  chirality pdb=" CB  VAL A  70 "
            pdb=" CA  VAL A  70 "
            pdb=" CG1 VAL A  70 "
            pdb=" CG2 VAL A  70 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.36   -0.27 2.00e-01 2.50e+01 1.85e+00
  ... (remaining 1111 not shown)

  Planarity restraints: 1298
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR E 231 "    0.027 2.00e-02 2.50e+03   5.45e-02 2.98e+01
        pdb=" C   THR E 231 "   -0.094 2.00e-02 2.50e+03
        pdb=" O   THR E 231 "    0.035 2.00e-02 2.50e+03
        pdb=" N  BLYS E 232 "    0.033 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA AARG B 104 "   -0.026 2.00e-02 2.50e+03   5.42e-02 2.93e+01
        pdb=" C  AARG B 104 "    0.094 2.00e-02 2.50e+03
        pdb=" O  AARG B 104 "   -0.035 2.00e-02 2.50e+03
        pdb=" N   LEU B 105 "   -0.032 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS E 266 "    0.026 2.00e-02 2.50e+03   5.33e-02 2.84e+01
        pdb=" C   LYS E 266 "   -0.092 2.00e-02 2.50e+03
        pdb=" O   LYS E 266 "    0.034 2.00e-02 2.50e+03
        pdb=" N   PHE E 267 "    0.032 2.00e-02 2.50e+03
  ... (remaining 1295 not shown)

  Histogram of nonbonded interaction distances:
        2.56 -     3.03: 4121
        3.03 -     3.49: 7699
        3.49 -     3.96: 12608
        3.96 -     4.43: 14872
        4.43 -     4.90: 22478
  Nonbonded interactions: 61778
  Sorted by model distance:
  nonbonded pdb=" N   THR A 118 "
            pdb=" O   THR A 118 "
     model   vdw
     2.557 2.496
  nonbonded pdb=" N   THR C 118 "
            pdb=" O   THR C 118 "
     model   vdw
     2.557 2.496
  nonbonded pdb=" O   TYR C 140 "
            pdb=" C   ARG C 141 "
     model   vdw
     2.557 3.270
  nonbonded pdb=" O   TYR D  35 "
            pdb=" OG1 THR D  38 "
     model   vdw
     2.564 3.040
  nonbonded pdb=" O   TYR E 391 "
            pdb=" N   HIS E 434 "
     model   vdw
     2.567 3.120
  ... (remaining 61773 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 1 through 55 or resid 57 through 141 or resid 201))
  selection = (chain 'C' and (resid 1 through 55 or resid 57 through 141 or resid 201))
}
ncs_group {
  reference = (chain 'B' and (resid 1 through 64 or (resid 65 and (name N or name CA or name C \ 
 or name O or name CB )) or resid 66 through 103 or resid 105 through 119 or (re \ 
sid 120 through 121 and (name N or name CA or name C or name O or name CB )) or  \ 
resid 122 through 146 or resid 201))
  selection = (chain 'D' and (resid 1 through 103 or resid 105 through 146 or resid 201))
}

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=0.00 max=1.00 mean=0.99
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.730
  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:          0.300
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     23.900
  Find NCS groups from input model:        0.220
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.970
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.280
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8035
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      :  0.014   0.246   7557  Z= 0.937
  Angle     :  1.548  11.328  10293  Z= 1.156
  Chirality :  0.098   0.307   1114
  Planarity :  0.008   0.055   1298
  Dihedral  : 13.616  89.634   2707
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 1.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  0.78 %
    Allowed  :  5.58 %
    Favored  : 93.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.72 (0.27), residues: 910
  helix:  2.24 (0.22), residues: 525
  sheet: -0.47 (0.57), residues: 78
  loop : -0.33 (0.33), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP C  14 
 HIS   0.005   0.001   HIS C 122 
 PHE   0.010   0.002   PHE E 225 
 TYR   0.015   0.002   TYR E 251 
 ARG   0.007   0.001   ARG E 414 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.18934 (  471)
  hydrogen bonds       : angle       7.38637 ( 1340)
  covalent geometry    : bond        0.01284 ( 7553)
  covalent geometry    : angle       1.54795 (10293)
  Misc. bond           : bond        0.20433 (    4)

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

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

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 170
  time to evaluate  : 0.865 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   27 GLU cc_start: 0.8609 (tt0) cc_final: 0.8055 (tt0)
REVERT: A   39 THR cc_start: 0.8882 (p) cc_final: 0.7824 (p)
REVERT: B    7 GLU cc_start: 0.8740 (mt-10) cc_final: 0.8495 (mt-10)
REVERT: B   35 TYR cc_start: 0.8799 (m-80) cc_final: 0.8596 (m-10)
REVERT: B   47 ASP cc_start: 0.8397 (t0) cc_final: 0.8156 (t0)
REVERT: B   98 VAL cc_start: 0.9513 (t) cc_final: 0.9114 (p)
REVERT: B  105 LEU cc_start: 0.9260 (mt) cc_final: 0.9060 (mt)
REVERT: B  108 ASN cc_start: 0.9230 (m-40) cc_final: 0.8907 (t0)
REVERT: B  127 GLN cc_start: 0.8895 (tt0) cc_final: 0.8234 (tm-30)
REVERT: B  131 GLN cc_start: 0.8995 (mm110) cc_final: 0.8478 (mm110)
REVERT: C   14 TRP cc_start: 0.8183 (t-100) cc_final: 0.7827 (t-100)
REVERT: D   31 LEU cc_start: 0.9406 (tp) cc_final: 0.9200 (tt)
REVERT: D   38 THR cc_start: 0.8975 (p) cc_final: 0.8725 (p)
  outliers start: 5
  outliers final: 2
  residues processed: 175
  average time/residue: 0.2302
  time to fit residues: 52.0717
Evaluate side-chains
  99 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 97
  time to evaluate  : 0.895 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain E residue  416 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 75 optimal weight:    2.9990
   chunk 67 optimal weight:    9.9990
   chunk 37 optimal weight:    1.9990
   chunk 23 optimal weight:    0.0870
   chunk 45 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 69 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 42 optimal weight:    5.9990
   chunk 51 optimal weight:    9.9990
   chunk 80 optimal weight:    0.7980
   overall best weight:    1.3764

