Starting phenix.real_space_refine
on Wed Mar  4 00:56:58 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6wbv_21599/03_2026/6wbv_21599.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6wbv_21599/03_2026/6wbv_21599.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6wbv_21599/03_2026/6wbv_21599.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6wbv_21599/03_2026/6wbv_21599.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6wbv_21599/03_2026/6wbv_21599.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6wbv_21599/03_2026/6wbv_21599.map"
  }
  resolution = 2.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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=  -0.013 sd=   0.959
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 3344 atoms to isotropic.
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: 6
    Type Number    sf(0)   Gaussians
     Co      2      6.85       5
     P       2      5.49       5
     S      47      5.16       5
     C    4398      2.51       5
     N    1114      2.21       5
     O    1297      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 22 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6860
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "B"
      Number of atoms: 181
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 25, 181
          Classifications: {'peptide': 25}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 23}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "A"
      Number of atoms: 3262
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 429, 3262
          Classifications: {'peptide': 429}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 10, 'TRANS': 418}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 30
          Unresolved non-hydrogen angles: 37
          Unresolved non-hydrogen dihedrals: 25
          Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 2, 'PHE:plan': 1, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 27
    Chain: "L"
      Number of atoms: 1670
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 218, 1670
          Classifications: {'peptide': 218}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PCIS': 4, 'PTRANS': 10, 'TRANS': 203}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 17
          Unresolved non-hydrogen angles: 19
          Unresolved non-hydrogen dihedrals: 15
          Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 7
    Chain: "H"
      Number of atoms: 1674
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 220, 1666
          Classifications: {'peptide': 220}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 205}
          Unresolved non-hydrogen bonds: 13
          Unresolved non-hydrogen angles: 15
          Unresolved non-hydrogen dihedrals: 11
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 9
      Conformer: "B"
        Number of residues, atoms: 220, 1666
          Classifications: {'peptide': 220}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 205}
          Unresolved non-hydrogen bonds: 13
          Unresolved non-hydrogen angles: 15
          Unresolved non-hydrogen dihedrals: 11
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 9
          bond proxies already assigned to first conformer: 1703
    Chain: "A"
      Number of atoms: 62
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 62
          Unusual residues: {' CO': 2, 'AGA': 2}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
    Chain: "A"
      Number of atoms: 10
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 10
          Classifications: {'water': 10}
          Link IDs: {None: 9}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   2181  SG  CYS A 326      78.631  63.845  45.666  1.00 49.12           S

  Time building chain proxies: 1.36, per 1000 atoms: 0.20
  Number of scatterers: 6860
  At special positions: 0
  Unit cell: (113.424, 110.088, 111.756, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Co      2     26.99
     S      47     16.00
     P       2     15.00
     O    1297      8.00
     N    1114      7.00
     C    4398      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=9, symmetry=0
    Simple disulfide: pdb=" SG  CYS B   7 " - pdb=" SG  CYS B  23 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  10 " - pdb=" SG  CYS B  13 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B  11 " - pdb=" SG  CYS B  19 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  14 " - pdb=" SG  CYS B  22 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  92 " distance=2.05
    Simple disulfide: pdb=" SG  CYS L 138 " - pdb=" SG  CYS L 198 " distance=2.04
    Simple disulfide: pdb=" SG  CYS L 218 " - pdb=" SG  CYS H 133 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  95 " distance=2.04
    Simple disulfide: pdb=" SG  CYS H 145 " - pdb=" SG  CYS H 200 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.56
  Conformation dependent library (CDL) restraints added in 221.6 milliseconds
  

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1650

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 13 sheets defined
      47.6% alpha, 27.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.15
  Creating SS restraints...
    Processing helix  chain 'A' and resid 17 through 21
    Processing helix  chain 'A' and resid 23 through 54
    Processing helix  chain 'A' and resid 58 through 86
      removed outlier: 3.503A  pdb=" N   ALA A  62 " --> pdb=" O   LEU A  58 " (cutoff:3.500A)
      removed outlier: 5.850A  pdb=" N   ALA A  77 " --> pdb=" O   LEU A  73 " (cutoff:3.500A)
      removed outlier: 5.084A  pdb=" N   ILE A  78 " --> pdb=" O   VAL A  74 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   ASN A  86 " --> pdb=" O   TRP A  82 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 87 through 116
    Processing helix  chain 'A' and resid 116 through 123
    Processing helix  chain 'A' and resid 125 through 156
      removed outlier: 4.247A  pdb=" N   LEU A 129 " --> pdb=" O   HIS A 125 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 157 through 163
    Processing helix  chain 'A' and resid 166 through 199
      removed outlier: 3.811A  pdb=" N   LEU A 170 " --> pdb=" O   ASP A 166 " (cutoff:3.500A)
      removed outlier: 3.956A  pdb=" N   ILE A 186 " --> pdb=" O   GLN A 182 " (cutoff:3.500A)
      Proline residue:  A 189  - end of helix
    Processing helix  chain 'A' and resid 200 through 230
      removed outlier: 3.975A  pdb=" N   CYS A 217 " --> pdb=" O   LEU A 213 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 231 through 235
    Processing helix  chain 'A' and resid 290 through 304
    Processing helix  chain 'A' and resid 307 through 317
    Processing helix  chain 'A' and resid 327 through 335
    Processing helix  chain 'A' and resid 338 through 367
    Processing helix  chain 'A' and resid 368 through 391
      removed outlier: 3.540A  pdb=" N   LEU A 374 " --> pdb=" O   VAL A 370 " (cutoff:3.500A)
      removed outlier: 4.409A  pdb=" N   LEU A 386 " --> pdb=" O   SER A 382 " (cutoff:3.500A)
      removed outlier: 4.150A  pdb=" N   CYS A 387 " --> pdb=" O   CYS A 383 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 452 through 484
      removed outlier: 4.491A  pdb=" N   ILE A 467 " --> pdb=" O   ILE A 463 " (cutoff:3.500A)
      removed outlier: 4.512A  pdb=" N   GLY A 468 " --> pdb=" O   ALA A 464 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 485 through 487
      No H-bonds generated for 'chain 'A' and resid 485 through 487'
    Processing helix  chain 'A' and resid 488 through 514
      removed outlier: 3.591A  pdb=" N   ILE A 512 " --> pdb=" O   PHE A 508 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 516 through 546
      removed outlier: 3.573A  pdb=" N   GLY A 521 " --> pdb=" O   PRO A 517 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 83 through 87
    Processing helix  chain 'L' and resid 125 through 131
    Processing helix  chain 'L' and resid 187 through 191
    Processing helix  chain 'H' and resid 86 through 90
    Processing helix  chain 'H' and resid 161 through 163
      No H-bonds generated for 'chain 'H' and resid 161 through 163'
    Processing helix  chain 'H' and resid 205 through 208
    Processing sheet with id=AA1, first strand: chain 'B' and resid 7 through 11
    Processing sheet with id=AA2, first strand: chain 'L' and resid 4 through 7
    Processing sheet with id=AA3, first strand: chain 'L' and resid 10 through 13
      removed outlier: 7.014A  pdb=" N   MET L  37 " --> pdb=" O   TYR L  53 " (cutoff:3.500A)
      removed outlier: 5.030A  pdb=" N   TYR L  53 " --> pdb=" O   MET L  37 " (cutoff:3.500A)
      removed outlier: 6.523A  pdb=" N   TRP L  39 " --> pdb=" O   LEU L  51 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'L' and resid 10 through 13
      removed outlier: 4.141A  pdb=" N   THR L 101 " --> pdb=" O   HIS L  94 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'L' and resid 30 through 31
    Processing sheet with id=AA6, first strand: chain 'L' and resid 118 through 122
      removed outlier: 5.815A  pdb=" N   TYR L 177 " --> pdb=" O   ASN L 142 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'L' and resid 157 through 159
      removed outlier: 4.240A  pdb=" N   TRP L 152 " --> pdb=" O   ARG L 159 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'H' and resid 3 through 7
      removed outlier: 4.616A  pdb=" N   GLN H  66 " --> pdb=" O   ASN H  83 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'H' and resid 11 through 12
      removed outlier: 6.551A  pdb=" N   TRP H  34 " --> pdb=" O   TYR H  50 " (cutoff:3.500A)
      removed outlier: 4.490A  pdb=" N   TYR H  50 " --> pdb=" O   TRP H  34 " (cutoff:3.500A)
      removed outlier: 6.650A  pdb=" N   TRP H  36 " --> pdb=" O   MET H  48 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'H' and resid 11 through 12
      removed outlier: 3.987A  pdb=" N   VAL H 107 " --> pdb=" O   ARG H  97 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'H' and resid 125 through 129
      removed outlier: 5.261A  pdb=" N   THR H 142 " --> pdb=" O   VAL H 188 " (cutoff:3.500A)
      removed outlier: 7.189A  pdb=" N   VAL H 188 " --> pdb=" O   THR H 142 " (cutoff:3.500A)
      removed outlier: 5.131A  pdb=" N   GLY H 144 " --> pdb=" O   VAL H 186 " (cutoff:3.500A)
      removed outlier: 6.842A  pdb=" N   VAL H 186 " --> pdb=" O   GLY H 144 " (cutoff:3.500A)
      removed outlier: 5.333A  pdb=" N   LEU H 146 " --> pdb=" O   SER H 184 " (cutoff:3.500A)
      removed outlier: 7.221A  pdb=" N   SER H 184 " --> pdb=" O   LEU H 146 " (cutoff:3.500A)
      removed outlier: 4.685A  pdb=" N   LYS H 148 " --> pdb=" O   LEU H 182 " (cutoff:3.500A)
      removed outlier: 7.089A  pdb=" N   LEU H 182 " --> pdb=" O   LYS H 148 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'H' and resid 125 through 129
      removed outlier: 5.261A  pdb=" N   THR H 142 " --> pdb=" O   VAL H 188 " (cutoff:3.500A)
      removed outlier: 7.189A  pdb=" N   VAL H 188 " --> pdb=" O   THR H 142 " (cutoff:3.500A)
      removed outlier: 5.131A  pdb=" N   GLY H 144 " --> pdb=" O   VAL H 186 " (cutoff:3.500A)
      removed outlier: 6.842A  pdb=" N   VAL H 186 " --> pdb=" O   GLY H 144 " (cutoff:3.500A)
      removed outlier: 5.333A  pdb=" N   LEU H 146 " --> pdb=" O   SER H 184 " (cutoff:3.500A)
      removed outlier: 7.221A  pdb=" N   SER H 184 " --> pdb=" O   LEU H 146 " (cutoff:3.500A)
      removed outlier: 4.685A  pdb=" N   LYS H 148 " --> pdb=" O   LEU H 182 " (cutoff:3.500A)
      removed outlier: 7.089A  pdb=" N   LEU H 182 " --> pdb=" O   LYS H 148 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'H' and resid 156 through 159

