Starting phenix.real_space_refine
on Wed Mar 12 07:42:17 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7pcq_13325/03_2025/7pcq_13325_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7pcq_13325/03_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_13325/03_2025/7pcq_13325.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7pcq_13325/03_2025/7pcq_13325.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7pcq_13325/03_2025/7pcq_13325_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7pcq_13325/03_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-5624/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: 7.68, 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: 2.02
  Conformation dependent library (CDL) restraints added in 1.3 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: 0.98
  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: 2.96

  Time building geometry restraints manager: 2.25 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:             2.940
  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:          0.280
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     24.840
  Find NCS groups from input model:        0.240
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.010
  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:2.980
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.460
-------------------------------------------------------------------------------
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      :  0.013   0.089   7553  Z= 0.861
  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 

*********************** 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  : 0.896 
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: 0.2257
  time to fit residues: 51.2137
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  : 0.777 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 45 optimal weight:    1.9990
   chunk 36 optimal weight:    4.9990
   chunk 69 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 42 optimal weight:    5.9990
   chunk 51 optimal weight:    5.9990
   chunk 80 optimal weight:    0.7980
   overall best weight:    1.5588

-------------------------------------------------------------------------------
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
** D  63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 339 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2797 r_free = 0.2797 target = 0.032864 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2388 r_free = 0.2388 target = 0.022277 restraints weight = 163490.374|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2443 r_free = 0.2443 target = 0.023845 restraints weight = 56816.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2487 r_free = 0.2487 target = 0.025021 restraints weight = 32108.825|
|-----------------------------------------------------------------------------|
r_work (final): 0.2469
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2469
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2469 r_free = 0.2469    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 = 0.2466 r_free = 0.2466    target_work(ls_wunit_k1) = 0.025         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.2466
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8692
moved from start:          0.3146

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062   7553  Z= 0.264
  Angle     :  0.625   6.489  10293  Z= 0.323
  Chirality :  0.042   0.146   1114
  Planarity :  0.004   0.038   1298
  Dihedral  :  8.713  89.029   1007
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 8.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.11 %
    Favored  : 98.89 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 13.25 %
    Favored  : 85.06 %
  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 (0.27), residues: 910
  helix:  2.79 (0.22), residues: 521
  sheet:  0.36 (0.57), residues: 81
  loop :  0.23 (0.34), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP C  14 
 HIS   0.004   0.001   HIS E 369 
 PHE   0.016   0.002   PHE E 178 
 TYR   0.010   0.001   TYR B 130 
 ARG   0.006   0.001   ARG E 403 

*********************** 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
  116 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 104
  time to evaluate  : 0.837 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   27 GLU cc_start: 0.9317 (tt0) cc_final: 0.8795 (tt0)
REVERT: A   94 ASP cc_start: 0.9189 (t0) cc_final: 0.8984 (t0)
REVERT: B    7 GLU cc_start: 0.9507 (mt-10) cc_final: 0.9159 (mt-10)
REVERT: B   21 ASP cc_start: 0.9428 (p0) cc_final: 0.8402 (p0)
REVERT: B   47 ASP cc_start: 0.9015 (t0) cc_final: 0.8661 (t0)
REVERT: B   99 ASP cc_start: 0.8873 (t0) cc_final: 0.8543 (t0)
REVERT: B  101 GLU cc_start: 0.9517 (mm-30) cc_final: 0.8924 (mp0)
REVERT: B  108 ASN cc_start: 0.9417 (m-40) cc_final: 0.9089 (t0)
REVERT: B  127 GLN cc_start: 0.9474 (tt0) cc_final: 0.8691 (tm-30)
REVERT: B  131 GLN cc_start: 0.9461 (mm110) cc_final: 0.9091 (mm110)
REVERT: C   27 GLU cc_start: 0.9378 (tt0) cc_final: 0.9176 (tt0)
REVERT: D   26 GLU cc_start: 0.9271 (mm-30) cc_final: 0.9005 (mm-30)
REVERT: D  127 GLN cc_start: 0.9786 (tt0) cc_final: 0.9209 (tm-30)
REVERT: D  139 ASN cc_start: 0.9768 (m-40) cc_final: 0.9552 (t0)
REVERT: D  144 LYS cc_start: 0.9223 (mmtt) cc_final: 0.8870 (mmtp)
REVERT: E  155 MET cc_start: 0.8812 (mmm) cc_final: 0.8577 (mmp)
REVERT: E  439 ASP cc_start: 0.9245 (t0) cc_final: 0.9044 (t0)
  outliers start: 12
  outliers final: 8
  residues processed: 109
  average time/residue: 0.2029
  time to fit residues: 29.8127
Evaluate side-chains
  92 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 84
  time to evaluate  : 0.772 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    2 LEU
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
Chi-restraints excluded: chain E residue  416 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 76 optimal weight:    1.9990
   chunk 43 optimal weight:    0.8980
   chunk 15 optimal weight:    0.9990
   chunk 44 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9990
   chunk 68 optimal weight:    4.9990
   chunk 17 optimal weight:    0.9980
   chunk 29 optimal weight:    2.9990
   chunk 52 optimal weight:    1.9990
   chunk 58 optimal weight:    6.9990
   chunk 21 optimal weight:    0.8980
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
B  39 GLN
B  63 HIS
C 122 HIS
D  39 GLN
** D  63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2778 r_free = 0.2778 target = 0.032277 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2388 r_free = 0.2388 target = 0.022431 restraints weight = 175953.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2442 r_free = 0.2442 target = 0.023950 restraints weight = 57221.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2486 r_free = 0.2486 target = 0.025108 restraints weight = 31598.251|
|-----------------------------------------------------------------------------|
r_work (final): 0.2456
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2457
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2457 r_free = 0.2457    target_work(ls_wunit_k1) = 0.024         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| 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:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.2455
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8756
moved from start:          0.3773