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

Flipped N/Q/H residues before XYZ refinement:
A  58 HIS
B  63 HIS
B 102 ASN
C  58 HIS
C 122 HIS
** D  63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 339 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2805 r_free = 0.2805 target = 0.033195 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2393 r_free = 0.2393 target = 0.022524 restraints weight = 162881.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2448 r_free = 0.2448 target = 0.024117 restraints weight = 56772.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2493 r_free = 0.2493 target = 0.025295 restraints weight = 31928.775|
|-----------------------------------------------------------------------------|
r_work (final): 0.2473
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2473
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2473 r_free = 0.2473    target_work(ls_wunit_k1) = 0.025         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2470 r_free = 0.2470    target_work(ls_wunit_k1) = 0.025         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.2470
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8681
moved from start:          0.3184

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.110   7557  Z= 0.145
  Angle     :  0.633   6.887  10293  Z= 0.325
  Chirality :  0.042   0.146   1114
  Planarity :  0.004   0.036   1298
  Dihedral  :  8.719  89.839   1007
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 7.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.11 %
    Favored  : 98.89 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 13.25 %
    Favored  : 85.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.49 (0.27), residues: 910
  helix:  2.72 (0.22), residues: 523
  sheet:  0.17 (0.56), residues: 85
  loop :  0.21 (0.35), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP C  14 
 HIS   0.005   0.001   HIS E 369 
 PHE   0.017   0.002   PHE E 178 
 TYR   0.011   0.001   TYR B 130 
 ARG   0.007   0.001   ARG E 403 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03598 (  471)
  hydrogen bonds       : angle       5.14875 ( 1340)
  covalent geometry    : bond        0.00380 ( 7553)
  covalent geometry    : angle       0.63279 (10293)
  Misc. bond           : bond        0.06323 (    4)

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

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

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 104
  time to evaluate  : 0.790 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   27 GLU cc_start: 0.9311 (tt0) cc_final: 0.8790 (tt0)
REVERT: A   94 ASP cc_start: 0.9192 (t0) cc_final: 0.8987 (t0)
REVERT: B    7 GLU cc_start: 0.9509 (mt-10) cc_final: 0.9239 (mt-10)
REVERT: B   21 ASP cc_start: 0.9441 (p0) cc_final: 0.8419 (p0)
REVERT: B   47 ASP cc_start: 0.9023 (t0) cc_final: 0.8672 (t0)
REVERT: B  108 ASN cc_start: 0.9412 (m-40) cc_final: 0.9092 (t0)
REVERT: B  127 GLN cc_start: 0.9469 (tt0) cc_final: 0.8673 (tm-30)
REVERT: B  131 GLN cc_start: 0.9454 (mm110) cc_final: 0.9086 (mm110)
REVERT: D    6 GLU cc_start: 0.9258 (pm20) cc_final: 0.9057 (pm20)
REVERT: D   26 GLU cc_start: 0.9310 (mm-30) cc_final: 0.8971 (mm-30)
REVERT: D  127 GLN cc_start: 0.9781 (tt0) cc_final: 0.9205 (tm-30)
REVERT: D  139 ASN cc_start: 0.9768 (m-40) cc_final: 0.9557 (t0)
REVERT: D  144 LYS cc_start: 0.9222 (mmtt) cc_final: 0.8864 (mmtp)
REVERT: E  155 MET cc_start: 0.8825 (mmm) cc_final: 0.8589 (mmp)
REVERT: E  190 GLN cc_start: 0.9357 (mt0) cc_final: 0.8753 (mp10)
REVERT: E  439 ASP cc_start: 0.9227 (t0) cc_final: 0.9014 (t0)
  outliers start: 10
  outliers final: 6
  residues processed: 108
  average time/residue: 0.1982
  time to fit residues: 28.7608
Evaluate side-chains
  90 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 84
  time to evaluate  : 0.788 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  104 CYS
Chi-restraints excluded: chain A residue  126 ASP
Chi-restraints excluded: chain C residue  126 ASP
Chi-restraints excluded: chain D residue    4 THR
Chi-restraints excluded: chain D residue   49 SER
Chi-restraints excluded: chain D residue  112 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 76 optimal weight:    0.5980
   chunk 43 optimal weight:    0.9990
   chunk 15 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9980
   chunk 2 optimal weight:    1.9990
   chunk 68 optimal weight:    6.9990
   chunk 17 optimal weight:    2.9990
   chunk 29 optimal weight:    1.9990
   chunk 52 optimal weight:    0.7980
   chunk 58 optimal weight:    6.9990
   chunk 21 optimal weight:    1.9990
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
B  63 HIS
** D  63 HIS ** 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 = 0.2778 r_free = 0.2778 target = 0.032337 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2389 r_free = 0.2389 target = 0.022514 restraints weight = 175592.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2443 r_free = 0.2443 target = 0.024024 restraints weight = 57004.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2485 r_free = 0.2485 target = 0.025153 restraints weight = 31566.219|
|-----------------------------------------------------------------------------|
r_work (final): 0.2455
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2455
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2455 r_free = 0.2455    target_work(ls_wunit_k1) = 0.024         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2452 r_free = 0.2452    target_work(ls_wunit_k1) = 0.024         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.2452
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8757
moved from start:          0.3752

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.120   7557  Z= 0.123
  Angle     :  0.602   9.374  10293  Z= 0.301
  Chirality :  0.040   0.157   1114
  Planarity :  0.004   0.041   1298
  Dihedral  :  8.451  89.896   1004
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 7.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 14.03 %
    Favored  : 84.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.52 (0.28), residues: 910
  helix:  2.69 (0.22), residues: 523
  sheet:  0.17 (0.52), residues: 101
  loop :  0.36 (0.36), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A  14 
 HIS   0.004   0.001   HIS E 369 
 PHE   0.010   0.001   PHE E 178 
 TYR   0.013   0.001   TYR B  35 
 ARG   0.004   0.001   ARG D  40 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03220 (  471)
  hydrogen bonds       : angle       4.81910 ( 1340)
  covalent geometry    : bond        0.00328 ( 7553)
  covalent geometry    : angle       0.60204 (10293)
  Misc. bond           : bond        0.08180 (    4)