    470 hydrogen bonds defined for protein.
    1308 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: 0.95

  Time building geometry restraints manager: 0.72 seconds

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

  Histogram of bond lengths:
        1.11 -     1.26: 1060
        1.26 -     1.40: 1747
        1.40 -     1.55: 4118
        1.55 -     1.69: 12
        1.69 -     1.83: 68
  Bond restraints: 7005
  Sorted by residual:
  bond pdb=" C   SER L  32 "
       pdb=" O   SER L  32 "
    ideal  model  delta    sigma   weight residual
    1.243  1.122  0.121 9.50e-03 1.11e+04 1.63e+02
  bond pdb=" C   TYR L  34 "
       pdb=" O   TYR L  34 "
    ideal  model  delta    sigma   weight residual
    1.234  1.114  0.120 1.28e-02 6.10e+03 8.84e+01
  bond pdb=" CA  ALA L  31 "
       pdb=" C   ALA L  31 "
    ideal  model  delta    sigma   weight residual
    1.520  1.427  0.093 1.16e-02 7.43e+03 6.44e+01
  bond pdb=" CA  TYR L  34 "
       pdb=" C   TYR L  34 "
    ideal  model  delta    sigma   weight residual
    1.523  1.429  0.094 1.21e-02 6.83e+03 6.10e+01
  bond pdb=" C   ALA L  31 "
       pdb=" O   ALA L  31 "
    ideal  model  delta    sigma   weight residual
    1.235  1.175  0.059 1.13e-02 7.83e+03 2.77e+01
  ... (remaining 7000 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.30: 9427
        3.30 -     6.60: 101
        6.60 -     9.90: 14
        9.90 -    13.20: 3
       13.20 -    16.49: 2
  Bond angle restraints: 9547
  Sorted by residual:
  angle pdb=" C   ASN A 516 "
        pdb=" N   PRO A 517 "
        pdb=" CA  PRO A 517 "
      ideal   model   delta    sigma   weight residual
     119.28  127.37   -8.09 1.10e+00 8.26e-01 5.41e+01
  angle pdb=" C   ALA L  55 "
        pdb=" CA  ALA L  55 "
        pdb=" CB  ALA L  55 "
      ideal   model   delta    sigma   weight residual
     110.04  100.16    9.88 1.51e+00 4.39e-01 4.28e+01
  angle pdb=" O5  AGA A 701 "
        pdb=" P1  AGA A 701 "
        pdb=" O6  AGA A 701 "
      ideal   model   delta    sigma   weight residual
      93.68  110.17  -16.49 3.00e+00 1.11e-01 3.02e+01
  angle pdb=" O5  AGA A 702 "
        pdb=" P1  AGA A 702 "
        pdb=" O6  AGA A 702 "
      ideal   model   delta    sigma   weight residual
      93.68  109.83  -16.15 3.00e+00 1.11e-01 2.90e+01
  angle pdb=" N   PRO A 515 "
        pdb=" CA  PRO A 515 "
        pdb=" C   PRO A 515 "
      ideal   model   delta    sigma   weight residual
     112.47  121.47   -9.00 2.06e+00 2.36e-01 1.91e+01
  ... (remaining 9542 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.21: 3720
       17.21 -    34.42: 284
       34.42 -    51.63: 96
       51.63 -    68.84: 28
       68.84 -    86.05: 14
  Dihedral angle restraints: 4142
    sinusoidal: 1565
      harmonic: 2577
  Sorted by residual:
  dihedral pdb=" C   SER L  32 "
           pdb=" N   SER L  32 "
           pdb=" CA  SER L  32 "
           pdb=" CB  SER L  32 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -135.46   12.86     0      2.50e+00 1.60e-01 2.65e+01
  dihedral pdb=" C   ALA L  55 "
           pdb=" N   ALA L  55 "
           pdb=" CA  ALA L  55 "
           pdb=" CB  ALA L  55 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -110.94  -11.66     0      2.50e+00 1.60e-01 2.17e+01
  dihedral pdb=" CA  TYR H  50 "
           pdb=" C   TYR H  50 "
           pdb=" N   ILE H  51 "
           pdb=" CA  ILE H  51 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.54   21.46     0      5.00e+00 4.00e-02 1.84e+01
  ... (remaining 4139 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.111: 1086
       0.111 -    0.221: 33
       0.221 -    0.331: 2
       0.331 -    0.442: 2
       0.442 -    0.552: 1
  Chirality restraints: 1124
  Sorted by residual:
  chirality pdb=" CA  SER L  32 "
            pdb=" N   SER L  32 "
            pdb=" C   SER L  32 "
            pdb=" CB  SER L  32 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.96    0.55 2.00e-01 2.50e+01 7.63e+00
  chirality pdb=" CA  TRP H 103 "
            pdb=" N   TRP H 103 "
            pdb=" C   TRP H 103 "
            pdb=" CB  TRP H 103 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.10    0.41 2.00e-01 2.50e+01 4.20e+00
  chirality pdb=" CA  PRO A 515 "
            pdb=" N   PRO A 515 "
            pdb=" C   PRO A 515 "
            pdb=" CB  PRO A 515 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.36    0.36 2.00e-01 2.50e+01 3.19e+00
  ... (remaining 1121 not shown)

