Starting phenix.real_space_refine
on Wed Feb 12 07:41:13 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7pcq_13325/02_2025/7pcq_13325_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7pcq_13325/02_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_13325/02_2025/7pcq_13325.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7pcq_13325/02_2025/7pcq_13325.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7pcq_13325/02_2025/7pcq_13325_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7pcq_13325/02_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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 7.33, per 1000 atoms: 1.00
  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: 2.04
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      41 helices and 5 sheets defined
      64.0% alpha, 13.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.73
  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: 2.12

  Time building geometry restraints manager: 2.35 seconds

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

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

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

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

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

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

  Histogram of nonbonded interaction distances:
        2.56 -     3.03: 4121
        3.03 -     3.49: 7699
        3.49 -     3.96: 12608
        3.96 -     4.43: 14872
        4.43 -     4.90: 22478
  Nonbonded interactions: 61778
  Sorted by model distance:
  nonbonded pdb=" N   THR A 118 "
            pdb=" O   THR A 118 "
     model   vdw
     2.557 2.496
  nonbonded pdb=" N   THR C 118 "
            pdb=" O   THR C 118 "
     model   vdw
     2.557 2.496
  nonbonded pdb=" O   TYR C 140 "
            pdb=" C   ARG C 141 "
     model   vdw
     2.557 3.270
  nonbonded pdb=" O   TYR D  35 "
            pdb=" OG1 THR D  38 "
     model   vdw
     2.564 3.040
  nonbonded pdb=" O   TYR E 391 "
            pdb=" N   HIS E 434 "
     model   vdw
     2.567 3.120
  ... (remaining 61773 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 1 through 55 or resid 57 through 141 or resid 201))
  selection = (chain 'C' and (resid 1 through 55 or resid 57 through 141 or resid 201))
}
ncs_group {
  reference = (chain 'B' and (resid 1 through 64 or (resid 65 and (name N or name CA or name C \ 
 or name O or name CB )) or resid 66 through 103 or resid 105 through 119 or (re \ 
sid 120 through 121 and (name N or name CA or name C or name O or name CB )) or  \ 
resid 122 through 146 or resid 201))
  selection = (chain 'D' and (resid 1 through 103 or resid 105 through 146 or resid 201))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=0.99
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.880
  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:             0.020
  Extract box with map and model:          0.340
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     23.700
  Find NCS groups from input model:        0.220
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.090
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.410
-------------------------------------------------------------------------------
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  : 0.815 
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: 0.2503
  time to fit residues: 56.0275
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  : 1.002 
-------------------------------------------------------------------------------
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 = 0.032865 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2389 r_free = 0.2389 target = 0.022293 restraints weight = 163487.950|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2443 r_free = 0.2443 target = 0.023859 restraints weight = 56470.800|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2487 r_free = 0.2487 target = 0.025027 restraints weight = 31919.457|
|-----------------------------------------------------------------------------|
r_work (final): 0.2470
-------------------------------------------------------------------------------
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:          0.3145

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   0.147   1114
  Planarity :  0.004   0.038   1298
  Dihedral  :  8.714  89.030   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  : 0.805 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   27 GLU cc_start: 0.9318 (tt0) cc_final: 0.8796 (tt0)
REVERT: A   94 ASP cc_start: 0.9189 (t0) cc_final: 0.8985 (t0)
REVERT: B    7 GLU cc_start: 0.9507 (mt-10) cc_final: 0.9159 (mt-10)
REVERT: B   21 ASP cc_start: 0.9429 (p0) cc_final: 0.8404 (p0)
REVERT: B   47 ASP cc_start: 0.9015 (t0) cc_final: 0.8661 (t0)
REVERT: B   99 ASP cc_start: 0.8872 (t0) cc_final: 0.8542 (t0)
REVERT: B  101 GLU cc_start: 0.9518 (mm-30) cc_final: 0.8924 (mp0)
REVERT: B  108 ASN cc_start: 0.9418 (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: 0.9092 (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: 0.9224 (mmtt) cc_final: 0.8870 (mmtp)
REVERT: E  155 MET cc_start: 0.8812 (mmm) cc_final: 0.8578 (mmp)
REVERT: E  190 GLN cc_start: 0.9371 (mt0) cc_final: 0.8766 (mp10)
REVERT: E  439 ASP cc_start: 0.9246 (t0) cc_final: 0.9044 (t0)
  outliers start: 12
  outliers final: 8
  residues processed: 109
  average time/residue: 0.2175
  time to fit residues: 31.7232
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  : 0.891 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 43 optimal weight:    0.8980
   chunk 15 optimal weight:    0.9990
   chunk 44 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 68 optimal weight:    3.9990
   chunk 17 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 52 optimal weight:    2.9990
   chunk 58 optimal weight:    5.9990
   chunk 21 optimal weight:    0.9980
   overall best weight:    1.1584