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

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

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 91
  time to evaluate  : 0.861 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 ASP cc_start: 0.9296 (t0) cc_final: 0.9025 (t0)
REVERT: B    7 GLU cc_start: 0.9538 (mt-10) cc_final: 0.9186 (mt-10)
REVERT: B   21 ASP cc_start: 0.9054 (p0) cc_final: 0.8558 (p0)
REVERT: B   22 GLU cc_start: 0.9288 (mm-30) cc_final: 0.8936 (mm-30)
REVERT: B   47 ASP cc_start: 0.9139 (t0) cc_final: 0.8831 (t0)
REVERT: B   99 ASP cc_start: 0.8719 (t0) cc_final: 0.8288 (t0)
REVERT: B  101 GLU cc_start: 0.9446 (mm-30) cc_final: 0.8868 (mp0)
REVERT: B  108 ASN cc_start: 0.9427 (m-40) cc_final: 0.9128 (t0)
REVERT: B  127 GLN cc_start: 0.9502 (tt0) cc_final: 0.8735 (tm-30)
REVERT: B  131 GLN cc_start: 0.9404 (mm110) cc_final: 0.9055 (mm110)
REVERT: C   68 ASN cc_start: 0.9527 (t0) cc_final: 0.9303 (t0)
REVERT: D   22 GLU cc_start: 0.8793 (tm-30) cc_final: 0.8381 (tm-30)
REVERT: D   26 GLU cc_start: 0.9396 (mm-30) cc_final: 0.9003 (mm-30)
REVERT: D   71 PHE cc_start: 0.9718 (m-80) cc_final: 0.9346 (m-80)
REVERT: D   99 ASP cc_start: 0.8777 (t0) cc_final: 0.8230 (t0)
REVERT: D  104 ARG cc_start: 0.9547 (ptm-80) cc_final: 0.9299 (mtm-85)
REVERT: D  127 GLN cc_start: 0.9770 (tt0) cc_final: 0.9223 (tm-30)
REVERT: E  382 MET cc_start: 0.8644 (OUTLIER) cc_final: 0.8422 (mpp)
REVERT: E  439 ASP cc_start: 0.9340 (t0) cc_final: 0.9099 (t0)
  outliers start: 9
  outliers final: 7
  residues processed: 95
  average time/residue: 0.1988
  time to fit residues: 25.7642
Evaluate side-chains
  89 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 81
  time to evaluate  : 0.915 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 SER
Chi-restraints excluded: chain A residue  126 ASP
Chi-restraints excluded: chain C residue  126 ASP
Chi-restraints excluded: chain D residue   49 SER
Chi-restraints excluded: chain D residue  112 CYS
Chi-restraints excluded: chain E residue  382 MET
Chi-restraints excluded: chain E residue  386 THR
Chi-restraints excluded: chain E residue  416 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 55 optimal weight:    7.9990
   chunk 7 optimal weight:    8.9990
   chunk 77 optimal weight:    6.9990
   chunk 15 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9990
   chunk 80 optimal weight:    0.0870
   chunk 14 optimal weight:    0.7980
   chunk 23 optimal weight:    7.9990
   chunk 32 optimal weight:    2.9990
   chunk 62 optimal weight:    9.9990
   overall best weight:    1.1764

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

Flipped N/Q/H residues before XYZ refinement:
A  78 ASN
B  63 HIS
** D  63 HIS ** 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 = 0.2751 r_free = 0.2751 target = 0.031326 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2358 r_free = 0.2358 target = 0.021774 restraints weight = 172817.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2414 r_free = 0.2414 target = 0.023226 restraints weight = 56569.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.2459 r_free = 0.2459 target = 0.024336 restraints weight = 31510.685|
|-----------------------------------------------------------------------------|
r_work (final): 0.2427
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2427
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2427 r_free = 0.2427    target_work(ls_wunit_k1) = 0.023         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2426 r_free = 0.2426    target_work(ls_wunit_k1) = 0.023         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.2426
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8812
moved from start:          0.4225

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.122   7557  Z= 0.121
  Angle     :  0.590   9.662  10293  Z= 0.291
  Chirality :  0.039   0.166   1114
  Planarity :  0.004   0.045   1298
  Dihedral  :  8.421  84.923   1004
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 8.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.11 %
    Favored  : 98.89 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 13.90 %
    Favored  : 84.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.58 (0.28), residues: 910
  helix:  2.76 (0.22), residues: 523
  sheet:  0.22 (0.53), residues: 102
  loop :  0.33 (0.37), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A  14 
 HIS   0.003   0.001   HIS A  87 
 PHE   0.011   0.001   PHE E 178 
 TYR   0.016   0.001   TYR B  35 
 ARG   0.007   0.001   ARG E 403 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02991 (  471)
  hydrogen bonds       : angle       4.63261 ( 1340)
  covalent geometry    : bond        0.00333 ( 7553)
  covalent geometry    : angle       0.58965 (10293)
  Misc. bond           : bond        0.08760 (    4)

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

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

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 87
  time to evaluate  : 0.879 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 ASP cc_start: 0.9335 (t0) cc_final: 0.8873 (t0)
REVERT: B    7 GLU cc_start: 0.9533 (mt-10) cc_final: 0.9134 (mt-10)
REVERT: B   21 ASP cc_start: 0.9077 (p0) cc_final: 0.8317 (p0)
REVERT: B   22 GLU cc_start: 0.9271 (mm-30) cc_final: 0.8758 (mm-30)
REVERT: B   47 ASP cc_start: 0.9216 (t0) cc_final: 0.8942 (t0)
REVERT: B  108 ASN cc_start: 0.9423 (m-40) cc_final: 0.9114 (t0)
REVERT: B  127 GLN cc_start: 0.9498 (tt0) cc_final: 0.8775 (tm-30)
REVERT: B  131 GLN cc_start: 0.9399 (mm110) cc_final: 0.9074 (mm110)
REVERT: C   32 MET cc_start: 0.9631 (ttm) cc_final: 0.9318 (mmm)
REVERT: C   68 ASN cc_start: 0.9551 (t0) cc_final: 0.9322 (t0)
REVERT: D   22 GLU cc_start: 0.8849 (tm-30) cc_final: 0.8338 (tm-30)
REVERT: D   26 GLU cc_start: 0.9461 (mm-30) cc_final: 0.9052 (mm-30)
REVERT: D   99 ASP cc_start: 0.8910 (t0) cc_final: 0.8436 (t0)
REVERT: D  127 GLN cc_start: 0.9762 (tt0) cc_final: 0.9226 (tm-30)
REVERT: E  254 MET cc_start: 0.9539 (ttt) cc_final: 0.9256 (tpp)
REVERT: E  392 TRP cc_start: 0.9174 (m100) cc_final: 0.8487 (m100)
REVERT: E  439 ASP cc_start: 0.9395 (t0) cc_final: 0.9173 (t0)
  outliers start: 12
  outliers final: 7
  residues processed: 95
  average time/residue: 0.2028
  time to fit residues: 26.4500
Evaluate side-chains
  87 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 80
  time to evaluate  : 0.792 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 SER
Chi-restraints excluded: chain C residue  105 LEU
Chi-restraints excluded: chain C residue  126 ASP
Chi-restraints excluded: chain D residue    4 THR
Chi-restraints excluded: chain D residue   49 SER
Chi-restraints excluded: chain D residue  112 CYS
Chi-restraints excluded: chain E residue  416 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 46 optimal weight:    6.9990
   chunk 80 optimal weight:    0.3980
   chunk 77 optimal weight:   10.0000
   chunk 60 optimal weight:   10.0000
   chunk 84 optimal weight:    5.9990
   chunk 62 optimal weight:    4.9990
   chunk 40 optimal weight:    3.9990
   chunk 78 optimal weight:    2.9990
   chunk 55 optimal weight:    4.9990
   chunk 47 optimal weight:    6.9990
   chunk 19 optimal weight:    0.8980
   overall best weight:    2.6586