  Planarity restraints: 1176
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN A 516 "   -0.015 2.00e-02 2.50e+03   2.99e-02 8.95e+00
        pdb=" C   ASN A 516 "    0.052 2.00e-02 2.50e+03
        pdb=" O   ASN A 516 "   -0.020 2.00e-02 2.50e+03
        pdb=" N   PRO A 517 "   -0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER L  71 "   -0.013 2.00e-02 2.50e+03   2.74e-02 7.52e+00
        pdb=" C   SER L  71 "    0.047 2.00e-02 2.50e+03
        pdb=" O   SER L  71 "   -0.018 2.00e-02 2.50e+03
        pdb=" N   GLY L  72 "   -0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN H  35 "    0.013 2.00e-02 2.50e+03   2.72e-02 7.42e+00
        pdb=" C   ASN H  35 "   -0.047 2.00e-02 2.50e+03
        pdb=" O   ASN H  35 "    0.018 2.00e-02 2.50e+03
        pdb=" N   TRP H  36 "    0.016 2.00e-02 2.50e+03
  ... (remaining 1173 not shown)

  Histogram of nonbonded interaction distances:
        1.80 -     2.42: 25
        2.42 -     3.04: 4166
        3.04 -     3.66: 10377
        3.66 -     4.28: 16019
        4.28 -     4.90: 26508
  Nonbonded interactions: 57095
  Sorted by model distance:
  nonbonded pdb="CO    CO A 704 "
            pdb=" O   HOH A 806 "
     model   vdw
     1.797 2.220
  nonbonded pdb=" O   THR B  25 "
            pdb="CO    CO A 704 "
     model   vdw
     1.798 2.220
  nonbonded pdb=" ND2 ASN L  95 "
            pdb=" O   TRP H 103 "
     model   vdw
     1.887 3.120
  nonbonded pdb=" NE2 HIS A 507 "
            pdb="CO    CO A 704 "
     model   vdw
     2.111 2.300
  nonbonded pdb=" OG  SER A  35 "
            pdb=" OE1 GLU A 219 "
     model   vdw
     2.113 3.040
  ... (remaining 57090 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.650
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.020
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     6.590
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:5.960
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.460
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8538
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      :  0.006   0.121   7014  Z= 0.389
  Angle     :  0.936  16.494   9565  Z= 0.502
  Chirality :  0.054   0.552   1124
  Planarity :  0.007   0.067   1176
  Dihedral  : 15.749  86.050   2465
  Min Nonbonded Distance : 1.797

Molprobity Statistics.
  All-atom Clashscore : 7.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  4.26 %
    Allowed  :  9.05 %
    Favored  : 86.68 %
  Cbeta Deviations :  0.24 %
  Peptide Plane:
    Cis-proline     : 18.42 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.54 (0.26), residues: 879
  helix: -0.19 (0.22), residues: 382
  sheet:  0.01 (0.33), residues: 226
  loop : -0.63 (0.37), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG H  97 
 TYR   0.024   0.002   TYR H  78 
 PHE   0.023   0.002   PHE L  75 
 TRP   0.041   0.003   TRP L 167 
 HIS   0.005   0.001   HIS L  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00648 ( 7005)
  covalent geometry    : angle       0.93528 ( 9547)
  SS BOND              : bond        0.00872 (    9)
  SS BOND              : angle       1.24634 (   18)
  hydrogen bonds       : bond        0.12386 (  450)
  hydrogen bonds       : angle       6.04241 ( 1308)

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 133
  time to evaluate  : 0.168 
Fit side-chains
   revert: symmetry clash
REVERT: A  317 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8695 (mp)
REVERT: A  341 ILE cc_start: 0.8536 (mp) cc_final: 0.8291 (mm)
REVERT: A  364 ARG cc_start: 0.8649 (OUTLIER) cc_final: 0.7895 (ttp-110)
REVERT: A  366 LYS cc_start: 0.8414 (tppt) cc_final: 0.8202 (mptp)
REVERT: A  516 ASN cc_start: 0.7799 (OUTLIER) cc_final: 0.7554 (m-40)
REVERT: L   49 LYS cc_start: 0.8392 (OUTLIER) cc_final: 0.8009 (tptp)
REVERT: H   16 GLN cc_start: 0.8131 (mt0) cc_final: 0.7927 (mt0)
REVERT: H  216 GLU cc_start: 0.7216 (OUTLIER) cc_final: 0.6492 (pm20)
  outliers start: 32
  outliers final: 11
  residues processed: 157
  average time/residue: 0.4371
  time to fit residues: 72.6776
Evaluate side-chains
  125 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 109
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   95 SER
Chi-restraints excluded: chain A residue  317 LEU
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  364 ARG
Chi-restraints excluded: chain A residue  474 LEU
Chi-restraints excluded: chain A residue  507 HIS
Chi-restraints excluded: chain A residue  511 VAL
Chi-restraints excluded: chain A residue  516 ASN
Chi-restraints excluded: chain L residue   49 LYS
Chi-restraints excluded: chain L residue  118 THR
Chi-restraints excluded: chain L residue  201 THR
Chi-restraints excluded: chain L residue  203 LYS
Chi-restraints excluded: chain L residue  218 CYS
Chi-restraints excluded: chain H residue  114 VAL
Chi-restraints excluded: chain H residue  216 GLU
Chi-restraints excluded: chain H residue  219 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    6.9990
   chunk 62 optimal weight:   10.0000
   chunk 51 optimal weight:    5.9990
   chunk 38 optimal weight:    0.4980
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:   10.0000
   chunk 74 optimal weight:    2.9990
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
B  15 HIS
A  86 ASN
A  99 GLN
A 141 ASN
A 155 GLN
A 174 ASN
A 185 ASN
A 481 GLN
A 496 GLN
L 142 ASN
L 149 ASN
L 194 ASN
L 216 ASN
H   3 GLN
H  77 HIS
H  83 ASN
H  98 GLN
H 196 GLN