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   7553  Z= 0.209
  Angle     :  0.592   8.449  10293  Z= 0.297
  Chirality :  0.040   0.151   1114
  Planarity :  0.004   0.042   1298
  Dihedral  :  8.462  89.145   1006
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 7.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 13.12 %
    Favored  : 84.94 %
  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:  2.51 (0.28), residues: 910
  helix:  2.69 (0.22), residues: 523
  sheet:  0.15 (0.53), residues: 101
  loop :  0.35 (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   0.010   0.001   TYR B  35 
 ARG   0.003   0.000   ARG E 403 

*********************** 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
  107 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 93
  time to evaluate  : 0.850 
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: 0.9296 (t0) cc_final: 0.9037 (t0)
REVERT: B    7 GLU cc_start: 0.9525 (mt-10) cc_final: 0.9154 (mt-10)
REVERT: B   21 ASP cc_start: 0.9020 (p0) cc_final: 0.8547 (p0)
REVERT: B   22 GLU cc_start: 0.9257 (mm-30) cc_final: 0.8929 (mm-30)
REVERT: B   47 ASP cc_start: 0.9157 (t0) cc_final: 0.8855 (t0)
REVERT: B  101 GLU cc_start: 0.9545 (mm-30) cc_final: 0.9298 (mm-30)
REVERT: B  108 ASN cc_start: 0.9423 (m-40) cc_final: 0.9125 (t0)
REVERT: B  127 GLN cc_start: 0.9499 (tt0) cc_final: 0.8728 (tm-30)
REVERT: B  131 GLN cc_start: 0.9395 (mm110) cc_final: 0.9041 (mm110)
REVERT: C   27 GLU cc_start: 0.9533 (tt0) cc_final: 0.9102 (tt0)
REVERT: C   32 MET cc_start: 0.9616 (OUTLIER) cc_final: 0.9368 (mmm)
REVERT: C   68 ASN cc_start: 0.9525 (t0) cc_final: 0.9299 (t0)
REVERT: C   92 ARG cc_start: 0.8843 (mpp80) cc_final: 0.8574 (mmt90)
REVERT: D   71 PHE cc_start: 0.9718 (m-80) cc_final: 0.9349 (m-80)
REVERT: D   99 ASP cc_start: 0.8816 (t0) cc_final: 0.8351 (t0)
REVERT: D  127 GLN cc_start: 0.9767 (tt0) cc_final: 0.9147 (tm-30)
REVERT: D  132 LYS cc_start: 0.9633 (mtpp) cc_final: 0.9349 (mtmm)
REVERT: E  382 MET cc_start: 0.8647 (OUTLIER) cc_final: 0.8440 (mpp)
REVERT: E  384 MET cc_start: 0.9666 (ttm) cc_final: 0.9431 (ttm)
REVERT: E  439 ASP cc_start: 0.9330 (t0) cc_final: 0.9096 (t0)
  outliers start: 14
  outliers final: 10
  residues processed: 101
  average time/residue: 0.2057
  time to fit residues: 28.2504
Evaluate side-chains
  94 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 82
  time to evaluate  : 0.901 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 SER
Chi-restraints excluded: chain A residue  126 ASP
Chi-restraints excluded: chain B residue   39 GLN
Chi-restraints excluded: chain C residue   32 MET
Chi-restraints excluded: chain C residue  105 LEU
Chi-restraints excluded: chain C residue  126 ASP
Chi-restraints excluded: chain D residue   39 GLN
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:    2.9990
   chunk 77 optimal weight:    8.9990
   chunk 15 optimal weight:    2.9990
   chunk 34 optimal weight:    3.9990
   chunk 16 optimal weight:    0.9990
   chunk 80 optimal weight:    7.9990
   chunk 14 optimal weight:    1.9990
   chunk 23 optimal weight:    7.9990
   chunk 32 optimal weight:    6.9990
   chunk 62 optimal weight:    6.9990
   overall best weight:    2.5990

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

Flipped N/Q/H residues before XYZ refinement:
A  78 ASN
B  39 GLN
** 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2693 r_free = 0.2693 target = 0.029419 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2294 r_free = 0.2294 target = 0.020214 restraints weight = 179341.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2349 r_free = 0.2349 target = 0.021585 restraints weight = 57749.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2392 r_free = 0.2392 target = 0.022620 restraints weight = 31862.654|
|-----------------------------------------------------------------------------|
r_work (final): 0.2372
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2372
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2372 r_free = 0.2372    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 = 0.2371 r_free = 0.2371    target_work(ls_wunit_k1) = 0.022         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.2371
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8914
moved from start:          0.4489