-------------------------------------------------------------------------------
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 = 0.2769 r_free = 0.2769 target = 0.032016 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2380 r_free = 0.2380 target = 0.022191 restraints weight = 175886.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2433 r_free = 0.2433 target = 0.023692 restraints weight = 57237.948|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2477 r_free = 0.2477 target = 0.024831 restraints weight = 31681.441|
|-----------------------------------------------------------------------------|
r_work (final): 0.2446
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2445
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2445 r_free = 0.2445    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 = 0.2442 r_free = 0.2442    target_work(ls_wunit_k1) = 0.024         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.2442
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8771
moved from start:          0.3808

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   7553  Z= 0.222
  Angle     :  0.594   8.248  10293  Z= 0.297
  Chirality :  0.040   0.150   1114
  Planarity :  0.004   0.040   1298
  Dihedral  :  8.479  89.553   1006
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 7.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 13.25 %
    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:  2.52 (0.28), residues: 910
  helix:  2.69 (0.22), residues: 523
  sheet:  0.17 (0.52), 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   0.004   0.001   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
  104 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 91
  time to evaluate  : 0.834 
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   94 ASP cc_start: 0.9319 (t0) cc_final: 0.9056 (t0)
REVERT: B    7 GLU cc_start: 0.9529 (mt-10) cc_final: 0.9157 (mt-10)
REVERT: B   47 ASP cc_start: 0.9168 (t0) cc_final: 0.8875 (t0)
REVERT: B  101 GLU cc_start: 0.9552 (mm-30) cc_final: 0.9310 (mm-30)
REVERT: B  108 ASN cc_start: 0.9428 (m-40) cc_final: 0.9126 (t0)
REVERT: B  127 GLN cc_start: 0.9503 (tt0) cc_final: 0.8734 (tm-30)
REVERT: B  131 GLN cc_start: 0.9408 (mm110) cc_final: 0.9054 (mm110)
REVERT: C   27 GLU cc_start: 0.9532 (tt0) cc_final: 0.9096 (tt0)
REVERT: C   32 MET cc_start: 0.9614 (OUTLIER) cc_final: 0.9373 (mmm)
REVERT: C   68 ASN cc_start: 0.9526 (t0) cc_final: 0.9294 (t0)
REVERT: C   92 ARG cc_start: 0.8855 (mpp80) cc_final: 0.8592 (mmt90)
REVERT: D   71 PHE cc_start: 0.9722 (m-80) cc_final: 0.9354 (m-80)
REVERT: D   99 ASP cc_start: 0.8831 (t0) cc_final: 0.8373 (t0)
REVERT: D  127 GLN cc_start: 0.9767 (tt0) cc_final: 0.9145 (tm-30)
REVERT: E  439 ASP cc_start: 0.9353 (t0) cc_final: 0.9124 (t0)
  outliers start: 13
  outliers final: 9
  residues processed: 99
  average time/residue: 0.2059
  time to fit residues: 27.7023
Evaluate side-chains
  90 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 80
  time to evaluate  : 0.944 
-------------------------------------------------------------------------------
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  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:    0.3980
   chunk 77 optimal weight:    6.9990
   chunk 15 optimal weight:    0.6980
   chunk 34 optimal weight:    5.9990
   chunk 16 optimal weight:    0.9980
   chunk 80 optimal weight:    0.6980
   chunk 14 optimal weight:    1.9990
   chunk 23 optimal weight:    5.9990
   chunk 32 optimal weight:    0.9980
   chunk 62 optimal weight:   10.0000
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A  78 ASN
B  63 HIS
** D  39 GLN ** 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 = 0.2763 r_free = 0.2763 target = 0.031684 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2371 r_free = 0.2371 target = 0.022088 restraints weight = 172590.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2427 r_free = 0.2427 target = 0.023570 restraints weight = 56500.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2470 r_free = 0.2470 target = 0.024660 restraints weight = 31291.534|
|-----------------------------------------------------------------------------|
r_work (final): 0.2437
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2437
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2437 r_free = 0.2437    target_work(ls_wunit_k1) = 0.024         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2437 r_free = 0.2437    target_work(ls_wunit_k1) = 0.024         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.2437
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8790
moved from start:          0.4140