Total number of N/Q/H flips: 18

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.162881 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.112769 restraints weight = 15381.858|
|-----------------------------------------------------------------------------|
r_work (start): 0.3465 rms_B_bonded: 2.30
r_work: 0.3379 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3283 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.3283
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3242
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3242 r_free = 0.3242    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3242 r_free = 0.3242    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3242
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8782
moved from start:          0.1612

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7014  Z= 0.137
  Angle     :  0.587   8.279   9565  Z= 0.308
  Chirality :  0.042   0.176   1124
  Planarity :  0.005   0.051   1176
  Dihedral  : 11.071  90.534   1036
  Min Nonbonded Distance : 1.951

Molprobity Statistics.
  All-atom Clashscore : 4.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 13.45 %
    Favored  : 83.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.42 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.37 (0.28), residues: 879
  helix:  1.86 (0.25), residues: 393
  sheet:  0.69 (0.35), residues: 222
  loop : -0.26 (0.37), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H  71 
 TYR   0.023   0.001   TYR H  78 
 PHE   0.015   0.002   PHE L 213 
 TRP   0.018   0.002   TRP H  34 
 HIS   0.004   0.001   HIS A  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 7005)
  covalent geometry    : angle       0.58636 ( 9547)
  SS BOND              : bond        0.00594 (    9)
  SS BOND              : angle       0.87902 (   18)
  hydrogen bonds       : bond        0.05688 (  450)
  hydrogen bonds       : angle       4.44045 ( 1308)

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 105
  time to evaluate  : 0.254 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   24 LYS cc_start: 0.8872 (mmtp) cc_final: 0.8442 (mttt)
REVERT: A  317 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8707 (mp)
REVERT: A  341 ILE cc_start: 0.8538 (mp) cc_final: 0.8263 (mm)
REVERT: A  378 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8304 (mp)
REVERT: L   49 LYS cc_start: 0.8989 (ttmm) cc_final: 0.8768 (mttt)
REVERT: H   16 GLN cc_start: 0.8373 (mt0) cc_final: 0.8059 (mt0)
REVERT: H   81 GLN cc_start: 0.8282 (tt0) cc_final: 0.8061 (tt0)
REVERT: H  183 SER cc_start: 0.9026 (p) cc_final: 0.8810 (p)
  outliers start: 22
  outliers final: 11
  residues processed: 120
  average time/residue: 0.5171
  time to fit residues: 65.3171
Evaluate side-chains
  112 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 99
  time to evaluate  : 0.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   14 CYS
Chi-restraints excluded: chain A residue  317 LEU
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  364 ARG
Chi-restraints excluded: chain A residue  378 LEU
Chi-restraints excluded: chain A residue  474 LEU
Chi-restraints excluded: chain A residue  507 HIS
Chi-restraints excluded: chain L residue  169 ASP
Chi-restraints excluded: chain L residue  201 THR
Chi-restraints excluded: chain L residue  203 LYS
Chi-restraints excluded: chain H residue   74 SER
Chi-restraints excluded: chain H residue  114 VAL
Chi-restraints excluded: chain H residue  219 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 5 optimal weight:    6.9990
   chunk 31 optimal weight:    4.9990
   chunk 54 optimal weight:    0.9990
   chunk 83 optimal weight:    6.9990
   chunk 11 optimal weight:    5.9990
   chunk 48 optimal weight:    2.9990
   chunk 60 optimal weight:    0.8980
   chunk 76 optimal weight:   10.0000
   chunk 26 optimal weight:    4.9990
   chunk 14 optimal weight:    1.9990
   chunk 34 optimal weight:    0.8980
   overall best weight:    1.5586

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

Flipped N/Q/H residues before XYZ refinement:
H   3 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4040 r_free = 0.4040 target = 0.162110 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.112460 restraints weight = 12330.307|
|-----------------------------------------------------------------------------|
r_work (start): 0.3450 rms_B_bonded: 2.06
r_work: 0.3368 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3274 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.3274
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3233
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3233 r_free = 0.3233    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3233 r_free = 0.3233    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3233
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8804
moved from start:          0.1837

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7014  Z= 0.151
  Angle     :  0.588   9.181   9565  Z= 0.306
  Chirality :  0.042   0.195   1124
  Planarity :  0.005   0.052   1176
  Dihedral  : 10.445  84.553   1022
  Min Nonbonded Distance : 1.939

Molprobity Statistics.
  All-atom Clashscore : 4.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 14.65 %
    Favored  : 82.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.42 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.85 (0.28), residues: 879
  helix:  2.30 (0.26), residues: 393
  sheet:  1.09 (0.35), residues: 213
  loop : -0.23 (0.38), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H  97 
 TYR   0.025   0.002   TYR H  78 
 PHE   0.012   0.002   PHE A 295 
 TRP   0.020   0.002   TRP H  34 
 HIS   0.004   0.001   HIS L  94 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 7005)
  covalent geometry    : angle       0.58734 ( 9547)
  SS BOND              : bond        0.00635 (    9)
  SS BOND              : angle       1.00921 (   18)
  hydrogen bonds       : bond        0.05892 (  450)
  hydrogen bonds       : angle       4.33974 ( 1308)

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 105
  time to evaluate  : 0.240 
Fit side-chains
   revert: symmetry clash
REVERT: B   24 LYS cc_start: 0.8829 (mmtp) cc_final: 0.8421 (mttt)
REVERT: A  317 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8653 (mp)
REVERT: A  341 ILE cc_start: 0.8601 (mp) cc_final: 0.8275 (mm)
REVERT: A  364 ARG cc_start: 0.8562 (OUTLIER) cc_final: 0.7724 (ttp-110)
REVERT: A  378 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8375 (mp)
REVERT: L   49 LYS cc_start: 0.8930 (ttmm) cc_final: 0.8381 (tptp)
REVERT: H   16 GLN cc_start: 0.8376 (mt0) cc_final: 0.8045 (mt0)
  outliers start: 25
  outliers final: 12
  residues processed: 123
  average time/residue: 0.5177
  time to fit residues: 67.1635
Evaluate side-chains
  117 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 102
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  195 ILE
Chi-restraints excluded: chain A residue  317 LEU
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  361 THR
Chi-restraints excluded: chain A residue  364 ARG
Chi-restraints excluded: chain A residue  378 LEU
Chi-restraints excluded: chain A residue  474 LEU
Chi-restraints excluded: chain A residue  507 HIS
Chi-restraints excluded: chain A residue  511 VAL
Chi-restraints excluded: chain L residue  169 ASP
Chi-restraints excluded: chain L residue  201 THR
Chi-restraints excluded: chain H residue   54 SER
Chi-restraints excluded: chain H residue  102 ASN
Chi-restraints excluded: chain H residue  114 VAL
Chi-restraints excluded: chain H residue  219 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 10 optimal weight:    1.9990
   chunk 79 optimal weight:    1.9990
   chunk 52 optimal weight:    8.9990
   chunk 84 optimal weight:    0.5980
   chunk 22 optimal weight:    0.9990
   chunk 21 optimal weight:    1.9990
   chunk 42 optimal weight:    0.7980
   chunk 35 optimal weight:    7.9990
   chunk 45 optimal weight:    9.9990
   chunk 55 optimal weight:    6.9990
   chunk 29 optimal weight:    0.8980
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
H   3 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.163676 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.114709 restraints weight = 11134.641|
|-----------------------------------------------------------------------------|
r_work (start): 0.3480 rms_B_bonded: 1.96
r_work: 0.3401 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.3308 rms_B_bonded: 3.77 restraints_weight: 0.2500
r_work (final): 0.3308
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3284
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3284 r_free = 0.3284    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3284 r_free = 0.3284    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3284
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8770
moved from start:          0.2136