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

Flipped N/Q/H residues before XYZ refinement:
** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  63 HIS ** 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 = 0.2685 r_free = 0.2685 target = 0.029176 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2283 r_free = 0.2283 target = 0.019863 restraints weight = 205174.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2338 r_free = 0.2338 target = 0.021277 restraints weight = 61658.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2380 r_free = 0.2380 target = 0.022281 restraints weight = 33358.111|
|-----------------------------------------------------------------------------|
r_work (final): 0.2361
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2362
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2362 r_free = 0.2362    target_work(ls_wunit_k1) = 0.022         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2361 r_free = 0.2361    target_work(ls_wunit_k1) = 0.022         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.2361
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8943
moved from start:          0.4807

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.219   7557  Z= 0.195
  Angle     :  0.665  10.144  10293  Z= 0.322
  Chirality :  0.041   0.328   1114
  Planarity :  0.004   0.044   1298
  Dihedral  :  8.583  88.744   1004
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 9.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 14.03 %
    Favored  : 84.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.63 (0.28), residues: 910
  helix:  2.73 (0.22), residues: 523
  sheet:  0.44 (0.55), residues: 98
  loop :  0.41 (0.36), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A  14 
 HIS   0.004   0.001   HIS A  87 
 PHE   0.022   0.001   PHE E 418 
 TYR   0.017   0.001   TYR B  35 
 ARG   0.004   0.001   ARG E 403 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03213 (  471)
  hydrogen bonds       : angle       4.66287 ( 1340)
  covalent geometry    : bond        0.00518 ( 7553)
  covalent geometry    : angle       0.66473 (10293)
  Misc. bond           : bond        0.16113 (    4)

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

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

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 79
  time to evaluate  : 0.786 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   30 GLU cc_start: 0.9509 (pt0) cc_final: 0.9155 (tt0)
REVERT: A   94 ASP cc_start: 0.9489 (t0) cc_final: 0.9103 (t0)
REVERT: B    7 GLU cc_start: 0.9564 (mt-10) cc_final: 0.9181 (mt-10)
REVERT: B   21 ASP cc_start: 0.9140 (p0) cc_final: 0.8360 (p0)
REVERT: B   22 GLU cc_start: 0.9287 (mm-30) cc_final: 0.8754 (mm-30)
REVERT: B   73 ASP cc_start: 0.9401 (m-30) cc_final: 0.9101 (t0)
REVERT: B  108 ASN cc_start: 0.9466 (m-40) cc_final: 0.9072 (t0)
REVERT: B  127 GLN cc_start: 0.9524 (tt0) cc_final: 0.8801 (tm-30)
REVERT: B  131 GLN cc_start: 0.9522 (mm110) cc_final: 0.9055 (mm110)
REVERT: C   68 ASN cc_start: 0.9578 (t0) cc_final: 0.9357 (t0)
REVERT: D   22 GLU cc_start: 0.8988 (tm-30) cc_final: 0.8385 (tm-30)
REVERT: D   26 GLU cc_start: 0.9473 (mm-30) cc_final: 0.8992 (mm-30)
REVERT: D   55 MET cc_start: 0.9292 (mmp) cc_final: 0.8970 (mmp)
REVERT: D   71 PHE cc_start: 0.9693 (m-80) cc_final: 0.9449 (m-80)
REVERT: D   99 ASP cc_start: 0.9015 (t0) cc_final: 0.8657 (t0)
REVERT: D  127 GLN cc_start: 0.9745 (tt0) cc_final: 0.9234 (tm-30)
REVERT: D  144 LYS cc_start: 0.9230 (mmtt) cc_final: 0.8904 (mmtp)
REVERT: E  382 MET cc_start: 0.8758 (mpp) cc_final: 0.8538 (mpp)
REVERT: E  384 MET cc_start: 0.9706 (ttm) cc_final: 0.9441 (ttm)
  outliers start: 13
  outliers final: 8
  residues processed: 88
  average time/residue: 0.2061
  time to fit residues: 24.7330
Evaluate side-chains
  83 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 75
  time to evaluate  : 1.009 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain A residue  126 ASP
Chi-restraints excluded: chain B residue   32 LEU
Chi-restraints excluded: chain C residue  126 ASP
Chi-restraints excluded: chain D residue    4 THR
Chi-restraints excluded: chain D residue   49 SER
Chi-restraints excluded: chain D residue  112 CYS
Chi-restraints excluded: chain E residue  416 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 42 optimal weight:    7.9990
   chunk 39 optimal weight:    0.9980
   chunk 25 optimal weight:    0.9990
   chunk 45 optimal weight:    2.9990
   chunk 71 optimal weight:    0.6980
   chunk 0 optimal weight:   10.0000
   chunk 18 optimal weight:    6.9990
   chunk 16 optimal weight:    0.6980
   chunk 5 optimal weight:    0.9980
   chunk 80 optimal weight:    0.6980
   chunk 54 optimal weight:    1.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  63 HIS ** 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 = 0.2714 r_free = 0.2714 target = 0.029789 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2304 r_free = 0.2304 target = 0.019996 restraints weight = 195506.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2357 r_free = 0.2357 target = 0.021375 restraints weight = 58794.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2398 r_free = 0.2398 target = 0.022425 restraints weight = 32352.658|
|-----------------------------------------------------------------------------|
r_work (final): 0.2371
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2375
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2375 r_free = 0.2375    target_work(ls_wunit_k1) = 0.022         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2375 r_free = 0.2375    target_work(ls_wunit_k1) = 0.022         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.2375
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8903
moved from start:          0.4977