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   7553  Z= 0.201
  Angle     :  0.597   9.716  10293  Z= 0.294
  Chirality :  0.039   0.162   1114
  Planarity :  0.004   0.045   1298
  Dihedral  :  8.475  86.583   1006
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 8.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 14.03 %
    Favored  : 84.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.68 (0.28), residues: 910
  helix:  2.87 (0.22), residues: 509
  sheet:  0.19 (0.53), residues: 102
  loop :  0.49 (0.37), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A  14 
 HIS   0.003   0.001   HIS E 369 
 PHE   0.014   0.001   PHE E 418 
 TYR   0.015   0.001   TYR B  35 
 ARG   0.007   0.000   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
  97 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 88
  time to evaluate  : 0.824 
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   94 ASP cc_start: 0.9314 (t0) cc_final: 0.8849 (t0)
REVERT: B    7 GLU cc_start: 0.9535 (mt-10) cc_final: 0.9188 (mt-10)
REVERT: B   21 ASP cc_start: 0.9039 (p0) cc_final: 0.8363 (p0)
REVERT: B   22 GLU cc_start: 0.9224 (mm-30) cc_final: 0.8778 (mm-30)
REVERT: B   47 ASP cc_start: 0.9205 (t0) cc_final: 0.8935 (t0)
REVERT: B  108 ASN cc_start: 0.9417 (m-40) cc_final: 0.9128 (t0)
REVERT: B  127 GLN cc_start: 0.9499 (tt0) cc_final: 0.8758 (tm-30)
REVERT: B  131 GLN cc_start: 0.9376 (mm110) cc_final: 0.9046 (mm110)
REVERT: C   27 GLU cc_start: 0.9566 (tt0) cc_final: 0.9138 (tt0)
REVERT: C   68 ASN cc_start: 0.9547 (t0) cc_final: 0.9316 (t0)
REVERT: C   92 ARG cc_start: 0.8877 (mpp80) cc_final: 0.8622 (mmt90)
REVERT: C  116 GLU cc_start: 0.9478 (mp0) cc_final: 0.9267 (pm20)
REVERT: D   99 ASP cc_start: 0.8899 (t0) cc_final: 0.8456 (t0)
REVERT: D  127 GLN cc_start: 0.9764 (tt0) cc_final: 0.9150 (tm-30)
REVERT: E  155 MET cc_start: 0.8982 (mmp) cc_final: 0.8033 (mmp)
REVERT: E  254 MET cc_start: 0.9561 (ttt) cc_final: 0.9261 (tpp)
REVERT: E  439 ASP cc_start: 0.9375 (t0) cc_final: 0.9146 (t0)
  outliers start: 9
  outliers final: 6
  residues processed: 95
  average time/residue: 0.2137
  time to fit residues: 27.4183
Evaluate side-chains
  88 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 82
  time to evaluate  : 0.817 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 SER
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 46 optimal weight:    2.9990
   chunk 80 optimal weight:    3.9990
   chunk 77 optimal weight:    4.9990
   chunk 60 optimal weight:   10.0000
   chunk 84 optimal weight:    0.9990
   chunk 62 optimal weight:    3.9990
   chunk 40 optimal weight:    5.9990
   chunk 78 optimal weight:    7.9990
   chunk 55 optimal weight:    2.9990
   chunk 47 optimal weight:    8.9990
   chunk 19 optimal weight:    0.9980
   overall best weight:    2.3988

-------------------------------------------------------------------------------
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 = 0.2693 r_free = 0.2693 target = 0.029477 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2290 r_free = 0.2290 target = 0.020116 restraints weight = 203920.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2344 r_free = 0.2344 target = 0.021509 restraints weight = 61239.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.2383 r_free = 0.2383 target = 0.022494 restraints weight = 33495.929|
|-----------------------------------------------------------------------------|
r_work (final): 0.2363
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2363
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2363 r_free = 0.2363    target_work(ls_wunit_k1) = 0.022         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2362 r_free = 0.2362    target_work(ls_wunit_k1) = 0.022         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.2362
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8937
moved from start:          0.4716

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.081   7553  Z= 0.321
  Angle     :  0.637   9.152  10293  Z= 0.311
  Chirality :  0.040   0.181   1114
  Planarity :  0.004   0.044   1298
  Dihedral  :  8.606  89.821   1004
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 9.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 13.77 %
    Favored  : 84.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.63 (0.28), residues: 910
  helix:  2.76 (0.22), residues: 521
  sheet:  0.43 (0.55), residues: 98
  loop :  0.39 (0.36), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A  14 
 HIS   0.004   0.001   HIS A  87 
 PHE   0.019   0.001   PHE E 418 
 TYR   0.019   0.001   TYR B  35 
 ARG   0.004   0.001   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
  92 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 78
  time to evaluate  : 0.847 
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   92 ARG cc_start: 0.9257 (OUTLIER) cc_final: 0.8777 (mmm-85)
REVERT: A   94 ASP cc_start: 0.9483 (t0) cc_final: 0.9088 (t0)
REVERT: B    7 GLU cc_start: 0.9557 (mt-10) cc_final: 0.9158 (mt-10)
REVERT: B   21 ASP cc_start: 0.9039 (p0) cc_final: 0.8324 (p0)
REVERT: B   22 GLU cc_start: 0.9231 (mm-30) cc_final: 0.8808 (mm-30)
REVERT: B   73 ASP cc_start: 0.9417 (m-30) cc_final: 0.9106 (t0)
REVERT: B  101 GLU cc_start: 0.9566 (mm-30) cc_final: 0.9357 (mm-30)
REVERT: B  108 ASN cc_start: 0.9446 (m-40) cc_final: 0.9060 (t0)
REVERT: B  127 GLN cc_start: 0.9524 (tt0) cc_final: 0.8816 (tm-30)
REVERT: B  131 GLN cc_start: 0.9503 (mm110) cc_final: 0.9173 (mm110)
REVERT: C   27 GLU cc_start: 0.9575 (tt0) cc_final: 0.9160 (tt0)
REVERT: C   68 ASN cc_start: 0.9580 (t0) cc_final: 0.9352 (t0)
REVERT: D   55 MET cc_start: 0.9223 (mmp) cc_final: 0.8946 (mmp)
REVERT: D   71 PHE cc_start: 0.9691 (m-80) cc_final: 0.9420 (m-80)
REVERT: D   99 ASP cc_start: 0.9065 (t0) cc_final: 0.8609 (t0)
REVERT: D  127 GLN cc_start: 0.9766 (tt0) cc_final: 0.9160 (tm-30)
REVERT: E  124 MET cc_start: 0.8129 (mmm) cc_final: 0.6297 (tmm)
  outliers start: 14
  outliers final: 10
  residues processed: 89
  average time/residue: 0.2334
  time to fit residues: 27.6136
Evaluate side-chains
  86 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 75
  time to evaluate  : 0.833 
-------------------------------------------------------------------------------
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  105 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:    8.9990
   chunk 39 optimal weight:   10.0000
   chunk 25 optimal weight:    0.9980
   chunk 45 optimal weight:    3.9990
   chunk 71 optimal weight:    0.9980
   chunk 0 optimal weight:   10.0000
   chunk 18 optimal weight:    6.9990
   chunk 16 optimal weight:    0.7980
   chunk 5 optimal weight:   10.0000
   chunk 80 optimal weight:    0.9980
   chunk 54 optimal weight:    6.9990
   overall best weight:    1.5582