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7014  Z= 0.125
  Angle     :  0.551  10.026   9565  Z= 0.283
  Chirality :  0.041   0.179   1124
  Planarity :  0.005   0.050   1176
  Dihedral  : 10.166  79.437   1018
  Min Nonbonded Distance : 1.972

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  : 14.78 %
    Favored  : 81.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.42 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.13 (0.28), residues: 879
  helix:  2.56 (0.26), residues: 393
  sheet:  1.16 (0.35), residues: 210
  loop : -0.07 (0.37), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H  97 
 TYR   0.022   0.001   TYR H  78 
 PHE   0.011   0.001   PHE L 213 
 TRP   0.016   0.001   TRP H  34 
 HIS   0.004   0.001   HIS L  94 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 7005)
  covalent geometry    : angle       0.54623 ( 9547)
  SS BOND              : bond        0.00536 (    9)
  SS BOND              : angle       1.71607 (   18)
  hydrogen bonds       : bond        0.05203 (  450)
  hydrogen bonds       : angle       4.16301 ( 1308)

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 103
  time to evaluate  : 0.243 
Fit side-chains
   revert: symmetry clash
REVERT: B   24 LYS cc_start: 0.8843 (mmtp) cc_final: 0.8422 (mttt)
REVERT: A  317 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8705 (mp)
REVERT: A  341 ILE cc_start: 0.8600 (mp) cc_final: 0.8276 (mm)
REVERT: L   18 ARG cc_start: 0.7883 (OUTLIER) cc_final: 0.7411 (ptm160)
REVERT: L   49 LYS cc_start: 0.8892 (ttmm) cc_final: 0.8337 (tptm)
REVERT: H   16 GLN cc_start: 0.8314 (mt0) cc_final: 0.7955 (mt0)
  outliers start: 28
  outliers final: 17
  residues processed: 123
  average time/residue: 0.5132
  time to fit residues: 66.6129
Evaluate side-chains
  117 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 98
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 CYS
Chi-restraints excluded: chain A residue  195 ILE
Chi-restraints excluded: chain A residue  317 LEU
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  352 THR
Chi-restraints excluded: chain A residue  474 LEU
Chi-restraints excluded: chain A residue  507 HIS
Chi-restraints excluded: chain A residue  511 VAL
Chi-restraints excluded: chain L residue   18 ARG
Chi-restraints excluded: chain L residue   97 GLU
Chi-restraints excluded: chain L residue  169 ASP
Chi-restraints excluded: chain L residue  201 THR
Chi-restraints excluded: chain L residue  203 LYS
Chi-restraints excluded: chain H residue   13 LYS
Chi-restraints excluded: chain H residue   54 SER
Chi-restraints excluded: chain H residue   74 SER
Chi-restraints excluded: chain H residue  102 ASN
Chi-restraints excluded: chain H residue  114 VAL
Chi-restraints excluded: chain H residue  219 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 1 optimal weight:    0.0470
   chunk 86 optimal weight:    5.9990
   chunk 42 optimal weight:    2.9990
   chunk 58 optimal weight:    9.9990
   chunk 61 optimal weight:   10.0000
   chunk 70 optimal weight:    3.9990
   chunk 85 optimal weight:    0.9990
   chunk 84 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9980
   chunk 23 optimal weight:    0.6980
   chunk 73 optimal weight:    3.9990
   overall best weight:    1.1482

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

Flipped N/Q/H residues before XYZ refinement:
H   3 GLN
H 160 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.163214 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.114053 restraints weight = 11136.789|
|-----------------------------------------------------------------------------|
r_work (start): 0.3470 rms_B_bonded: 1.97
r_work: 0.3391 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.3297 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.3297
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3270
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3270 r_free = 0.3270    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3270 r_free = 0.3270    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3270
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8778
moved from start:          0.2242

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   7014  Z= 0.129
  Angle     :  0.549  10.186   9565  Z= 0.283
  Chirality :  0.041   0.195   1124
  Planarity :  0.005   0.049   1176
  Dihedral  :  9.787  74.575   1014
  Min Nonbonded Distance : 1.973

Molprobity Statistics.
  All-atom Clashscore : 4.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 15.05 %
    Favored  : 81.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.42 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.25 (0.29), residues: 879
  helix:  2.63 (0.26), residues: 393
  sheet:  1.28 (0.35), residues: 208
  loop : -0.02 (0.38), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG L 112 
 TYR   0.023   0.001   TYR H  78 
 PHE   0.011   0.001   PHE A 295 
 TRP   0.016   0.001   TRP H  34 
 HIS   0.005   0.001   HIS L  94 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 7005)
  covalent geometry    : angle       0.54475 ( 9547)
  SS BOND              : bond        0.00605 (    9)
  SS BOND              : angle       1.58666 (   18)
  hydrogen bonds       : bond        0.05273 (  450)
  hydrogen bonds       : angle       4.13361 ( 1308)

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 99
  time to evaluate  : 0.247 
Fit side-chains
   revert: symmetry clash
REVERT: B   24 LYS cc_start: 0.8851 (mmtp) cc_final: 0.8426 (mttt)
REVERT: A  317 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8680 (mp)
REVERT: A  341 ILE cc_start: 0.8577 (mp) cc_final: 0.8275 (mm)
REVERT: L   18 ARG cc_start: 0.7866 (OUTLIER) cc_final: 0.7377 (ptm160)
REVERT: L   49 LYS cc_start: 0.8911 (ttmm) cc_final: 0.8350 (tptm)
REVERT: L  182 THR cc_start: 0.8109 (m) cc_final: 0.7628 (t)
REVERT: H   16 GLN cc_start: 0.8320 (mt0) cc_final: 0.7979 (mt0)
  outliers start: 29
  outliers final: 18
  residues processed: 119
  average time/residue: 0.5156
  time to fit residues: 64.6527
Evaluate side-chains
  117 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 97
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 CYS
Chi-restraints excluded: chain A residue  195 ILE
Chi-restraints excluded: chain A residue  317 LEU
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  352 THR
Chi-restraints excluded: chain A residue  361 THR
Chi-restraints excluded: chain A residue  474 LEU
Chi-restraints excluded: chain A residue  507 HIS
Chi-restraints excluded: chain A residue  511 VAL
Chi-restraints excluded: chain L residue   18 ARG
Chi-restraints excluded: chain L residue  169 ASP
Chi-restraints excluded: chain L residue  201 THR
Chi-restraints excluded: chain L residue  203 LYS
Chi-restraints excluded: chain H residue   13 LYS
Chi-restraints excluded: chain H residue   54 SER
Chi-restraints excluded: chain H residue   74 SER
Chi-restraints excluded: chain H residue  102 ASN
Chi-restraints excluded: chain H residue  114 VAL
Chi-restraints excluded: chain H residue  219 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 32 optimal weight:    0.7980
   chunk 42 optimal weight:    1.9990
   chunk 40 optimal weight:    5.9990
   chunk 68 optimal weight:    0.9990
   chunk 47 optimal weight:    9.9990
   chunk 75 optimal weight:    0.6980
   chunk 84 optimal weight:    0.9980
   chunk 1 optimal weight:    0.3980
   chunk 46 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9990
   chunk 29 optimal weight:    5.9990
   overall best weight:    0.7782