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.139   7557  Z= 0.114
  Angle     :  0.608  10.983  10293  Z= 0.298
  Chirality :  0.040   0.317   1114
  Planarity :  0.004   0.045   1298
  Dihedral  :  8.364  86.706   1004
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 8.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 13.90 %
    Favored  : 84.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.64 (0.28), residues: 910
  helix:  2.78 (0.22), residues: 521
  sheet:  0.53 (0.55), residues: 98
  loop :  0.30 (0.36), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  14 
 HIS   0.004   0.001   HIS A  87 
 PHE   0.015   0.001   PHE E 418 
 TYR   0.013   0.001   TYR C 140 
 ARG   0.008   0.001   ARG E 403 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02854 (  471)
  hydrogen bonds       : angle       4.47954 ( 1340)
  covalent geometry    : bond        0.00309 ( 7553)
  covalent geometry    : angle       0.60806 (10293)
  Misc. bond           : bond        0.08547 (    4)

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

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

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 84
  time to evaluate  : 0.884 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   27 GLU cc_start: 0.9372 (tt0) cc_final: 0.8745 (tt0)
REVERT: A   30 GLU cc_start: 0.9498 (pt0) cc_final: 0.9040 (tt0)
REVERT: A   94 ASP cc_start: 0.9449 (t0) cc_final: 0.9028 (t0)
REVERT: B    7 GLU cc_start: 0.9580 (mt-10) cc_final: 0.9170 (mt-10)
REVERT: B   21 ASP cc_start: 0.9127 (p0) cc_final: 0.8263 (p0)
REVERT: B   22 GLU cc_start: 0.9253 (mm-30) cc_final: 0.8672 (mm-30)
REVERT: B  127 GLN cc_start: 0.9473 (tt0) cc_final: 0.8739 (tm-30)
REVERT: C   32 MET cc_start: 0.9602 (ttm) cc_final: 0.9311 (mtp)
REVERT: C   68 ASN cc_start: 0.9584 (t0) cc_final: 0.9375 (t0)
REVERT: D   22 GLU cc_start: 0.8920 (tm-30) cc_final: 0.8301 (tm-30)
REVERT: D   26 GLU cc_start: 0.9504 (mm-30) cc_final: 0.9006 (mm-30)
REVERT: D   55 MET cc_start: 0.9305 (mmp) cc_final: 0.8997 (mmp)
REVERT: D   99 ASP cc_start: 0.9011 (t0) cc_final: 0.8519 (t0)
REVERT: D  127 GLN cc_start: 0.9757 (tt0) cc_final: 0.9216 (tm-30)
REVERT: E  124 MET cc_start: 0.8090 (mmm) cc_final: 0.6469 (tmm)
REVERT: E  382 MET cc_start: 0.8748 (mpp) cc_final: 0.8399 (mpp)
REVERT: E  384 MET cc_start: 0.9734 (ttm) cc_final: 0.9497 (ttm)
REVERT: E  396 MET cc_start: 0.9222 (tpp) cc_final: 0.8944 (tpp)
  outliers start: 9
  outliers final: 7
  residues processed: 91
  average time/residue: 0.2059
  time to fit residues: 25.5920
Evaluate side-chains
  85 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 78
  time to evaluate  : 0.784 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain B residue   32 LEU
Chi-restraints excluded: chain C residue  126 ASP
Chi-restraints excluded: chain D residue    4 THR
Chi-restraints excluded: chain D residue   49 SER
Chi-restraints excluded: chain D residue  112 CYS
Chi-restraints excluded: chain E residue  416 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 4 optimal weight:    5.9990
   chunk 53 optimal weight:    1.9990
   chunk 2 optimal weight:    5.9990
   chunk 82 optimal weight:    4.9990
   chunk 5 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   chunk 81 optimal weight:    7.9990
   chunk 25 optimal weight:    0.8980
   chunk 57 optimal weight:    9.9990
   chunk 73 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9990
   overall best weight:    1.5788

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

Flipped N/Q/H residues before XYZ refinement:
** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  63 HIS ** 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 = 0.2708 r_free = 0.2708 target = 0.029578 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2295 r_free = 0.2295 target = 0.019843 restraints weight = 181474.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2348 r_free = 0.2348 target = 0.021202 restraints weight = 58247.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2389 r_free = 0.2389 target = 0.022199 restraints weight = 32507.912|
|-----------------------------------------------------------------------------|
r_work (final): 0.2363
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2363
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2363 r_free = 0.2363    target_work(ls_wunit_k1) = 0.022         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2364 r_free = 0.2364    target_work(ls_wunit_k1) = 0.022         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.2364
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8949
moved from start:          0.5199

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.176   7557  Z= 0.139
  Angle     :  0.633  11.532  10293  Z= 0.307
  Chirality :  0.040   0.284   1114
  Planarity :  0.004   0.045   1298
  Dihedral  :  8.278  86.039   1004
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 8.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.66 %
    Favored  : 98.34 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 14.81 %
    Favored  : 83.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.57 (0.28), residues: 910
  helix:  2.73 (0.22), residues: 523
  sheet:  0.46 (0.56), residues: 98
  loop :  0.24 (0.36), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A  14 
 HIS   0.004   0.001   HIS A  87 
 PHE   0.015   0.001   PHE E 418 
 TYR   0.014   0.001   TYR C 140 
 ARG   0.006   0.001   ARG E 403 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02948 (  471)
  hydrogen bonds       : angle       4.49409 ( 1340)
  covalent geometry    : bond        0.00387 ( 7553)
  covalent geometry    : angle       0.63315 (10293)
  Misc. bond           : bond        0.11360 (    4)