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.082   7553  Z= 0.333
  Angle     :  0.650   8.884  10293  Z= 0.319
  Chirality :  0.040   0.162   1114
  Planarity :  0.004   0.041   1298
  Dihedral  :  8.648  87.673   1006
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 10.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 13.12 %
    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:  2.74 (0.28), residues: 910
  helix:  2.87 (0.22), residues: 507
  sheet:  0.35 (0.54), residues: 98
  loop :  0.56 (0.36), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A  14 
 HIS   0.004   0.001   HIS C  87 
 PHE   0.018   0.002   PHE E 178 
 TYR   0.017   0.001   TYR B  35 
 ARG   0.007   0.001   ARG E 403 

*********************** 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
  96 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 80
  time to evaluate  : 0.768 
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: 0.9459 (t0) cc_final: 0.9062 (t0)
REVERT: B    7 GLU cc_start: 0.9527 (mt-10) cc_final: 0.9108 (mt-10)
REVERT: B   21 ASP cc_start: 0.9091 (p0) cc_final: 0.8350 (p0)
REVERT: B   22 GLU cc_start: 0.9271 (mm-30) cc_final: 0.8764 (mm-30)
REVERT: B   47 ASP cc_start: 0.9235 (t0) cc_final: 0.9011 (t0)
REVERT: B  108 ASN cc_start: 0.9459 (m-40) cc_final: 0.9080 (t0)
REVERT: B  127 GLN cc_start: 0.9546 (tt0) cc_final: 0.8813 (tm-30)
REVERT: B  131 GLN cc_start: 0.9515 (mm110) cc_final: 0.9033 (mm110)
REVERT: C   27 GLU cc_start: 0.9559 (tt0) cc_final: 0.9131 (tt0)
REVERT: C   68 ASN cc_start: 0.9558 (t0) cc_final: 0.9328 (t0)
REVERT: C  116 GLU cc_start: 0.9490 (mp0) cc_final: 0.9279 (pm20)
REVERT: D   55 MET cc_start: 0.9230 (mmp) cc_final: 0.8931 (mmp)
REVERT: D   99 ASP cc_start: 0.9025 (t0) cc_final: 0.8616 (t0)
REVERT: D  127 GLN cc_start: 0.9766 (tt0) cc_final: 0.9161 (tm-30)
REVERT: D  144 LYS cc_start: 0.9250 (mmtt) cc_final: 0.8921 (mmtp)
REVERT: E  254 MET cc_start: 0.9572 (ttt) cc_final: 0.9285 (tpp)
  outliers start: 16
  outliers final: 11
  residues processed: 92
  average time/residue: 0.2008
  time to fit residues: 25.2924
Evaluate side-chains
  87 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 76
  time to evaluate  : 0.847 
-------------------------------------------------------------------------------
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 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   28 LEU
Chi-restraints excluded: chain D residue   39 GLN
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:    3.9990
   chunk 80 optimal weight:    5.9990
   chunk 77 optimal weight:    2.9990
   chunk 60 optimal weight:    0.8980
   chunk 84 optimal weight:    6.9990
   chunk 62 optimal weight:    0.8980
   chunk 40 optimal weight:    4.9990
   chunk 78 optimal weight:    9.9990
   chunk 55 optimal weight:    2.9990
   chunk 47 optimal weight:    4.9990
   chunk 19 optimal weight:    0.5980
   overall best weight:    1.6784

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

Flipped N/Q/H residues before XYZ refinement:
B  39 GLN
** 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2702 r_free = 0.2702 target = 0.029690 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2301 r_free = 0.2301 target = 0.020424 restraints weight = 204697.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2359 r_free = 0.2359 target = 0.021826 restraints weight = 60209.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2400 r_free = 0.2400 target = 0.022864 restraints weight = 32425.918|
|-----------------------------------------------------------------------------|
r_work (final): 0.2383
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2383
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2383 r_free = 0.2383    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 = 0.2382 r_free = 0.2382    target_work(ls_wunit_k1) = 0.022         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.2382
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8922
moved from start:          0.4810

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.065   7553  Z= 0.260
  Angle     :  0.607  10.275  10293  Z= 0.298
  Chirality :  0.040   0.203   1114
  Planarity :  0.004   0.043   1298
  Dihedral  :  8.544  89.818   1006
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 8.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 14.42 %
    Favored  : 83.64 %
  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:  2.62 (0.28), residues: 910
  helix:  2.77 (0.22), residues: 521
  sheet:  0.40 (0.55), residues: 98
  loop :  0.34 (0.36), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A  14 
 HIS   0.003   0.001   HIS A  87 
 PHE   0.016   0.001   PHE E 418 
 TYR   0.012   0.001   TYR B  35 
 ARG   0.004   0.000   ARG E 403 

