Starting phenix.real_space_refine
on Fri Feb 14 03:07:36 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6wbv_21599/02_2025/6wbv_21599.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6wbv_21599/02_2025/6wbv_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6wbv_21599/02_2025/6wbv_21599.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6wbv_21599/02_2025/6wbv_21599.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6wbv_21599/02_2025/6wbv_21599.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6wbv_21599/02_2025/6wbv_21599.cif"
  }
  resolution = 2.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.013 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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 1}
          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: 5.17, per 1000 atoms: 0.75
  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: 1.74
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  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: 1.08
  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: 2.36

  Time building geometry restraints manager: 1.99 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:             1.670
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.060
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.310
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     21.130
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.030
  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:14.760
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.180
-------------------------------------------------------------------------------
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   7005  Z= 0.415
  Angle     :  0.935  16.494   9547  Z= 0.501
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.54 (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
 TRP   0.041   0.003   TRP L 167 
 HIS   0.005   0.001   HIS L  38 
 PHE   0.023   0.002   PHE L  75 
 TYR   0.024   0.002   TYR H  78 
 ARG   0.009   0.001   ARG H  97 

*********************** 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  : 0.921 
Fit side-chains
   revert: symmetry clash
REVERT: A  317 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8696 (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: 0.7896 (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: 1.0583
  time to fit residues: 176.4483
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  : 0.745 
-------------------------------------------------------------------------------
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 73 optimal weight:   10.0000
   chunk 65 optimal weight:    6.9990
   chunk 36 optimal weight:    0.9990
   chunk 22 optimal weight:    5.9990
   chunk 44 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 68 optimal weight:    3.9990
   chunk 26 optimal weight:    4.9990
   chunk 41 optimal weight:    0.6980
   chunk 50 optimal weight:    8.9990
   chunk 79 optimal weight:    5.9990
   overall best weight:    1.9388

-------------------------------------------------------------------------------
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 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: 17

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.161332 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.110410 restraints weight = 16608.249|
|-----------------------------------------------------------------------------|
r_work (start): 0.3425 rms_B_bonded: 2.36
r_work: 0.3339 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3242 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.3242
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3240
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3240 r_free = 0.3240    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 = 0.3240 r_free = 0.3240    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3240
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8829
moved from start:          0.1572

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   7005  Z= 0.256
  Angle     :  0.633   8.498   9547  Z= 0.333
  Chirality :  0.044   0.204   1124
  Planarity :  0.006   0.051   1176
  Dihedral  : 11.181  91.166   1036
  Min Nonbonded Distance : 1.923

Molprobity Statistics.
  All-atom Clashscore : 4.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 12.65 %
    Favored  : 83.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.42 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.21 (0.28), residues: 879
  helix:  1.70 (0.25), residues: 393
  sheet:  0.67 (0.34), residues: 222
  loop : -0.34 (0.37), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP H  34 
 HIS   0.004   0.001   HIS A  32 
 PHE   0.015   0.002   PHE L 213 
 TYR   0.026   0.002   TYR H  78 
 ARG   0.003   0.001   ARG H  97 

*********************** 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
  132 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 105
  time to evaluate  : 0.771 
Fit side-chains
   revert: symmetry clash
REVERT: B   24 LYS cc_start: 0.8871 (mmtp) cc_final: 0.8435 (mttt)
REVERT: A  317 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8653 (mp)
REVERT: A  341 ILE cc_start: 0.8550 (mp) cc_final: 0.8276 (mm)
REVERT: A  378 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8341 (mp)
REVERT: L   49 LYS cc_start: 0.9032 (ttmm) cc_final: 0.8807 (mttt)
REVERT: H   16 GLN cc_start: 0.8456 (mt0) cc_final: 0.8142 (mt0)
REVERT: H  183 SER cc_start: 0.9015 (p) cc_final: 0.8809 (p)
  outliers start: 27
  outliers final: 14
  residues processed: 124
  average time/residue: 1.0928
  time to fit residues: 143.6324
Evaluate side-chains
  114 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 98
  time to evaluate  : 0.727 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  457 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 L residue  203 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=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 77 optimal weight:    4.9990
   chunk 51 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   chunk 55 optimal weight:    0.6980
   chunk 74 optimal weight:    7.9990
   chunk 8 optimal weight:    3.9990
   chunk 16 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9990
   chunk 3 optimal weight:    0.8980
   chunk 33 optimal weight:    4.9990
   chunk 50 optimal weight:    7.9990
   overall best weight:    1.7186

-------------------------------------------------------------------------------
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 = 0.4031 r_free = 0.4031 target = 0.160655 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.110148 restraints weight = 15308.700|
|-----------------------------------------------------------------------------|
r_work (start): 0.3433 rms_B_bonded: 2.29
r_work: 0.3349 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3253 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.3253
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3245
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3245 r_free = 0.3245    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3245 r_free = 0.3245    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3245
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8823
moved from start:          0.1843

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   7005  Z= 0.227
  Angle     :  0.599  10.145   9547  Z= 0.310
  Chirality :  0.042   0.190   1124
  Planarity :  0.005   0.053   1176
  Dihedral  : 10.450  84.959   1023
  Min Nonbonded Distance : 1.938