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

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

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 78
  time to evaluate  : 0.809 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   27 GLU cc_start: 0.9402 (tt0) cc_final: 0.8754 (tt0)
REVERT: A   30 GLU cc_start: 0.9502 (pt0) cc_final: 0.9035 (tt0)
REVERT: A   94 ASP cc_start: 0.9448 (t0) cc_final: 0.9035 (t0)
REVERT: B    7 GLU cc_start: 0.9589 (mt-10) cc_final: 0.9214 (mt-10)
REVERT: B   21 ASP cc_start: 0.9114 (p0) cc_final: 0.8259 (p0)
REVERT: B   22 GLU cc_start: 0.9207 (mm-30) cc_final: 0.8665 (mm-30)
REVERT: B   73 ASP cc_start: 0.9342 (m-30) cc_final: 0.9091 (t0)
REVERT: B  121 GLU cc_start: 0.9120 (tp30) cc_final: 0.8748 (tp30)
REVERT: B  127 GLN cc_start: 0.9510 (tt0) cc_final: 0.8802 (tm-30)
REVERT: C   32 MET cc_start: 0.9569 (ttm) cc_final: 0.9316 (mtp)
REVERT: C   68 ASN cc_start: 0.9576 (t0) cc_final: 0.9364 (t0)
REVERT: C  116 GLU cc_start: 0.8990 (pm20) cc_final: 0.8725 (pm20)
REVERT: D   22 GLU cc_start: 0.8944 (tm-30) cc_final: 0.8306 (tm-30)
REVERT: D   26 GLU cc_start: 0.9515 (mm-30) cc_final: 0.9035 (mm-30)
REVERT: D   55 MET cc_start: 0.9365 (mmp) cc_final: 0.9057 (mmp)
REVERT: D   71 PHE cc_start: 0.9631 (m-80) cc_final: 0.9371 (m-80)
REVERT: D   99 ASP cc_start: 0.9039 (t0) cc_final: 0.8568 (t0)
REVERT: D  127 GLN cc_start: 0.9764 (tt0) cc_final: 0.9238 (tm-30)
REVERT: D  132 LYS cc_start: 0.9692 (mtpp) cc_final: 0.9371 (mtmm)
REVERT: E  124 MET cc_start: 0.8110 (mmm) cc_final: 0.6544 (tmm)
REVERT: E  382 MET cc_start: 0.8772 (mpp) cc_final: 0.8414 (mpp)
REVERT: E  384 MET cc_start: 0.9755 (ttm) cc_final: 0.9495 (mtp)
  outliers start: 9
  outliers final: 8
  residues processed: 85
  average time/residue: 0.2227
  time to fit residues: 25.9386
Evaluate side-chains
  83 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 75
  time to evaluate  : 0.881 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 SER
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain B residue   32 LEU
Chi-restraints excluded: chain C residue  126 ASP
Chi-restraints excluded: chain D residue    4 THR
Chi-restraints excluded: chain D residue   49 SER
Chi-restraints excluded: chain D residue  112 CYS
Chi-restraints excluded: chain E residue  416 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 82 optimal weight:    3.9990
   chunk 79 optimal weight:    4.9990
   chunk 45 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9990
   chunk 55 optimal weight:    9.9990
   chunk 59 optimal weight:    7.9990
   chunk 83 optimal weight:    6.9990
   chunk 56 optimal weight:    9.9990
   chunk 47 optimal weight:    5.9990
   chunk 24 optimal weight:    0.9980
   chunk 53 optimal weight:    0.8980
   overall best weight:    1.5784

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

Flipped N/Q/H residues before XYZ refinement:
** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  63 HIS ** 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 = 0.2703 r_free = 0.2703 target = 0.029337 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2289 r_free = 0.2289 target = 0.019648 restraints weight = 184238.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2345 r_free = 0.2345 target = 0.021036 restraints weight = 58845.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2385 r_free = 0.2385 target = 0.022040 restraints weight = 32585.342|
|-----------------------------------------------------------------------------|
r_work (final): 0.2352
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2352
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2352 r_free = 0.2352    target_work(ls_wunit_k1) = 0.022         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2352 r_free = 0.2352    target_work(ls_wunit_k1) = 0.022         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.2352
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8951
moved from start:          0.5378

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.181   7557  Z= 0.138
  Angle     :  0.638  11.805  10293  Z= 0.309
  Chirality :  0.040   0.259   1114
  Planarity :  0.004   0.045   1298
  Dihedral  :  8.169  87.048   1004
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 9.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 15.45 %
    Favored  : 83.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.55 (0.28), residues: 910
  helix:  2.75 (0.22), residues: 521
  sheet:  0.39 (0.56), residues: 98
  loop :  0.21 (0.37), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  14 
 HIS   0.004   0.001   HIS A  87 
 PHE   0.015   0.001   PHE E 418 
 TYR   0.015   0.001   TYR C 140 
 ARG   0.008   0.001   ARG E 403 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02852 (  471)
  hydrogen bonds       : angle       4.46428 ( 1340)
  covalent geometry    : bond        0.00386 ( 7553)
  covalent geometry    : angle       0.63849 (10293)
  Misc. bond           : bond        0.11471 (    4)

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

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

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 75
  time to evaluate  : 0.875 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 ASP cc_start: 0.9440 (t0) cc_final: 0.9038 (t0)
REVERT: B    7 GLU cc_start: 0.9569 (mt-10) cc_final: 0.9197 (mt-10)
REVERT: B   21 ASP cc_start: 0.9088 (p0) cc_final: 0.8234 (p0)
REVERT: B   22 GLU cc_start: 0.9214 (mm-30) cc_final: 0.8666 (mm-30)
REVERT: B   26 GLU cc_start: 0.9372 (tp30) cc_final: 0.9154 (tp30)
REVERT: B   73 ASP cc_start: 0.9333 (m-30) cc_final: 0.9105 (t0)
REVERT: B  121 GLU cc_start: 0.9169 (tp30) cc_final: 0.8778 (tp30)
REVERT: B  127 GLN cc_start: 0.9507 (tt0) cc_final: 0.8816 (tm-30)
REVERT: C  116 GLU cc_start: 0.8954 (pm20) cc_final: 0.8740 (pm20)
REVERT: D   22 GLU cc_start: 0.8950 (tm-30) cc_final: 0.8249 (tm-30)
REVERT: D   26 GLU cc_start: 0.9526 (mm-30) cc_final: 0.9016 (mm-30)
REVERT: D   55 MET cc_start: 0.9367 (mmp) cc_final: 0.9053 (mmp)
REVERT: D   99 ASP cc_start: 0.9043 (t0) cc_final: 0.8579 (t0)
REVERT: D  127 GLN cc_start: 0.9774 (tt0) cc_final: 0.9246 (tm-30)
REVERT: D  132 LYS cc_start: 0.9694 (mtpp) cc_final: 0.9373 (mtmm)
REVERT: E  124 MET cc_start: 0.8136 (mmm) cc_final: 0.6690 (tmm)
REVERT: E  382 MET cc_start: 0.8794 (mpp) cc_final: 0.8393 (mpp)
REVERT: E  384 MET cc_start: 0.9758 (ttm) cc_final: 0.9516 (mtp)
  outliers start: 10
  outliers final: 8
  residues processed: 82
  average time/residue: 0.2123
  time to fit residues: 23.7649
Evaluate side-chains
  81 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 73
  time to evaluate  : 0.866 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain A residue  126 ASP
Chi-restraints excluded: chain B residue   32 LEU
Chi-restraints excluded: chain C residue  106 LEU
Chi-restraints excluded: chain C residue  126 ASP
Chi-restraints excluded: chain D residue    4 THR
Chi-restraints excluded: chain D residue  112 CYS
Chi-restraints excluded: chain E residue  416 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 63 optimal weight:    5.9990
   chunk 78 optimal weight:    8.9990
   chunk 15 optimal weight:    0.9990
   chunk 41 optimal weight:    0.9990
   chunk 46 optimal weight:    0.0170
   chunk 42 optimal weight:    0.4980
   chunk 17 optimal weight:    0.9980
   chunk 81 optimal weight:   10.0000
   chunk 13 optimal weight:   10.0000
   chunk 48 optimal weight:    3.9990
   chunk 72 optimal weight:    4.9990
   overall best weight:    0.7022