*********************** 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
  94 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 80
  time to evaluate  : 0.836 
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: 0.9398 (tt0) cc_final: 0.8869 (tt0)
REVERT: A   92 ARG cc_start: 0.9260 (OUTLIER) cc_final: 0.8800 (mmm-85)
REVERT: A   94 ASP cc_start: 0.9464 (t0) cc_final: 0.9077 (t0)
REVERT: B    7 GLU cc_start: 0.9569 (mt-10) cc_final: 0.9181 (mt-10)
REVERT: B   21 ASP cc_start: 0.9144 (p0) cc_final: 0.8338 (p0)
REVERT: B   22 GLU cc_start: 0.9296 (mm-30) cc_final: 0.8778 (mm-30)
REVERT: B   47 ASP cc_start: 0.9255 (t0) cc_final: 0.9051 (t0)
REVERT: B  101 GLU cc_start: 0.9569 (mm-30) cc_final: 0.9367 (mm-30)
REVERT: B  108 ASN cc_start: 0.9444 (m-40) cc_final: 0.9081 (t0)
REVERT: B  127 GLN cc_start: 0.9492 (tt0) cc_final: 0.8789 (tm-30)
REVERT: B  131 GLN cc_start: 0.9484 (mm110) cc_final: 0.9196 (mm110)
REVERT: C   27 GLU cc_start: 0.9592 (tt0) cc_final: 0.9188 (tt0)
REVERT: C   68 ASN cc_start: 0.9594 (t0) cc_final: 0.9377 (t0)
REVERT: D   55 MET cc_start: 0.9218 (mmp) cc_final: 0.8939 (mmp)
REVERT: D   71 PHE cc_start: 0.9650 (m-80) cc_final: 0.9415 (m-80)
REVERT: D   99 ASP cc_start: 0.9005 (t0) cc_final: 0.8575 (t0)
REVERT: D  127 GLN cc_start: 0.9760 (tt0) cc_final: 0.9145 (tm-30)
REVERT: E  124 MET cc_start: 0.8124 (mmm) cc_final: 0.6254 (tmm)
REVERT: E  254 MET cc_start: 0.9517 (ttt) cc_final: 0.9278 (tpp)
  outliers start: 14
  outliers final: 9
  residues processed: 91
  average time/residue: 0.2097
  time to fit residues: 25.7943
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  : 0.760 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 ARG
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  126 ASP
Chi-restraints excluded: chain D residue    4 THR
Chi-restraints excluded: chain D residue   39 GLN
Chi-restraints excluded: chain D residue   49 SER
Chi-restraints excluded: chain D residue  112 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 42 optimal weight:    0.0770
   chunk 39 optimal weight:    0.1980
   chunk 25 optimal weight:    0.7980
   chunk 45 optimal weight:    1.9990
   chunk 71 optimal weight:    0.9990
   chunk 0 optimal weight:   10.0000
   chunk 18 optimal weight:    5.9990
   chunk 16 optimal weight:    0.7980
   chunk 5 optimal weight:    3.9990
   chunk 80 optimal weight:    5.9990
   chunk 54 optimal weight:    0.5980
   overall best weight:    0.4938

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

Flipped N/Q/H residues before XYZ refinement:
B  39 GLN
B  63 HIS
** 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2733 r_free = 0.2733 target = 0.030392 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2339 r_free = 0.2339 target = 0.021046 restraints weight = 194782.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2393 r_free = 0.2393 target = 0.022456 restraints weight = 58883.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2434 r_free = 0.2434 target = 0.023517 restraints weight = 31812.882|
|-----------------------------------------------------------------------------|
r_work (final): 0.2409
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2409
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2409 r_free = 0.2409    target_work(ls_wunit_k1) = 0.023         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2409 r_free = 0.2409    target_work(ls_wunit_k1) = 0.023         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.2409
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8901
moved from start:          0.4965

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7553  Z= 0.190
  Angle     :  0.601  10.932  10293  Z= 0.294
  Chirality :  0.040   0.188   1114
  Planarity :  0.004   0.045   1298
  Dihedral  :  8.384  88.039   1004
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 8.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 14.42 %
    Favored  : 84.55 %
  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:  2.54 (0.28), residues: 910
  helix:  2.71 (0.22), residues: 523
  sheet:  0.42 (0.55), residues: 98
  loop :  0.27 (0.36), residues: 289

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   0.016   0.001   PHE E 418 
 TYR   0.010   0.001   TYR B  35 
 ARG   0.007   0.000   ARG E 403 