Molprobity Statistics.
  All-atom Clashscore : 4.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 15.18 %
    Favored  : 81.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.42 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.80 (0.28), residues: 879
  helix:  2.24 (0.26), residues: 393
  sheet:  1.08 (0.35), residues: 213
  loop : -0.25 (0.38), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP H  34 
 HIS   0.004   0.001   HIS A  32 
 PHE   0.012   0.002   PHE A 295 
 TYR   0.025   0.002   TYR H  78 
 ARG   0.003   0.000   ARG H  97 

*********************** 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
  128 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 102
  time to evaluate  : 0.748 
Fit side-chains
   revert: symmetry clash
REVERT: B   24 LYS cc_start: 0.8852 (mmtp) cc_final: 0.8420 (mttt)
REVERT: A  317 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8665 (mp)
REVERT: A  341 ILE cc_start: 0.8562 (mp) cc_final: 0.8272 (mm)
REVERT: A  378 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8375 (mp)
REVERT: L   49 LYS cc_start: 0.9003 (ttmm) cc_final: 0.8450 (tptp)
REVERT: H   16 GLN cc_start: 0.8382 (mt0) cc_final: 0.8038 (mt0)
  outliers start: 26
  outliers final: 15
  residues processed: 120
  average time/residue: 1.1965
  time to fit residues: 151.4613
Evaluate side-chains
  115 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 98
  time to evaluate  : 0.872 
-------------------------------------------------------------------------------
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  321 VAL
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  352 THR
Chi-restraints excluded: chain A residue  364 ARG
Chi-restraints excluded: chain A residue  378 LEU
Chi-restraints excluded: chain A residue  457 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   17 THR
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 65 optimal weight:    5.9990
   chunk 51 optimal weight:    5.9990
   chunk 70 optimal weight:    0.0670
   chunk 80 optimal weight:    7.9990
   chunk 7 optimal weight:    0.6980
   chunk 69 optimal weight:    0.9990
   chunk 54 optimal weight:    5.9990
   chunk 2 optimal weight:    5.9990
   chunk 71 optimal weight:    0.0980
   chunk 82 optimal weight:    3.9990
   chunk 20 optimal weight:    5.9990
   overall best weight:    1.1722

-------------------------------------------------------------------------------
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 = 0.4048 r_free = 0.4048 target = 0.162824 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.113736 restraints weight = 11105.711|
|-----------------------------------------------------------------------------|
r_work (start): 0.3469 rms_B_bonded: 1.95
r_work: 0.3391 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3297 rms_B_bonded: 3.76 restraints_weight: 0.2500
r_work (final): 0.3297
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3271
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3271 r_free = 0.3271    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 = 0.3271 r_free = 0.3271    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3271
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8781
moved from start:          0.2100

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7005  Z= 0.177
  Angle     :  0.553   9.889   9547  Z= 0.286
  Chirality :  0.041   0.182   1124
  Planarity :  0.005   0.050   1176
  Dihedral  : 10.139  80.529   1019
  Min Nonbonded Distance : 1.969

Molprobity Statistics.
  All-atom Clashscore : 4.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  : 15.31 %
    Favored  : 80.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.42 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.08 (0.29), residues: 879
  helix:  2.54 (0.26), residues: 393
  sheet:  1.19 (0.35), residues: 212
  loop : -0.20 (0.38), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP H  34 
 HIS   0.004   0.001   HIS L  94 
 PHE   0.011   0.001   PHE A 295 
 TYR   0.023   0.001   TYR H  78 
 ARG   0.002   0.000   ARG L 112 

*********************** 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
  128 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 100
  time to evaluate  : 0.707 
Fit side-chains
   revert: symmetry clash
REVERT: B   24 LYS cc_start: 0.8838 (mmtp) cc_final: 0.8419 (mttt)
REVERT: A  317 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8711 (mp)
REVERT: A  341 ILE cc_start: 0.8527 (mp) cc_final: 0.8279 (mm)
REVERT: L   18 ARG cc_start: 0.7863 (OUTLIER) cc_final: 0.7414 (ptm160)
REVERT: L   49 LYS cc_start: 0.8935 (ttmm) cc_final: 0.8698 (mttt)
REVERT: H   16 GLN cc_start: 0.8354 (mt0) cc_final: 0.8025 (mt0)
  outliers start: 28
  outliers final: 17
  residues processed: 120
  average time/residue: 1.1848
  time to fit residues: 150.1010
Evaluate side-chains
  114 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 95
  time to evaluate  : 0.763 
-------------------------------------------------------------------------------
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  364 ARG
Chi-restraints excluded: chain A residue  367 CYS
Chi-restraints excluded: chain A residue  457 LEU
Chi-restraints excluded: chain A residue  474 LEU
Chi-restraints excluded: chain A residue  507 HIS
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  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 10 optimal weight:    3.9990
   chunk 66 optimal weight:    6.9990
   chunk 2 optimal weight:    4.9990
   chunk 18 optimal weight:    5.9990
   chunk 22 optimal weight:    0.9990
   chunk 54 optimal weight:    0.8980
   chunk 79 optimal weight:    5.9990
   chunk 50 optimal weight:    8.9990
   chunk 78 optimal weight:   30.0000
   chunk 71 optimal weight:    2.9990
   chunk 37 optimal weight:    5.9990
   overall best weight:    2.7788