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

Flipped N/Q/H residues before XYZ refinement:
** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  39 GLN
** D  63 HIS ** 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 = 0.2719 r_free = 0.2719 target = 0.029778 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2323 r_free = 0.2323 target = 0.020440 restraints weight = 129056.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2373 r_free = 0.2373 target = 0.021745 restraints weight = 50114.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2411 r_free = 0.2411 target = 0.022692 restraints weight = 29585.779|
|-----------------------------------------------------------------------------|
r_work (final): 0.2398
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2398
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2398 r_free = 0.2398    target_work(ls_wunit_k1) = 0.022         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2398 r_free = 0.2398    target_work(ls_wunit_k1) = 0.022         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.2398
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8936
moved from start:          0.5519

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.129   7557  Z= 0.113
  Angle     :  0.634  11.995  10293  Z= 0.307
  Chirality :  0.040   0.302   1114
  Planarity :  0.004   0.046   1298
  Dihedral  :  8.011  86.854   1004
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 8.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 15.32 %
    Favored  : 83.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.52 (0.28), residues: 910
  helix:  2.80 (0.22), residues: 513
  sheet:  0.44 (0.56), residues: 98
  loop :  0.12 (0.36), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A  14 
 HIS   0.003   0.001   HIS A  87 
 PHE   0.015   0.001   PHE E 418 
 TYR   0.016   0.001   TYR C 140 
 ARG   0.008   0.000   ARG E 403 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02719 (  471)
  hydrogen bonds       : angle       4.38154 ( 1340)
  covalent geometry    : bond        0.00307 ( 7553)
  covalent geometry    : angle       0.63401 (10293)
  Misc. bond           : bond        0.07620 (    4)

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

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

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 78
  time to evaluate  : 0.885 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   30 GLU cc_start: 0.9457 (pt0) cc_final: 0.8849 (tt0)
REVERT: A   68 ASN cc_start: 0.9772 (t0) cc_final: 0.9567 (t0)
REVERT: A   94 ASP cc_start: 0.9378 (t0) cc_final: 0.8954 (t0)
REVERT: B    7 GLU cc_start: 0.9572 (mt-10) cc_final: 0.9168 (mt-10)
REVERT: B   21 ASP cc_start: 0.9083 (p0) cc_final: 0.8229 (p0)
REVERT: B   22 GLU cc_start: 0.9190 (mm-30) cc_final: 0.8645 (mm-30)
REVERT: B   26 GLU cc_start: 0.9314 (tp30) cc_final: 0.9086 (tp30)
REVERT: B  121 GLU cc_start: 0.9175 (tp30) cc_final: 0.8771 (tp30)
REVERT: B  127 GLN cc_start: 0.9511 (tt0) cc_final: 0.8805 (tm-30)
REVERT: D   22 GLU cc_start: 0.8912 (tm-30) cc_final: 0.8228 (tm-30)
REVERT: D   26 GLU cc_start: 0.9515 (mm-30) cc_final: 0.9029 (mm-30)
REVERT: D   55 MET cc_start: 0.9380 (mmp) cc_final: 0.9086 (mmp)
REVERT: D   71 PHE cc_start: 0.9612 (m-80) cc_final: 0.9372 (m-80)
REVERT: D   99 ASP cc_start: 0.9010 (t0) cc_final: 0.8537 (t0)
REVERT: D  127 GLN cc_start: 0.9777 (tt0) cc_final: 0.9234 (tm-30)
REVERT: D  132 LYS cc_start: 0.9688 (mtpp) cc_final: 0.9284 (mtmm)
REVERT: E  124 MET cc_start: 0.8152 (mmm) cc_final: 0.6903 (tmm)
REVERT: E  382 MET cc_start: 0.8777 (mpp) cc_final: 0.8319 (mpp)
REVERT: E  384 MET cc_start: 0.9755 (ttm) cc_final: 0.9520 (ttm)
REVERT: E  396 MET cc_start: 0.9190 (tpp) cc_final: 0.8826 (tpp)
  outliers start: 10
  outliers final: 10
  residues processed: 85
  average time/residue: 0.1956
  time to fit residues: 22.8331
Evaluate side-chains
  83 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 73
  time to evaluate  : 0.798 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 SER
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain A residue  126 ASP
Chi-restraints excluded: chain B residue   32 LEU
Chi-restraints excluded: chain C residue  106 LEU
Chi-restraints excluded: chain C residue  126 ASP
Chi-restraints excluded: chain D residue    4 THR
Chi-restraints excluded: chain D residue   39 GLN
Chi-restraints excluded: chain D residue  112 CYS
Chi-restraints excluded: chain E residue  416 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 68 optimal weight:    0.0870
   chunk 41 optimal weight:    8.9990
   chunk 62 optimal weight:    0.7980
   chunk 56 optimal weight:   10.0000
   chunk 17 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9990
   chunk 74 optimal weight:    0.8980
   chunk 11 optimal weight:    7.9990
   chunk 70 optimal weight:    4.9990
   chunk 14 optimal weight:    0.7980
   chunk 75 optimal weight:    5.9990
   overall best weight:    0.7160