*********************** 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
  92 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 85
  time to evaluate  : 0.813 
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   27 GLU cc_start: 0.9370 (tt0) cc_final: 0.8731 (tt0)
REVERT: A   30 GLU cc_start: 0.9479 (pt0) cc_final: 0.8994 (tt0)
REVERT: A   94 ASP cc_start: 0.9387 (t0) cc_final: 0.8967 (t0)
REVERT: B    7 GLU cc_start: 0.9577 (mt-10) cc_final: 0.9193 (mt-10)
REVERT: B   21 ASP cc_start: 0.9138 (p0) cc_final: 0.8251 (p0)
REVERT: B   22 GLU cc_start: 0.9263 (mm-30) cc_final: 0.8698 (mm-30)
REVERT: B  127 GLN cc_start: 0.9475 (tt0) cc_final: 0.8687 (tm-30)
REVERT: B  131 GLN cc_start: 0.9401 (mm110) cc_final: 0.9119 (mm-40)
REVERT: C   27 GLU cc_start: 0.9608 (tt0) cc_final: 0.9222 (tt0)
REVERT: C   32 MET cc_start: 0.9611 (ttm) cc_final: 0.9282 (mtp)
REVERT: C   68 ASN cc_start: 0.9583 (t0) cc_final: 0.9374 (t0)
REVERT: D   55 MET cc_start: 0.9237 (mmp) cc_final: 0.8969 (mmp)
REVERT: D   99 ASP cc_start: 0.9004 (t0) cc_final: 0.8551 (t0)
REVERT: D  127 GLN cc_start: 0.9758 (tt0) cc_final: 0.9132 (tm-30)
REVERT: E  124 MET cc_start: 0.8061 (mmm) cc_final: 0.6433 (tmm)
REVERT: E  155 MET cc_start: 0.8879 (mmp) cc_final: 0.7717 (mmp)
REVERT: E  254 MET cc_start: 0.9512 (ttt) cc_final: 0.9221 (tpp)
REVERT: E  384 MET cc_start: 0.9718 (ttm) cc_final: 0.9482 (ttm)
REVERT: E  392 TRP cc_start: 0.9229 (m100) cc_final: 0.8561 (m100)
  outliers start: 7
  outliers final: 5
  residues processed: 91
  average time/residue: 0.2106
  time to fit residues: 25.8500
Evaluate side-chains
  81 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 76
  time to evaluate  : 0.864 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 SER
Chi-restraints excluded: chain A residue  104 CYS
Chi-restraints excluded: chain B residue   39 GLN
Chi-restraints excluded: chain C residue  126 ASP
Chi-restraints excluded: chain D residue    4 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 4 optimal weight:   10.0000
   chunk 53 optimal weight:    2.9990
   chunk 2 optimal weight:    3.9990
   chunk 82 optimal weight:    3.9990
   chunk 5 optimal weight:    2.9990
   chunk 37 optimal weight:    1.9990
   chunk 81 optimal weight:    4.9990
   chunk 25 optimal weight:    4.9990
   chunk 57 optimal weight:    0.9990
   chunk 73 optimal weight:    1.9990
   chunk 15 optimal weight:    0.8980
   overall best weight:    1.7788

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

Flipped N/Q/H residues before XYZ refinement:
B  39 GLN
** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  39 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2704 r_free = 0.2704 target = 0.029330 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2289 r_free = 0.2289 target = 0.019641 restraints weight = 182247.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2344 r_free = 0.2344 target = 0.021021 restraints weight = 58197.375|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2384 r_free = 0.2384 target = 0.022000 restraints weight = 32143.876|
|-----------------------------------------------------------------------------|
r_work (final): 0.2373
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2373
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2373 r_free = 0.2373    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 = 0.2372 r_free = 0.2372    target_work(ls_wunit_k1) = 0.022         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.2372
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8947
moved from start:          0.5129

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.067   7553  Z= 0.275
  Angle     :  0.644  10.771  10293  Z= 0.314
  Chirality :  0.041   0.317   1114
  Planarity :  0.004   0.043   1298
  Dihedral  :  8.348  86.680   1004
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 8.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.66 %
    Favored  : 98.34 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 14.29 %
    Favored  : 83.51 %
  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:  2.64 (0.22), residues: 523
  sheet:  0.41 (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   0.005   0.001   HIS D  92 
 PHE   0.017   0.001   PHE E 418 
 TYR   0.007   0.001   TYR B  35 
 ARG   0.008   0.000   ARG E 403 

*********************** 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
  95 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 79
  time to evaluate  : 0.857 
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   27 GLU cc_start: 0.9411 (tt0) cc_final: 0.8763 (tt0)
REVERT: A   30 GLU cc_start: 0.9496 (pt0) cc_final: 0.9015 (tt0)
REVERT: A   92 ARG cc_start: 0.9285 (OUTLIER) cc_final: 0.9029 (mmm-85)
REVERT: A   94 ASP cc_start: 0.9441 (t0) cc_final: 0.9041 (t0)
REVERT: B    7 GLU cc_start: 0.9580 (mt-10) cc_final: 0.9199 (mt-10)
REVERT: B   21 ASP cc_start: 0.9114 (p0) cc_final: 0.8225 (p0)
REVERT: B   22 GLU cc_start: 0.9231 (mm-30) cc_final: 0.8662 (mm-30)
REVERT: B  121 GLU cc_start: 0.9138 (tp30) cc_final: 0.8742 (tp30)
REVERT: B  127 GLN cc_start: 0.9506 (tt0) cc_final: 0.8727 (tm-30)
REVERT: B  131 GLN cc_start: 0.9492 (mm110) cc_final: 0.9102 (mm-40)
REVERT: C   27 GLU cc_start: 0.9602 (tt0) cc_final: 0.9217 (tt0)
REVERT: C   32 MET cc_start: 0.9594 (ttm) cc_final: 0.9298 (mtp)
REVERT: C   68 ASN cc_start: 0.9578 (t0) cc_final: 0.9363 (t0)
REVERT: D   55 MET cc_start: 0.9277 (mmp) cc_final: 0.9027 (mmp)
REVERT: D   71 PHE cc_start: 0.9634 (m-80) cc_final: 0.9376 (m-80)
REVERT: D   99 ASP cc_start: 0.9049 (t0) cc_final: 0.8590 (t0)
REVERT: D  127 GLN cc_start: 0.9778 (tt0) cc_final: 0.9172 (tm-30)
REVERT: D  132 LYS cc_start: 0.9692 (mtpp) cc_final: 0.9377 (mtmm)
REVERT: D  144 LYS cc_start: 0.9180 (mmtt) cc_final: 0.8875 (mmtm)
REVERT: E  124 MET cc_start: 0.8163 (mmm) cc_final: 0.6589 (tmm)
REVERT: E  384 MET cc_start: 0.9736 (ttm) cc_final: 0.9508 (ttm)
  outliers start: 16
  outliers final: 11
  residues processed: 92
  average time/residue: 0.2294
  time to fit residues: 28.2448
Evaluate side-chains
  87 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 75
  time to evaluate  : 1.084 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 ARG
Chi-restraints excluded: chain A residue  102 SER
Chi-restraints excluded: chain A residue  104 CYS
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 B residue   38 THR
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 82 optimal weight:    4.9990
   chunk 79 optimal weight:    1.9990
   chunk 45 optimal weight:    0.8980
   chunk 32 optimal weight:    1.9990
   chunk 55 optimal weight:    0.9980
   chunk 59 optimal weight:    8.9990
   chunk 83 optimal weight:    0.9980
   chunk 56 optimal weight:   20.0000
   chunk 47 optimal weight:    5.9990
   chunk 24 optimal weight:    8.9990
   chunk 53 optimal weight:    2.9990
   overall best weight:    1.3784