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4074 r_free = 0.4074 target = 0.165216 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.114203 restraints weight = 20270.190|
|-----------------------------------------------------------------------------|
r_work (start): 0.3469 rms_B_bonded: 2.57
r_work: 0.3383 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.3288 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.3288
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3268
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3268 r_free = 0.3268    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3268 r_free = 0.3268    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3268
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8774
moved from start:          0.2440

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043   7014  Z= 0.110
  Angle     :  0.523  10.402   9565  Z= 0.266
  Chirality :  0.040   0.176   1124
  Planarity :  0.004   0.048   1176
  Dihedral  :  9.140  66.896   1014
  Min Nonbonded Distance : 1.996

Molprobity Statistics.
  All-atom Clashscore : 4.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 15.98 %
    Favored  : 81.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.42 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.45 (0.29), residues: 879
  helix:  2.81 (0.26), residues: 393
  sheet:  1.39 (0.35), residues: 212
  loop :  0.05 (0.39), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG L 112 
 TYR   0.021   0.001   TYR H  78 
 PHE   0.011   0.001   PHE A 295 
 TRP   0.014   0.001   TRP H  34 
 HIS   0.006   0.001   HIS L  94 

Details of bonding type rmsd
  covalent geometry    : bond        0.00229 ( 7005)
  covalent geometry    : angle       0.52137 ( 9547)
  SS BOND              : bond        0.00467 (    9)
  SS BOND              : angle       1.15654 (   18)
  hydrogen bonds       : bond        0.04715 (  450)
  hydrogen bonds       : angle       4.00184 ( 1308)

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 99
  time to evaluate  : 0.247 
Fit side-chains
   revert: symmetry clash
REVERT: B   24 LYS cc_start: 0.8802 (mmtp) cc_final: 0.8403 (mttt)
REVERT: A  341 ILE cc_start: 0.8533 (mp) cc_final: 0.8239 (mm)
REVERT: A  378 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8396 (mp)
REVERT: L   49 LYS cc_start: 0.8933 (ttmm) cc_final: 0.8353 (tptm)
REVERT: L  182 THR cc_start: 0.8100 (m) cc_final: 0.7606 (t)
REVERT: H   16 GLN cc_start: 0.8331 (mt0) cc_final: 0.7999 (mt0)
  outliers start: 22
  outliers final: 14
  residues processed: 114
  average time/residue: 0.5453
  time to fit residues: 65.5924
Evaluate side-chains
  112 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 97
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 CYS
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  352 THR
Chi-restraints excluded: chain A residue  361 THR
Chi-restraints excluded: chain A residue  367 CYS
Chi-restraints excluded: chain A residue  378 LEU
Chi-restraints excluded: chain A residue  507 HIS
Chi-restraints excluded: chain A residue  511 VAL
Chi-restraints excluded: chain L residue   97 GLU
Chi-restraints excluded: chain L residue  169 ASP
Chi-restraints excluded: chain L residue  201 THR
Chi-restraints excluded: chain L residue  203 LYS
Chi-restraints excluded: chain H residue   13 LYS
Chi-restraints excluded: chain H residue  114 VAL
Chi-restraints excluded: chain H residue  219 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 59 optimal weight:    8.9990
   chunk 38 optimal weight:    1.9990
   chunk 28 optimal weight:    6.9990
   chunk 58 optimal weight:    4.9990
   chunk 22 optimal weight:    4.9990
   chunk 56 optimal weight:    9.9990
   chunk 40 optimal weight:    5.9990
   chunk 18 optimal weight:    0.9980
   chunk 17 optimal weight:    0.8980
   chunk 8 optimal weight:    3.9990
   chunk 70 optimal weight:    3.9990
   overall best weight:    2.3786

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

Flipped N/Q/H residues before XYZ refinement:
** L  94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.161026 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.111006 restraints weight = 12199.042|
|-----------------------------------------------------------------------------|
r_work (start): 0.3428 rms_B_bonded: 2.04
r_work: 0.3346 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.3251 rms_B_bonded: 3.85 restraints_weight: 0.2500
r_work (final): 0.3251
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3219
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3219 r_free = 0.3219    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3219 r_free = 0.3219    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3219
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8832
moved from start:          0.2275

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   7014  Z= 0.194
  Angle     :  0.619  10.616   9565  Z= 0.320
  Chirality :  0.044   0.226   1124
  Planarity :  0.005   0.049   1176
  Dihedral  :  8.926  62.596   1010
  Min Nonbonded Distance : 1.930

Molprobity Statistics.
  All-atom Clashscore : 4.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  : 15.18 %
    Favored  : 81.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.42 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.17 (0.28), residues: 879
  helix:  2.45 (0.25), residues: 393
  sheet:  1.50 (0.35), residues: 212
  loop : -0.12 (0.39), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG L 112 
 TYR   0.026   0.002   TYR H  78 
 PHE   0.013   0.002   PHE A 295 
 TRP   0.023   0.002   TRP H  34 
 HIS   0.007   0.001   HIS L  94 

Details of bonding type rmsd
  covalent geometry    : bond        0.00448 ( 7005)
  covalent geometry    : angle       0.61530 ( 9547)
  SS BOND              : bond        0.00762 (    9)
  SS BOND              : angle       1.74346 (   18)
  hydrogen bonds       : bond        0.06382 (  450)
  hydrogen bonds       : angle       4.32741 ( 1308)