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

Flipped N/Q/H residues before XYZ refinement:
** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  39 GLN
** D  63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 146 HIS ** 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 = 0.2727 r_free = 0.2727 target = 0.029958 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2314 r_free = 0.2314 target = 0.020250 restraints weight = 181108.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2369 r_free = 0.2369 target = 0.021657 restraints weight = 57920.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2411 r_free = 0.2411 target = 0.022694 restraints weight = 32126.804|
|-----------------------------------------------------------------------------|
r_work (final): 0.2398
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2398
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2398 r_free = 0.2398    target_work(ls_wunit_k1) = 0.022         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2398 r_free = 0.2398    target_work(ls_wunit_k1) = 0.022         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.2398
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8935
moved from start:          0.5556

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.121   7557  Z= 0.118
  Angle     :  0.651  11.631  10293  Z= 0.318
  Chirality :  0.041   0.295   1114
  Planarity :  0.004   0.046   1298
  Dihedral  :  8.011  87.675   1004
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 8.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.33 %
    Favored  : 98.67 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 15.58 %
    Favored  : 83.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.46 (0.28), residues: 910
  helix:  2.73 (0.22), residues: 513
  sheet:  0.52 (0.56), residues: 98
  loop :  0.09 (0.36), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  15 
 HIS   0.004   0.001   HIS D  92 
 PHE   0.014   0.001   PHE E 418 
 TYR   0.018   0.001   TYR B 130 
 ARG   0.009   0.000   ARG E 403 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02778 (  471)
  hydrogen bonds       : angle       4.35189 ( 1340)
  covalent geometry    : bond        0.00318 ( 7553)
  covalent geometry    : angle       0.65114 (10293)
  Misc. bond           : bond        0.07427 (    4)

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

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

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 76
  time to evaluate  : 0.801 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   68 ASN cc_start: 0.9769 (t0) cc_final: 0.9558 (t0)
REVERT: A   94 ASP cc_start: 0.9378 (t0) cc_final: 0.8945 (t0)
REVERT: B    7 GLU cc_start: 0.9574 (mt-10) cc_final: 0.9217 (mt-10)
REVERT: B   21 ASP cc_start: 0.9082 (p0) cc_final: 0.8262 (p0)
REVERT: B   22 GLU cc_start: 0.9193 (mm-30) cc_final: 0.8676 (mm-30)
REVERT: B   26 GLU cc_start: 0.9309 (tp30) cc_final: 0.9081 (tp30)
REVERT: B  121 GLU cc_start: 0.9186 (tp30) cc_final: 0.8777 (tp30)
REVERT: B  127 GLN cc_start: 0.9479 (tt0) cc_final: 0.8773 (tm-30)
REVERT: D   22 GLU cc_start: 0.8910 (tm-30) cc_final: 0.8243 (tm-30)
REVERT: D   26 GLU cc_start: 0.9525 (mm-30) cc_final: 0.9052 (mm-30)
REVERT: D   55 MET cc_start: 0.9388 (mmp) cc_final: 0.9095 (mmp)
REVERT: D   71 PHE cc_start: 0.9612 (m-80) cc_final: 0.9368 (m-80)
REVERT: D   99 ASP cc_start: 0.8995 (t0) cc_final: 0.8532 (t0)
REVERT: D  127 GLN cc_start: 0.9781 (tt0) cc_final: 0.9239 (tm-30)
REVERT: D  132 LYS cc_start: 0.9690 (mtpp) cc_final: 0.9286 (mtmm)
REVERT: E  382 MET cc_start: 0.8774 (mpp) cc_final: 0.8323 (mpp)
REVERT: E  384 MET cc_start: 0.9758 (ttm) cc_final: 0.9525 (ttm)
REVERT: E  396 MET cc_start: 0.9195 (tpp) cc_final: 0.8829 (tpp)
  outliers start: 7
  outliers final: 7
  residues processed: 80
  average time/residue: 0.2014
  time to fit residues: 22.0450
Evaluate side-chains
  79 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 72
  time to evaluate  : 0.799 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  126 ASP
Chi-restraints excluded: chain B residue   32 LEU
Chi-restraints excluded: chain C residue  106 LEU
Chi-restraints excluded: chain C residue  126 ASP
Chi-restraints excluded: chain D residue   39 GLN
Chi-restraints excluded: chain D residue  112 CYS
Chi-restraints excluded: chain E residue  416 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 8 optimal weight:    0.0370
   chunk 50 optimal weight:    8.9990
   chunk 12 optimal weight:    0.6980
   chunk 64 optimal weight:    0.9990
   chunk 39 optimal weight:    0.9980
   chunk 37 optimal weight:    5.9990
   chunk 44 optimal weight:    8.9990
   chunk 79 optimal weight:    0.0270
   chunk 24 optimal weight:    0.9980
   chunk 76 optimal weight:    0.3980
   chunk 46 optimal weight:    0.6980
   overall best weight:    0.3716

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

Flipped N/Q/H residues before XYZ refinement:
** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  39 GLN
** D  63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 146 HIS ** 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 = 0.2732 r_free = 0.2732 target = 0.030157 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2323 r_free = 0.2323 target = 0.020376 restraints weight = 185748.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.2376 r_free = 0.2376 target = 0.021794 restraints weight = 58837.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2418 r_free = 0.2418 target = 0.022842 restraints weight = 32598.178|
|-----------------------------------------------------------------------------|
r_work (final): 0.2402
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2402
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2402 r_free = 0.2402    target_work(ls_wunit_k1) = 0.022         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2402 r_free = 0.2402    target_work(ls_wunit_k1) = 0.022         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.2402
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8928
moved from start:          0.5619

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.101   7557  Z= 0.116
  Angle     :  0.659  12.040  10293  Z= 0.321
  Chirality :  0.041   0.299   1114
  Planarity :  0.004   0.046   1298
  Dihedral  :  7.968  87.732   1004
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 8.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.33 %
    Favored  : 98.67 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 15.97 %
    Favored  : 82.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.41 (0.28), residues: 910
  helix:  2.66 (0.22), residues: 515
  sheet:  0.56 (0.56), residues: 98
  loop :  0.09 (0.36), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A  14 
 HIS   0.003   0.001   HIS D  92 
 PHE   0.014   0.001   PHE E 418 
 TYR   0.017   0.001   TYR C 140 
 ARG   0.008   0.001   ARG E 403 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02827 (  471)
  hydrogen bonds       : angle       4.32023 ( 1340)
  covalent geometry    : bond        0.00298 ( 7553)
  covalent geometry    : angle       0.65891 (10293)
  Misc. bond           : bond        0.06196 (    4)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2997.33 seconds
wall clock time: 52 minutes 45.27 seconds (3165.27 seconds total)