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

Flipped N/Q/H residues before XYZ refinement:
B  39 GLN
** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  39 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2699 r_free = 0.2699 target = 0.029253 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2291 r_free = 0.2291 target = 0.019692 restraints weight = 184811.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2343 r_free = 0.2343 target = 0.021077 restraints weight = 58335.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2384 r_free = 0.2384 target = 0.022104 restraints weight = 31787.985|
|-----------------------------------------------------------------------------|
r_work (final): 0.2373
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2373
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2373 r_free = 0.2373    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 = 0.2372 r_free = 0.2372    target_work(ls_wunit_k1) = 0.022         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.2372
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8944
moved from start:          0.5306

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058   7553  Z= 0.245
  Angle     :  0.644  10.836  10293  Z= 0.315
  Chirality :  0.041   0.309   1114
  Planarity :  0.004   0.043   1298
  Dihedral  :  8.249  86.710   1004
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 8.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 14.81 %
    Favored  : 83.64 %
  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:  2.43 (0.28), residues: 910
  helix:  2.62 (0.22), residues: 523
  sheet:  0.41 (0.56), residues: 98
  loop :  0.20 (0.36), residues: 289

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   0.018   0.001   PHE E 418 
 TYR   0.008   0.001   TYR B  35 
 ARG   0.007   0.000   ARG E 403 

*********************** 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: 11
    poor density    : 74
  time to evaluate  : 0.772 
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   27 GLU cc_start: 0.9402 (tt0) cc_final: 0.8749 (tt0)
REVERT: A   30 GLU cc_start: 0.9481 (pt0) cc_final: 0.8970 (tt0)
REVERT: A   92 ARG cc_start: 0.9296 (OUTLIER) cc_final: 0.8915 (mmm-85)
REVERT: A   94 ASP cc_start: 0.9431 (t0) cc_final: 0.9041 (t0)
REVERT: B    7 GLU cc_start: 0.9575 (mt-10) cc_final: 0.9184 (mt-10)
REVERT: B   21 ASP cc_start: 0.9105 (p0) cc_final: 0.8224 (p0)
REVERT: B   22 GLU cc_start: 0.9202 (mm-30) cc_final: 0.8663 (mm-30)
REVERT: B  121 GLU cc_start: 0.9164 (tp30) cc_final: 0.8746 (tp30)
REVERT: B  127 GLN cc_start: 0.9489 (tt0) cc_final: 0.8701 (tm-30)
REVERT: B  131 GLN cc_start: 0.9474 (mm110) cc_final: 0.9093 (mm-40)
REVERT: C   27 GLU cc_start: 0.9612 (tt0) cc_final: 0.9225 (tt0)
REVERT: C   68 ASN cc_start: 0.9588 (t0) cc_final: 0.9381 (t0)
REVERT: C  116 GLU cc_start: 0.9014 (pm20) cc_final: 0.8731 (pm20)
REVERT: D   55 MET cc_start: 0.9288 (mmp) cc_final: 0.9052 (mmp)
REVERT: D   99 ASP cc_start: 0.9048 (t0) cc_final: 0.8605 (t0)
REVERT: D  127 GLN cc_start: 0.9782 (tt0) cc_final: 0.9174 (tm-30)
REVERT: D  132 LYS cc_start: 0.9693 (mtpp) cc_final: 0.9370 (mtmm)
REVERT: E  124 MET cc_start: 0.8181 (mmm) cc_final: 0.6815 (tmm)
REVERT: E  384 MET cc_start: 0.9748 (ttm) cc_final: 0.9536 (ttm)
  outliers start: 11
  outliers final: 8
  residues processed: 82
  average time/residue: 0.2237
  time to fit residues: 24.6104
Evaluate side-chains
  82 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 73
  time to evaluate  : 0.865 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 ARG
Chi-restraints excluded: chain A residue  102 SER
Chi-restraints excluded: chain A residue  104 CYS
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   39 GLN
Chi-restraints excluded: chain D residue  112 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 63 optimal weight:    3.9990
   chunk 78 optimal weight:    5.9990
   chunk 15 optimal weight:    0.7980
   chunk 41 optimal weight:    2.9990
   chunk 46 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9990
   chunk 17 optimal weight:    0.8980
   chunk 81 optimal weight:    8.9990
   chunk 13 optimal weight:    9.9990
   chunk 48 optimal weight:    0.9990
   chunk 72 optimal weight:    0.9980
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
B  39 GLN
** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  39 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2710 r_free = 0.2710 target = 0.029537 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2312 r_free = 0.2312 target = 0.020251 restraints weight = 127980.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2362 r_free = 0.2362 target = 0.021552 restraints weight = 49685.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2400 r_free = 0.2400 target = 0.022510 restraints weight = 29013.753|
|-----------------------------------------------------------------------------|
r_work (final): 0.2388
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2388
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2388 r_free = 0.2388    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 = 0.2388 r_free = 0.2388    target_work(ls_wunit_k1) = 0.022         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.2388
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8933
moved from start:          0.5411