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

Flipped N/Q/H residues before XYZ refinement:
** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  39 GLN
** D  63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2701 r_free = 0.2701 target = 0.029606 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2304 r_free = 0.2304 target = 0.020363 restraints weight = 196678.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2359 r_free = 0.2359 target = 0.021754 restraints weight = 59296.245|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2398 r_free = 0.2398 target = 0.022740 restraints weight = 32331.687|
|-----------------------------------------------------------------------------|
r_work (final): 0.2377
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2377
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2377 r_free = 0.2377    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 = 0.2377 r_free = 0.2377    target_work(ls_wunit_k1) = 0.022         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.2377
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8927
moved from start:          0.4916

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= 0.249
  Angle     :  0.612  11.046  10293  Z= 0.299
  Chirality :  0.039   0.179   1114
  Planarity :  0.004   0.044   1298
  Dihedral  :  8.468  86.841   1004
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 8.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.33 %
    Favored  : 98.67 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 13.77 %
    Favored  : 84.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.63 (0.28), residues: 910
  helix:  2.77 (0.22), residues: 523
  sheet:  0.41 (0.55), residues: 98
  loop :  0.35 (0.36), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A  14 
 HIS   0.003   0.001   HIS A  87 
 PHE   0.019   0.001   PHE E 418 
 TYR   0.015   0.001   TYR C 140 
 ARG   0.007   0.001   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
  94 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 80
  time to evaluate  : 0.869 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   30 GLU cc_start: 0.9490 (pt0) cc_final: 0.9094 (tt0)
REVERT: A   94 ASP cc_start: 0.9464 (t0) cc_final: 0.9072 (t0)
REVERT: B    7 GLU cc_start: 0.9566 (mt-10) cc_final: 0.9169 (mt-10)
REVERT: B   21 ASP cc_start: 0.9060 (p0) cc_final: 0.8310 (p0)
REVERT: B   22 GLU cc_start: 0.9224 (mm-30) cc_final: 0.8766 (mm-30)
REVERT: B   73 ASP cc_start: 0.9383 (m-30) cc_final: 0.9106 (t0)
REVERT: B  121 GLU cc_start: 0.9038 (tp30) cc_final: 0.8637 (tp30)
REVERT: B  127 GLN cc_start: 0.9496 (tt0) cc_final: 0.8761 (tm-30)
REVERT: B  131 GLN cc_start: 0.9466 (mm110) cc_final: 0.9259 (mm110)
REVERT: C   27 GLU cc_start: 0.9596 (tt0) cc_final: 0.9197 (tt0)
REVERT: C   68 ASN cc_start: 0.9579 (t0) cc_final: 0.9354 (t0)
REVERT: D   55 MET cc_start: 0.9235 (mmp) cc_final: 0.8955 (mmp)
REVERT: D   71 PHE cc_start: 0.9672 (m-80) cc_final: 0.9395 (m-80)
REVERT: D   99 ASP cc_start: 0.9030 (t0) cc_final: 0.8575 (t0)
REVERT: D  127 GLN cc_start: 0.9761 (tt0) cc_final: 0.9149 (tm-30)
REVERT: E  124 MET cc_start: 0.8118 (mmm) cc_final: 0.6365 (tmm)
REVERT: E  396 MET cc_start: 0.9222 (tpp) cc_final: 0.8947 (tpp)
  outliers start: 14
  outliers final: 9
  residues processed: 90
  average time/residue: 0.2182
  time to fit residues: 26.6048
Evaluate side-chains
  81 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 72
  time to evaluate  : 0.798 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 SER
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain A residue  126 ASP
Chi-restraints excluded: chain B residue   32 LEU
Chi-restraints excluded: chain C residue  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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 4 optimal weight:    0.6980
   chunk 53 optimal weight:    1.9990
   chunk 2 optimal weight:    4.9990
   chunk 82 optimal weight:    0.6980
   chunk 5 optimal weight:    5.9990
   chunk 37 optimal weight:    1.9990
   chunk 81 optimal weight:   10.0000
   chunk 25 optimal weight:    0.8980
   chunk 57 optimal weight:    7.9990
   chunk 73 optimal weight:    5.9990
   chunk 15 optimal weight:    1.9990
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  39 GLN
** D  63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2712 r_free = 0.2712 target = 0.029629 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2297 r_free = 0.2297 target = 0.019877 restraints weight = 180535.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2350 r_free = 0.2350 target = 0.021239 restraints weight = 57488.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2391 r_free = 0.2391 target = 0.022238 restraints weight = 32000.960|
|-----------------------------------------------------------------------------|
r_work (final): 0.2382
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2382
|-occupancy refinement: start-------------------------------------------------|
| 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:        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: 0.8931
moved from start:          0.5069