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 106
  time to evaluate  : 0.205 
Fit side-chains
   revert: symmetry clash
REVERT: B   24 LYS cc_start: 0.8852 (mmtp) cc_final: 0.8451 (mttt)
REVERT: A  341 ILE cc_start: 0.8567 (mp) cc_final: 0.8263 (mm)
REVERT: L   18 ARG cc_start: 0.7863 (OUTLIER) cc_final: 0.7377 (ptm160)
REVERT: L   43 LYS cc_start: 0.8689 (OUTLIER) cc_final: 0.8383 (mttt)
REVERT: L   49 LYS cc_start: 0.8968 (ttmm) cc_final: 0.8412 (tptp)
REVERT: L  169 ASP cc_start: 0.8304 (OUTLIER) cc_final: 0.8018 (m-30)
REVERT: H   16 GLN cc_start: 0.8339 (mt0) cc_final: 0.7999 (mt0)
  outliers start: 28
  outliers final: 19
  residues processed: 125
  average time/residue: 0.5071
  time to fit residues: 66.7749
Evaluate side-chains
  126 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 104
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 CYS
Chi-restraints excluded: chain A residue  147 SER
Chi-restraints excluded: chain A residue  195 ILE
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  352 THR
Chi-restraints excluded: chain A residue  361 THR
Chi-restraints excluded: chain A residue  367 CYS
Chi-restraints excluded: chain A residue  507 HIS
Chi-restraints excluded: chain A residue  511 VAL
Chi-restraints excluded: chain L residue   18 ARG
Chi-restraints excluded: chain L residue   43 LYS
Chi-restraints excluded: chain L residue   97 GLU
Chi-restraints excluded: chain L residue  136 VAL
Chi-restraints excluded: chain L residue  169 ASP
Chi-restraints excluded: chain L residue  201 THR
Chi-restraints excluded: chain L residue  203 LYS
Chi-restraints excluded: chain H residue   13 LYS
Chi-restraints excluded: chain H residue   17 THR
Chi-restraints excluded: chain H residue   74 SER
Chi-restraints excluded: chain H residue  114 VAL
Chi-restraints excluded: chain H residue  219 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 17 optimal weight:    2.9990
   chunk 80 optimal weight:    0.7980
   chunk 7 optimal weight:    0.6980
   chunk 25 optimal weight:    2.9990
   chunk 24 optimal weight:    1.9990
   chunk 70 optimal weight:    3.9990
   chunk 65 optimal weight:    4.9990
   chunk 66 optimal weight:    9.9990
   chunk 59 optimal weight:    7.9990
   chunk 51 optimal weight:    3.9990
   chunk 40 optimal weight:    2.9990
   overall best weight:    1.8986

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

Flipped N/Q/H residues before XYZ refinement:
L 170 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.160118 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.109732 restraints weight = 10782.459|
|-----------------------------------------------------------------------------|
r_work (start): 0.3444 rms_B_bonded: 1.94
r_work: 0.3364 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3269 rms_B_bonded: 3.70 restraints_weight: 0.2500
r_work (final): 0.3269
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3247
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3247 r_free = 0.3247    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3247 r_free = 0.3247    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3247
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8814
moved from start:          0.2348

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   7014  Z= 0.167
  Angle     :  0.598  10.715   9565  Z= 0.309
  Chirality :  0.043   0.212   1124
  Planarity :  0.005   0.048   1176
  Dihedral  :  8.722  56.529   1010
  Min Nonbonded Distance : 1.941

Molprobity Statistics.
  All-atom Clashscore : 4.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  : 15.85 %
    Favored  : 80.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.42 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.20 (0.29), residues: 879
  helix:  2.50 (0.25), residues: 393
  sheet:  1.58 (0.36), residues: 214
  loop : -0.20 (0.38), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG L 112 
 TYR   0.025   0.002   TYR H  78 
 PHE   0.012   0.002   PHE A 295 
 TRP   0.023   0.002   TRP H  34 
 HIS   0.006   0.001   HIS L  94 

Details of bonding type rmsd
  covalent geometry    : bond        0.00378 ( 7005)
  covalent geometry    : angle       0.59559 ( 9547)
  SS BOND              : bond        0.00694 (    9)
  SS BOND              : angle       1.44051 (   18)
  hydrogen bonds       : bond        0.05975 (  450)
  hydrogen bonds       : angle       4.27622 ( 1308)

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 99
  time to evaluate  : 0.250 
Fit side-chains
   revert: symmetry clash
REVERT: B   24 LYS cc_start: 0.8826 (mmtp) cc_final: 0.8441 (mttt)
REVERT: A  296 ARG cc_start: 0.8456 (mtm180) cc_final: 0.8041 (mtt-85)
REVERT: A  341 ILE cc_start: 0.8555 (mp) cc_final: 0.8282 (mm)
REVERT: L   18 ARG cc_start: 0.7911 (OUTLIER) cc_final: 0.7495 (ptm160)
REVERT: L   43 LYS cc_start: 0.8598 (OUTLIER) cc_final: 0.8154 (mttt)
REVERT: L   49 LYS cc_start: 0.8955 (ttmm) cc_final: 0.8400 (tptp)
REVERT: L  169 ASP cc_start: 0.8201 (OUTLIER) cc_final: 0.7986 (m-30)
REVERT: H   16 GLN cc_start: 0.8325 (mt0) cc_final: 0.7970 (mt0)
  outliers start: 28
  outliers final: 19
  residues processed: 119
  average time/residue: 0.5190
  time to fit residues: 65.0901
Evaluate side-chains
  119 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 97
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 CYS
Chi-restraints excluded: chain A residue  147 SER
Chi-restraints excluded: chain A residue  195 ILE
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  352 THR
Chi-restraints excluded: chain A residue  361 THR
Chi-restraints excluded: chain A residue  367 CYS
Chi-restraints excluded: chain A residue  507 HIS
Chi-restraints excluded: chain A residue  511 VAL
Chi-restraints excluded: chain L residue   18 ARG
Chi-restraints excluded: chain L residue   43 LYS
Chi-restraints excluded: chain L residue   97 GLU
Chi-restraints excluded: chain L residue  136 VAL
Chi-restraints excluded: chain L residue  169 ASP
Chi-restraints excluded: chain L residue  201 THR
Chi-restraints excluded: chain L residue  203 LYS
Chi-restraints excluded: chain H residue   13 LYS
Chi-restraints excluded: chain H residue   17 THR
Chi-restraints excluded: chain H residue   74 SER
Chi-restraints excluded: chain H residue  114 VAL
Chi-restraints excluded: chain H residue  219 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 37 optimal weight:    0.5980
   chunk 24 optimal weight:    3.9990
   chunk 14 optimal weight:    0.9980
   chunk 68 optimal weight:    2.9990
   chunk 49 optimal weight:    4.9990
   chunk 85 optimal weight:   20.0000
   chunk 10 optimal weight:    0.8980
   chunk 84 optimal weight:    0.0030
   chunk 8 optimal weight:    0.7980
   chunk 6 optimal weight:    4.9990
   chunk 65 optimal weight:    4.9990
   overall best weight:    0.6590

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4079 r_free = 0.4079 target = 0.165140 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.116886 restraints weight = 10479.547|
|-----------------------------------------------------------------------------|
r_work (start): 0.3519 rms_B_bonded: 1.90
r_work: 0.3442 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3351 rms_B_bonded: 3.72 restraints_weight: 0.2500
r_work (final): 0.3351
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3326
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3326 r_free = 0.3326    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3326 r_free = 0.3326    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3326
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8728
moved from start:          0.2680

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042   7014  Z= 0.107
  Angle     :  0.522  10.762   9565  Z= 0.268
  Chirality :  0.040   0.159   1124
  Planarity :  0.005   0.047   1176
  Dihedral  :  7.977  59.289   1010
  Min Nonbonded Distance : 2.001

Molprobity Statistics.
  All-atom Clashscore : 4.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 17.84 %
    Favored  : 79.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.42 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.55 (0.29), residues: 879
  helix:  2.85 (0.26), residues: 393
  sheet:  1.70 (0.36), residues: 210
  loop : -0.07 (0.38), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 178 
 TYR   0.021   0.001   TYR H  78 
 PHE   0.010   0.001   PHE A 295 
 TRP   0.015   0.001   TRP H  34 
 HIS   0.008   0.001   HIS L  94 