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   7553  Z= 0.223
  Angle     :  0.642  10.903  10293  Z= 0.314
  Chirality :  0.041   0.328   1114
  Planarity :  0.004   0.044   1298
  Dihedral  :  8.129  86.686   1004
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 8.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 14.68 %
    Favored  : 84.03 %
  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:  2.38 (0.28), residues: 910
  helix:  2.68 (0.23), residues: 511
  sheet:  0.45 (0.56), residues: 98
  loop :  0.06 (0.36), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C  14 
 HIS   0.004   0.001   HIS D  92 
 PHE   0.019   0.001   PHE E 418 
 TYR   0.008   0.001   TYR B  35 
 ARG   0.008   0.001   ARG E 403 

*********************** 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
  84 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 75
  time to evaluate  : 0.756 
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   30 GLU cc_start: 0.9456 (pt0) cc_final: 0.8905 (tt0)
REVERT: B    7 GLU cc_start: 0.9568 (mt-10) cc_final: 0.9176 (mt-10)
REVERT: B   21 ASP cc_start: 0.9083 (p0) cc_final: 0.8195 (p0)
REVERT: B   22 GLU cc_start: 0.9197 (mm-30) cc_final: 0.8659 (mm-30)
REVERT: B  121 GLU cc_start: 0.9183 (tp30) cc_final: 0.8756 (tp30)
REVERT: B  127 GLN cc_start: 0.9480 (tt0) cc_final: 0.8749 (tm-30)
REVERT: C   27 GLU cc_start: 0.9614 (tt0) cc_final: 0.9230 (tt0)
REVERT: C   68 ASN cc_start: 0.9590 (t0) cc_final: 0.9384 (t0)
REVERT: C  116 GLU cc_start: 0.8967 (pm20) cc_final: 0.8738 (pm20)
REVERT: D   55 MET cc_start: 0.9287 (mmp) cc_final: 0.9060 (mmp)
REVERT: D   71 PHE cc_start: 0.9617 (m-80) cc_final: 0.9376 (m-80)
REVERT: D   99 ASP cc_start: 0.9019 (t0) cc_final: 0.8682 (t0)
REVERT: D  127 GLN cc_start: 0.9787 (tt0) cc_final: 0.9169 (tm-30)
REVERT: D  132 LYS cc_start: 0.9691 (mtpp) cc_final: 0.9367 (mtmm)
REVERT: E  124 MET cc_start: 0.8211 (mmm) cc_final: 0.6910 (tmm)
REVERT: E  382 MET cc_start: 0.8712 (mpp) cc_final: 0.8205 (mpp)
REVERT: E  384 MET cc_start: 0.9752 (ttm) cc_final: 0.9521 (ttm)
REVERT: E  396 MET cc_start: 0.9189 (tpp) cc_final: 0.8847 (tpp)
  outliers start: 9
  outliers final: 8
  residues processed: 81
  average time/residue: 0.2065
  time to fit residues: 22.6965
Evaluate side-chains
  80 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 72
  time to evaluate  : 0.772 
-------------------------------------------------------------------------------
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   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:    3.9990
   chunk 41 optimal weight:    8.9990
   chunk 62 optimal weight:    8.9990
   chunk 56 optimal weight:    7.9990
   chunk 17 optimal weight:    0.9990
   chunk 29 optimal weight:    1.9990
   chunk 74 optimal weight:    6.9990
   chunk 11 optimal weight:    4.9990
   chunk 70 optimal weight:    2.9990
   chunk 14 optimal weight:    0.4980
   chunk 75 optimal weight:    0.8980
   overall best weight:    1.4786

-------------------------------------------------------------------------------
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 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 = 0.2708 r_free = 0.2708 target = 0.029648 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2298 r_free = 0.2298 target = 0.019979 restraints weight = 180281.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2350 r_free = 0.2350 target = 0.021367 restraints weight = 58092.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2390 r_free = 0.2390 target = 0.022369 restraints weight = 31946.239|
|-----------------------------------------------------------------------------|
r_work (final): 0.2360
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2359
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2359 r_free = 0.2359    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 = 0.2359 r_free = 0.2359    target_work(ls_wunit_k1) = 0.022         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.2359
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8944
moved from start:          0.5472