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   7553  Z= 0.238
  Angle     :  0.639  11.471  10293  Z= 0.311
  Chirality :  0.041   0.338   1114
  Planarity :  0.004   0.044   1298
  Dihedral  :  8.385  86.781   1004
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 8.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.66 %
    Favored  : 98.34 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 14.42 %
    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:  2.48 (0.28), residues: 910
  helix:  2.64 (0.22), residues: 525
  sheet:  0.42 (0.56), residues: 98
  loop :  0.23 (0.37), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  14 
 HIS   0.004   0.001   HIS D  92 
 PHE   0.017   0.001   PHE E 418 
 TYR   0.014   0.001   TYR C 140 
 ARG   0.006   0.001   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
  89 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 78
  time to evaluate  : 0.911 
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   94 ASP cc_start: 0.9446 (t0) cc_final: 0.9049 (t0)
REVERT: B    7 GLU cc_start: 0.9583 (mt-10) cc_final: 0.9179 (mt-10)
REVERT: B   21 ASP cc_start: 0.9028 (p0) cc_final: 0.8242 (p0)
REVERT: B   22 GLU cc_start: 0.9167 (mm-30) cc_final: 0.8728 (mm-30)
REVERT: B   73 ASP cc_start: 0.9358 (m-30) cc_final: 0.9085 (t0)
REVERT: B  127 GLN cc_start: 0.9493 (tt0) cc_final: 0.8691 (tm-30)
REVERT: B  131 GLN cc_start: 0.9495 (mm110) cc_final: 0.9101 (mm-40)
REVERT: C   27 GLU cc_start: 0.9607 (tt0) cc_final: 0.9221 (tt0)
REVERT: C   32 MET cc_start: 0.9598 (ttm) cc_final: 0.9190 (mtp)
REVERT: C   68 ASN cc_start: 0.9585 (t0) cc_final: 0.9372 (t0)
REVERT: D   55 MET cc_start: 0.9249 (mmp) cc_final: 0.8981 (mmp)
REVERT: D   99 ASP cc_start: 0.9048 (t0) cc_final: 0.8581 (t0)
REVERT: D  127 GLN cc_start: 0.9772 (tt0) cc_final: 0.9155 (tm-30)
REVERT: E  124 MET cc_start: 0.8121 (mmm) cc_final: 0.6461 (tmm)
REVERT: E  384 MET cc_start: 0.9732 (ttm) cc_final: 0.9510 (ttm)
  outliers start: 11
  outliers final: 11
  residues processed: 86
  average time/residue: 0.2216
  time to fit residues: 25.7972
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  : 0.909 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 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
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:    2.9990
   chunk 45 optimal weight:    0.6980
   chunk 32 optimal weight:    4.9990
   chunk 55 optimal weight:    9.9990
   chunk 59 optimal weight:    0.4980
   chunk 83 optimal weight:    1.9990
   chunk 56 optimal weight:   10.0000
   chunk 47 optimal weight:    0.7980
   chunk 24 optimal weight:    0.9980
   chunk 53 optimal weight:    1.9990
   overall best weight:    0.9982

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2723 r_free = 0.2723 target = 0.030001 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2310 r_free = 0.2310 target = 0.020200 restraints weight = 182069.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2363 r_free = 0.2363 target = 0.021585 restraints weight = 57587.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2403 r_free = 0.2403 target = 0.022582 restraints weight = 31960.430|
|-----------------------------------------------------------------------------|
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) = 0.023         |
| 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) = 0.023         |
| 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:          0.5199

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   7553  Z= 0.222
  Angle     :  0.643  11.710  10293  Z= 0.313
  Chirality :  0.041   0.324   1114
  Planarity :  0.004   0.045   1298
  Dihedral  :  8.254  86.413   1004
  Min Nonbonded Distance : 2.377