Details of bonding type rmsd
  covalent geometry    : bond        0.00220 ( 7005)
  covalent geometry    : angle       0.52091 ( 9547)
  SS BOND              : bond        0.00443 (    9)
  SS BOND              : angle       1.00447 (   18)
  hydrogen bonds       : bond        0.04587 (  450)
  hydrogen bonds       : angle       4.00021 ( 1308)

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 102
  time to evaluate  : 0.199 
Fit side-chains
   revert: symmetry clash
REVERT: B   24 LYS cc_start: 0.8810 (mmtp) cc_final: 0.8404 (tttt)
REVERT: A  296 ARG cc_start: 0.8422 (mtm180) cc_final: 0.8099 (mtt-85)
REVERT: A  341 ILE cc_start: 0.8503 (mp) cc_final: 0.8235 (mm)
REVERT: L   49 LYS cc_start: 0.8859 (ttmm) cc_final: 0.8288 (tptm)
REVERT: L  182 THR cc_start: 0.8099 (m) cc_final: 0.7611 (t)
REVERT: H   16 GLN cc_start: 0.8273 (mt0) cc_final: 0.7976 (mt0)
  outliers start: 18
  outliers final: 11
  residues processed: 115
  average time/residue: 0.5383
  time to fit residues: 65.2594
Evaluate side-chains
  108 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 97
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 CYS
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  352 THR
Chi-restraints excluded: chain A residue  361 THR
Chi-restraints excluded: chain A residue  507 HIS
Chi-restraints excluded: chain L residue   97 GLU
Chi-restraints excluded: chain L residue  201 THR
Chi-restraints excluded: chain L residue  203 LYS
Chi-restraints excluded: chain H residue   74 SER
Chi-restraints excluded: chain H residue  114 VAL
Chi-restraints excluded: chain H residue  219 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 26 optimal weight:    2.9990
   chunk 18 optimal weight:    0.9980
   chunk 3 optimal weight:    0.9990
   chunk 29 optimal weight:    0.9980
   chunk 44 optimal weight:    7.9990
   chunk 81 optimal weight:    0.3980
   chunk 40 optimal weight:    4.9990
   chunk 23 optimal weight:    0.3980
   chunk 42 optimal weight:    0.8980
   chunk 24 optimal weight:    0.6980
   chunk 41 optimal weight:    1.9990
   overall best weight:    0.6780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.165840 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.116747 restraints weight = 12682.577|
|-----------------------------------------------------------------------------|
r_work (start): 0.3504 rms_B_bonded: 2.09
r_work: 0.3427 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3333 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.3333
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3315
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3315 r_free = 0.3315    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3315 r_free = 0.3315    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3315
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8745
moved from start:          0.2719

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042   7014  Z= 0.108
  Angle     :  0.522  10.609   9565  Z= 0.268
  Chirality :  0.040   0.163   1124
  Planarity :  0.005   0.046   1176
  Dihedral  :  7.565  50.455   1010
  Min Nonbonded Distance : 2.003

Molprobity Statistics.
  All-atom Clashscore : 5.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 18.77 %
    Favored  : 79.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.42 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.64 (0.29), residues: 879
  helix:  2.92 (0.26), residues: 393
  sheet:  1.80 (0.36), residues: 210
  loop : -0.07 (0.38), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG L 112 
 TYR   0.020   0.001   TYR H  78 
 PHE   0.010   0.001   PHE A 295 
 TRP   0.014   0.001   TRP H  34 
 HIS   0.007   0.001   HIS L  94 

Details of bonding type rmsd
  covalent geometry    : bond        0.00223 ( 7005)
  covalent geometry    : angle       0.52044 ( 9547)
  SS BOND              : bond        0.00463 (    9)
  SS BOND              : angle       1.02345 (   18)
  hydrogen bonds       : bond        0.04615 (  450)
  hydrogen bonds       : angle       3.98202 ( 1308)

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 100
  time to evaluate  : 0.223 
Fit side-chains
   revert: symmetry clash
REVERT: B   24 LYS cc_start: 0.8802 (mmtp) cc_final: 0.8402 (tttt)
REVERT: A  296 ARG cc_start: 0.8425 (mtm180) cc_final: 0.8036 (mtt-85)
REVERT: A  341 ILE cc_start: 0.8485 (mp) cc_final: 0.8196 (mm)
REVERT: L   49 LYS cc_start: 0.8868 (ttmm) cc_final: 0.8300 (tptm)
REVERT: L  182 THR cc_start: 0.8126 (m) cc_final: 0.7623 (t)
REVERT: H   16 GLN cc_start: 0.8269 (mt0) cc_final: 0.7946 (mt0)
  outliers start: 11
  outliers final: 11
  residues processed: 107
  average time/residue: 0.5619
  time to fit residues: 63.1949
Evaluate side-chains
  109 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 98
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 CYS
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  361 THR
Chi-restraints excluded: chain A residue  366 LYS
Chi-restraints excluded: chain A residue  367 CYS
Chi-restraints excluded: chain A residue  507 HIS
Chi-restraints excluded: chain L residue   97 GLU
Chi-restraints excluded: chain L residue  201 THR
Chi-restraints excluded: chain L residue  203 LYS
Chi-restraints excluded: chain H residue  114 VAL
Chi-restraints excluded: chain H residue  219 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 6 optimal weight:    5.9990
   chunk 63 optimal weight:   10.0000
   chunk 75 optimal weight:    0.9990
   chunk 18 optimal weight:    0.9990
   chunk 2 optimal weight:    5.9990
   chunk 74 optimal weight:    0.5980
   chunk 79 optimal weight:    7.9990
   chunk 46 optimal weight:    3.9990
   chunk 27 optimal weight:    1.9990
   chunk 30 optimal weight:    5.9990
   chunk 52 optimal weight:   10.0000
   overall best weight:    1.7188

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.162355 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.113070 restraints weight = 10601.827|
|-----------------------------------------------------------------------------|
r_work (start): 0.3457 rms_B_bonded: 1.92
r_work: 0.3378 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3283 rms_B_bonded: 3.69 restraints_weight: 0.2500
r_work (final): 0.3283
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3295
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3295 r_free = 0.3295    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3295 r_free = 0.3295    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3295
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8801
moved from start:          0.2543

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   7014  Z= 0.158
  Angle     :  0.590  10.785   9565  Z= 0.303
  Chirality :  0.042   0.202   1124
  Planarity :  0.005   0.047   1176
  Dihedral  :  7.839  52.499   1010
  Min Nonbonded Distance : 1.948

Molprobity Statistics.
  All-atom Clashscore : 4.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 18.51 %
    Favored  : 79.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.42 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.40 (0.29), residues: 879
  helix:  2.65 (0.26), residues: 393
  sheet:  1.77 (0.36), residues: 210
  loop : -0.14 (0.38), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG L 112 
 TYR   0.026   0.002   TYR H  78 
 PHE   0.012   0.002   PHE A 295 
 TRP   0.019   0.002   TRP H  34 
 HIS   0.007   0.001   HIS L  94 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 ( 7005)
  covalent geometry    : angle       0.58765 ( 9547)
  SS BOND              : bond        0.00647 (    9)
  SS BOND              : angle       1.26869 (   18)
  hydrogen bonds       : bond        0.05778 (  450)
  hydrogen bonds       : angle       4.20554 ( 1308)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3783.30 seconds
wall clock time: 64 minutes 48.43 seconds (3888.43 seconds total)