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061   7553  Z= 0.254
  Angle     :  0.648  11.244  10293  Z= 0.317
  Chirality :  0.040   0.318   1114
  Planarity :  0.004   0.042   1298
  Dihedral  :  8.127  87.320   1004
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 9.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 14.68 %
    Favored  : 84.03 %
  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:  2.34 (0.28), residues: 910
  helix:  2.63 (0.23), residues: 511
  sheet:  0.46 (0.56), residues: 98
  loop :  0.06 (0.36), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C  14 
 HIS   0.004   0.001   HIS A 103 
 PHE   0.012   0.001   PHE E 418 
 TYR   0.008   0.001   TYR E 444 
 ARG   0.009   0.001   ARG E 403 

********************** 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: 9
    poor density    : 74
  time to evaluate  : 0.880 
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   30 GLU cc_start: 0.9460 (pt0) cc_final: 0.8962 (tt0)
REVERT: A  102 SER cc_start: 0.9643 (m) cc_final: 0.9363 (p)
REVERT: B    7 GLU cc_start: 0.9573 (mt-10) cc_final: 0.9189 (mt-10)
REVERT: B   21 ASP cc_start: 0.9092 (p0) cc_final: 0.8785 (p0)
REVERT: B  121 GLU cc_start: 0.9206 (tp30) cc_final: 0.8778 (tp30)
REVERT: B  127 GLN cc_start: 0.9488 (tt0) cc_final: 0.8798 (tm-30)
REVERT: C   27 GLU cc_start: 0.9616 (tt0) cc_final: 0.9234 (tt0)
REVERT: C   68 ASN cc_start: 0.9592 (t0) cc_final: 0.9388 (t0)
REVERT: C  116 GLU cc_start: 0.8970 (pm20) cc_final: 0.8753 (pm20)
REVERT: D   55 MET cc_start: 0.9298 (mmp) cc_final: 0.9080 (mmp)
REVERT: D   71 PHE cc_start: 0.9627 (m-80) cc_final: 0.9383 (m-80)
REVERT: D   99 ASP cc_start: 0.9019 (t0) cc_final: 0.8688 (t0)
REVERT: D  127 GLN cc_start: 0.9795 (tt0) cc_final: 0.9186 (tm-30)
REVERT: D  132 LYS cc_start: 0.9698 (mtpp) cc_final: 0.9376 (mtmm)
REVERT: E  382 MET cc_start: 0.8724 (mpp) cc_final: 0.8259 (mpp)
REVERT: E  384 MET cc_start: 0.9749 (ttm) cc_final: 0.9525 (ttm)
REVERT: E  396 MET cc_start: 0.9207 (tpp) cc_final: 0.8867 (tpp)
  outliers start: 9
  outliers final: 8
  residues processed: 80
  average time/residue: 0.2108
  time to fit residues: 22.9495
Evaluate side-chains
  82 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 74
  time to evaluate  : 0.811 
-------------------------------------------------------------------------------
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   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:    1.9990
   chunk 50 optimal weight:    3.9990
   chunk 12 optimal weight:    0.7980
   chunk 64 optimal weight:    0.0770
   chunk 39 optimal weight:    0.0070
   chunk 37 optimal weight:    0.7980
   chunk 44 optimal weight:    0.9980
   chunk 79 optimal weight:    0.8980
   chunk 24 optimal weight:    2.9990
   chunk 76 optimal weight:    4.9990
   chunk 46 optimal weight:    0.6980
   overall best weight:    0.4756

-------------------------------------------------------------------------------
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 = 0.2728 r_free = 0.2728 target = 0.029965 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2324 r_free = 0.2324 target = 0.020361 restraints weight = 185529.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2377 r_free = 0.2377 target = 0.021767 restraints weight = 58160.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2418 r_free = 0.2418 target = 0.022790 restraints weight = 31882.705|
|-----------------------------------------------------------------------------|
r_work (final): 0.2397
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2397
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2397 r_free = 0.2397    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 = 0.2397 r_free = 0.2397    target_work(ls_wunit_k1) = 0.022         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.2397
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8934
moved from start:          0.5509

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7553  Z= 0.202
  Angle     :  0.648  11.370  10293  Z= 0.316
  Chirality :  0.041   0.326   1114
  Planarity :  0.004   0.044   1298
  Dihedral  :  8.065  87.524   1004
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 8.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  : 14.81 %
    Favored  : 84.03 %
  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:  2.30 (0.28), residues: 910
  helix:  2.55 (0.22), residues: 513
  sheet:  0.51 (0.56), residues: 98
  loop :  0.09 (0.36), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP D  37 
 HIS   0.003   0.001   HIS A  87 
 PHE   0.014   0.001   PHE E 418 
 TYR   0.008   0.001   TYR B  35 
 ARG   0.008   0.000   ARG E 403 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2795.14 seconds
wall clock time: 49 minutes 19.80 seconds (2959.80 seconds total)