Molprobity Statistics.
  All-atom Clashscore : 8.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.33 %
    Favored  : 98.67 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 14.55 %
    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:  2.46 (0.28), residues: 910
  helix:  2.63 (0.22), residues: 525
  sheet:  0.41 (0.56), residues: 98
  loop :  0.22 (0.37), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  14 
 HIS   0.004   0.001   HIS A  87 
 PHE   0.015   0.001   PHE E 418 
 TYR   0.016   0.001   TYR C 140 
 ARG   0.008   0.001   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
  90 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 77
  time to evaluate  : 0.818 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   68 ASN cc_start: 0.9776 (t0) cc_final: 0.9537 (t0)
REVERT: A   92 ARG cc_start: 0.9278 (OUTLIER) cc_final: 0.8885 (mmm-85)
REVERT: A   94 ASP cc_start: 0.9418 (t0) cc_final: 0.9015 (t0)
REVERT: B    7 GLU cc_start: 0.9570 (mt-10) cc_final: 0.9179 (mt-10)
REVERT: B   21 ASP cc_start: 0.8988 (p0) cc_final: 0.8179 (p0)
REVERT: B   22 GLU cc_start: 0.9148 (mm-30) cc_final: 0.8703 (mm-30)
REVERT: B   26 GLU cc_start: 0.9351 (tp30) cc_final: 0.9132 (tp30)
REVERT: B   73 ASP cc_start: 0.9338 (m-30) cc_final: 0.9076 (t0)
REVERT: B  121 GLU cc_start: 0.9116 (tp30) cc_final: 0.8721 (tp30)
REVERT: B  127 GLN cc_start: 0.9482 (tt0) cc_final: 0.8760 (tm-30)
REVERT: C   27 GLU cc_start: 0.9615 (tt0) cc_final: 0.9240 (tt0)
REVERT: C   32 MET cc_start: 0.9582 (ttm) cc_final: 0.9287 (mtp)
REVERT: C   68 ASN cc_start: 0.9583 (t0) cc_final: 0.9367 (t0)
REVERT: C   92 ARG cc_start: 0.8857 (mpp80) cc_final: 0.8530 (mmt90)
REVERT: C  104 CYS cc_start: 0.9513 (m) cc_final: 0.9005 (t)
REVERT: C  116 GLU cc_start: 0.9012 (pm20) cc_final: 0.8715 (pm20)
REVERT: D   55 MET cc_start: 0.9260 (mmp) cc_final: 0.9001 (mmp)
REVERT: D   71 PHE cc_start: 0.9619 (m-80) cc_final: 0.9368 (m-80)
REVERT: D   99 ASP cc_start: 0.9039 (t0) cc_final: 0.8572 (t0)
REVERT: D  127 GLN cc_start: 0.9772 (tt0) cc_final: 0.9161 (tm-30)
REVERT: D  132 LYS cc_start: 0.9683 (mtpp) cc_final: 0.9280 (mtmm)
REVERT: E  124 MET cc_start: 0.8124 (mmm) cc_final: 0.6548 (tmm)
REVERT: E  254 MET cc_start: 0.9574 (ttt) cc_final: 0.9318 (tpp)
REVERT: E  384 MET cc_start: 0.9738 (ttm) cc_final: 0.9520 (ttm)
  outliers start: 13
  outliers final: 10
  residues processed: 86
  average time/residue: 0.2388
  time to fit residues: 27.1650
Evaluate side-chains
  84 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 73
  time to evaluate  : 0.855 
-------------------------------------------------------------------------------
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 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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 63 optimal weight:    3.9990
   chunk 78 optimal weight:    6.9990
   chunk 15 optimal weight:    0.7980
   chunk 41 optimal weight:    8.9990
   chunk 46 optimal weight:    0.9990
   chunk 42 optimal weight:    0.0040
   chunk 17 optimal weight:    0.9980
   chunk 81 optimal weight:    7.9990
   chunk 13 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9980
   chunk 72 optimal weight:    0.7980
   overall best weight:    0.7192

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2731 r_free = 0.2731 target = 0.030372 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2338 r_free = 0.2338 target = 0.020925 restraints weight = 125894.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2388 r_free = 0.2388 target = 0.022258 restraints weight = 49491.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2425 r_free = 0.2425 target = 0.023211 restraints weight = 28937.054|
|-----------------------------------------------------------------------------|
r_work (final): 0.2400
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2400
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2400 r_free = 0.2400    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 = 0.2399 r_free = 0.2399    target_work(ls_wunit_k1) = 0.023         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.2399
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8923
moved from start:          0.5331

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   7553  Z= 0.211
  Angle     :  0.643  11.825  10293  Z= 0.316
  Chirality :  0.041   0.318   1114
  Planarity :  0.004   0.045   1298
  Dihedral  :  8.147  86.108   1004
  Min Nonbonded Distance : 2.395

Molprobity Statistics.
  All-atom Clashscore : 7.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.33 %
    Favored  : 98.67 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 14.68 %
    Favored  : 83.77 %
  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:  2.39 (0.28), residues: 910
  helix:  2.66 (0.23), residues: 515
  sheet:  0.43 (0.56), residues: 98
  loop :  0.10 (0.36), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  14 
 HIS   0.004   0.001   HIS D  92 
 PHE   0.018   0.001   PHE E 418 
 TYR   0.017   0.001   TYR C 140 
 ARG   0.008   0.000   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
  87 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 76
  time to evaluate  : 1.005 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   68 ASN cc_start: 0.9776 (t0) cc_final: 0.9533 (t0)
REVERT: A   92 ARG cc_start: 0.9285 (OUTLIER) cc_final: 0.8805 (mmm-85)
REVERT: B    7 GLU cc_start: 0.9567 (mt-10) cc_final: 0.9176 (mt-10)
REVERT: B   21 ASP cc_start: 0.8954 (p0) cc_final: 0.8360 (p0)
REVERT: B   22 GLU cc_start: 0.9128 (mm-30) cc_final: 0.8655 (mm-30)
REVERT: B   26 GLU cc_start: 0.9325 (tp30) cc_final: 0.9093 (tp30)
REVERT: B  121 GLU cc_start: 0.9124 (tp30) cc_final: 0.8720 (tp30)
REVERT: B  127 GLN cc_start: 0.9481 (tt0) cc_final: 0.8776 (tm-30)
REVERT: C   27 GLU cc_start: 0.9626 (tt0) cc_final: 0.9255 (tt0)
REVERT: C   32 MET cc_start: 0.9566 (ttm) cc_final: 0.9282 (mtp)
REVERT: C   68 ASN cc_start: 0.9581 (t0) cc_final: 0.9369 (t0)
REVERT: C  104 CYS cc_start: 0.9496 (m) cc_final: 0.9007 (t)
REVERT: C  116 GLU cc_start: 0.8987 (pm20) cc_final: 0.8739 (pm20)
REVERT: D   55 MET cc_start: 0.9286 (mmp) cc_final: 0.9051 (mmp)
REVERT: D   71 PHE cc_start: 0.9614 (m-80) cc_final: 0.9348 (m-80)
REVERT: D   99 ASP cc_start: 0.9009 (t0) cc_final: 0.8654 (t0)
REVERT: D  127 GLN cc_start: 0.9776 (tt0) cc_final: 0.9165 (tm-30)
REVERT: D  132 LYS cc_start: 0.9681 (mtpp) cc_final: 0.9277 (mtmm)
REVERT: D  144 LYS cc_start: 0.9204 (mmtt) cc_final: 0.8846 (mmtm)
REVERT: E  124 MET cc_start: 0.8170 (mmm) cc_final: 0.6811 (tmm)
REVERT: E  254 MET cc_start: 0.9544 (ttt) cc_final: 0.9303 (tpp)
REVERT: E  382 MET cc_start: 0.8756 (mpp) cc_final: 0.8259 (mpp)
REVERT: E  384 MET cc_start: 0.9748 (ttm) cc_final: 0.9517 (ttm)
REVERT: E  396 MET cc_start: 0.9183 (tpp) cc_final: 0.8820 (tpp)
  outliers start: 11
  outliers final: 9
  residues processed: 83
  average time/residue: 0.2368
  time to fit residues: 26.0667
Evaluate side-chains
  84 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 74
  time to evaluate  : 0.849 
-------------------------------------------------------------------------------
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 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:   10.0000
   chunk 41 optimal weight:    9.9990
   chunk 62 optimal weight:    0.8980
   chunk 56 optimal weight:    8.9990
   chunk 17 optimal weight:    0.6980
   chunk 29 optimal weight:    3.9990
   chunk 74 optimal weight:    6.9990
   chunk 11 optimal weight:    1.9990
   chunk 70 optimal weight:    1.9990
   chunk 14 optimal weight:    6.9990
   chunk 75 optimal weight:    1.9990
   overall best weight:    1.5186

-------------------------------------------------------------------------------
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 = 0.2715 r_free = 0.2715 target = 0.029966 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2320 r_free = 0.2320 target = 0.020783 restraints weight = 181288.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2373 r_free = 0.2373 target = 0.022165 restraints weight = 57626.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2408 r_free = 0.2408 target = 0.023124 restraints weight = 31740.641|
|-----------------------------------------------------------------------------|
r_work (final): 0.2385
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2384
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2384 r_free = 0.2384    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 = 0.2384 r_free = 0.2384    target_work(ls_wunit_k1) = 0.022         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.2384
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8943
moved from start:          0.5406

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= 0.258
  Angle     :  0.651  11.550  10293  Z= 0.321
  Chirality :  0.040   0.310   1114
  Planarity :  0.004   0.044   1298
  Dihedral  :  8.132  86.825   1004
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 9.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 14.68 %
    Favored  : 83.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.42 (0.28), residues: 910
  helix:  2.69 (0.23), residues: 513
  sheet:  0.45 (0.56), residues: 98
  loop :  0.10 (0.36), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  14 
 HIS   0.004   0.001   HIS A  87 
 PHE   0.013   0.001   PHE E 418 
 TYR   0.017   0.001   TYR C 140 
 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: 10
    poor density    : 73
  time to evaluate  : 0.907 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   68 ASN cc_start: 0.9774 (t0) cc_final: 0.9557 (t0)
REVERT: B    7 GLU cc_start: 0.9573 (mt-10) cc_final: 0.9189 (mt-10)
REVERT: B   21 ASP cc_start: 0.8958 (p0) cc_final: 0.8377 (p0)
REVERT: B   22 GLU cc_start: 0.9128 (mm-30) cc_final: 0.8666 (mm-30)
REVERT: B   26 GLU cc_start: 0.9348 (tp30) cc_final: 0.9125 (tp30)
REVERT: B   73 ASP cc_start: 0.9336 (m-30) cc_final: 0.9070 (t0)
REVERT: B  121 GLU cc_start: 0.9206 (tp30) cc_final: 0.8814 (tp30)
REVERT: B  127 GLN cc_start: 0.9494 (tt0) cc_final: 0.8792 (tm-30)
REVERT: B  131 GLN cc_start: 0.9652 (mm-40) cc_final: 0.9384 (mm-40)
REVERT: C   27 GLU cc_start: 0.9617 (tt0) cc_final: 0.9244 (tt0)
REVERT: C   68 ASN cc_start: 0.9588 (t0) cc_final: 0.9376 (t0)
REVERT: C   92 ARG cc_start: 0.8880 (mpp80) cc_final: 0.8534 (mmt90)
REVERT: C  104 CYS cc_start: 0.9515 (m) cc_final: 0.9256 (t)
REVERT: C  116 GLU cc_start: 0.9004 (pm20) cc_final: 0.8778 (pm20)
REVERT: D   55 MET cc_start: 0.9307 (mmp) cc_final: 0.9068 (mmp)
REVERT: D   71 PHE cc_start: 0.9614 (m-80) cc_final: 0.9347 (m-80)
REVERT: D   99 ASP cc_start: 0.8982 (t0) cc_final: 0.8641 (t0)
REVERT: D  127 GLN cc_start: 0.9782 (tt0) cc_final: 0.9179 (tm-30)
REVERT: D  132 LYS cc_start: 0.9689 (mtpp) cc_final: 0.9369 (mtmm)
REVERT: E  124 MET cc_start: 0.8270 (mmm) cc_final: 0.6895 (tmm)
REVERT: E  254 MET cc_start: 0.9552 (ttt) cc_final: 0.9309 (tpp)
REVERT: E  382 MET cc_start: 0.8732 (mpp) cc_final: 0.8222 (mpp)
REVERT: E  384 MET cc_start: 0.9744 (ttm) cc_final: 0.9521 (ttm)
REVERT: E  396 MET cc_start: 0.9191 (tpp) cc_final: 0.8825 (tpp)
  outliers start: 10
  outliers final: 10
  residues processed: 81
  average time/residue: 0.2230
  time to fit residues: 24.1630
Evaluate side-chains
  82 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 72
  time to evaluate  : 0.900 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 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
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:    0.9990
   chunk 12 optimal weight:    3.9990
   chunk 64 optimal weight:    0.4980
   chunk 39 optimal weight:    7.9990
   chunk 37 optimal weight:    0.9990
   chunk 44 optimal weight:    0.2980
   chunk 79 optimal weight:    2.9990
   chunk 24 optimal weight:    5.9990
   chunk 76 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   overall best weight:    0.9586

-------------------------------------------------------------------------------
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 = 0.2725 r_free = 0.2725 target = 0.030275 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2330 r_free = 0.2330 target = 0.020981 restraints weight = 184814.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2383 r_free = 0.2383 target = 0.022396 restraints weight = 58083.950|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2422 r_free = 0.2422 target = 0.023423 restraints weight = 31886.912|
|-----------------------------------------------------------------------------|
r_work (final): 0.2402
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2402
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2402 r_free = 0.2402    target_work(ls_wunit_k1) = 0.023         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2402 r_free = 0.2402    target_work(ls_wunit_k1) = 0.023         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.2402
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8942
moved from start:          0.5463

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= 0.228
  Angle     :  0.648  11.337  10293  Z= 0.319
  Chirality :  0.040   0.309   1114
  Planarity :  0.004   0.045   1298
  Dihedral  :  8.096  87.233   1004
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 8.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.11 %
    Favored  : 98.89 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 15.06 %
    Favored  : 83.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.34 (0.28), residues: 910
  helix:  2.59 (0.22), residues: 515
  sheet:  0.47 (0.56), residues: 98
  loop :  0.12 (0.36), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D  37 
 HIS   0.004   0.001   HIS D  92 
 PHE   0.014   0.001   PHE E 418 
 TYR   0.017   0.001   TYR C 140 
 ARG   0.008   0.001   ARG E 403 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2771.83 seconds
wall clock time: 50 minutes 33.13 seconds (3033.13 seconds total)