-------------------------------------------------------------------------------
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**
H 160 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4010 r_free = 0.4010 target = 0.159499 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.108101 restraints weight = 16788.788|
|-----------------------------------------------------------------------------|
r_work (start): 0.3394 rms_B_bonded: 2.36
r_work: 0.3307 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3211 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.3211
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3180
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3180 r_free = 0.3180    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3180 r_free = 0.3180    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3180
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8863
moved from start:          0.2100

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.062   7005  Z= 0.330
  Angle     :  0.644  10.636   9547  Z= 0.335
  Chirality :  0.045   0.233   1124
  Planarity :  0.005   0.051   1176
  Dihedral  : 10.252  80.333   1018
  Min Nonbonded Distance : 1.916

Molprobity Statistics.
  All-atom Clashscore : 4.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  4.39 %
    Allowed  : 14.91 %
    Favored  : 80.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.42 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.89 (0.29), residues: 879
  helix:  2.27 (0.25), residues: 393
  sheet:  1.26 (0.35), residues: 213
  loop : -0.24 (0.39), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP H  34 
 HIS   0.005   0.001   HIS L  94 
 PHE   0.014   0.002   PHE A 295 
 TYR   0.027   0.002   TYR H  78 
 ARG   0.004   0.001   ARG H  97 

*********************** 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
  134 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 101
  time to evaluate  : 0.769 
Fit side-chains
   revert: symmetry clash
REVERT: B   24 LYS cc_start: 0.8884 (mmtp) cc_final: 0.8450 (mttt)
REVERT: A  317 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8699 (mp)
REVERT: A  364 ARG cc_start: 0.8637 (OUTLIER) cc_final: 0.7860 (ttp-110)
REVERT: L   18 ARG cc_start: 0.7920 (OUTLIER) cc_final: 0.7442 (ptm160)
REVERT: L   43 LYS cc_start: 0.8794 (OUTLIER) cc_final: 0.8564 (mttt)
REVERT: L   49 LYS cc_start: 0.9043 (ttmm) cc_final: 0.8786 (mttt)
REVERT: L  169 ASP cc_start: 0.8335 (OUTLIER) cc_final: 0.8049 (m-30)
REVERT: H   16 GLN cc_start: 0.8395 (mt0) cc_final: 0.8068 (mt0)
  outliers start: 33
  outliers final: 22
  residues processed: 124
  average time/residue: 1.1829
  time to fit residues: 154.7936
Evaluate side-chains
  126 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 99
  time to evaluate  : 0.818 
-------------------------------------------------------------------------------
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  364 ARG
Chi-restraints excluded: chain A residue  366 LYS
Chi-restraints excluded: chain A residue  367 CYS
Chi-restraints excluded: chain A residue  457 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   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  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 13 optimal weight:    0.9980
   chunk 41 optimal weight:    0.9990
   chunk 62 optimal weight:   20.0000
   chunk 0 optimal weight:    7.9990
   chunk 3 optimal weight:    1.9990
   chunk 26 optimal weight:    3.9990
   chunk 66 optimal weight:   10.0000
   chunk 28 optimal weight:    0.7980
   chunk 52 optimal weight:    7.9990
   chunk 11 optimal weight:    0.7980
   chunk 36 optimal weight:    2.9990
   overall best weight:    1.1184

-------------------------------------------------------------------------------
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 = 0.4049 r_free = 0.4049 target = 0.162878 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.113698 restraints weight = 20121.279|
|-----------------------------------------------------------------------------|
r_work (start): 0.3449 rms_B_bonded: 2.97
r_work: 0.3332 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.3236 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.3236
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3215
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3215 r_free = 0.3215    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 = 0.3215 r_free = 0.3215    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3215
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8816
moved from start:          0.2252

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   7005  Z= 0.173
  Angle     :  0.557  10.568   9547  Z= 0.287
  Chirality :  0.041   0.186   1124
  Planarity :  0.005   0.048   1176
  Dihedral  :  9.895  75.566   1018
  Min Nonbonded Distance : 1.972

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 15.58 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.22 (0.29), residues: 879
  helix:  2.58 (0.26), residues: 393
  sheet:  1.44 (0.36), residues: 210
  loop : -0.14 (0.39), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP H  34 
 HIS   0.005   0.001   HIS L  94 
 PHE   0.010   0.001   PHE A 295 
 TYR   0.023   0.001   TYR H  78 
 ARG   0.002   0.000   ARG L 112 

*********************** 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
  130 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 100
  time to evaluate  : 0.745 
Fit side-chains
   revert: symmetry clash
REVERT: B   24 LYS cc_start: 0.8845 (mmtp) cc_final: 0.8451 (mttt)
REVERT: A  317 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8759 (mp)
REVERT: L   18 ARG cc_start: 0.7943 (OUTLIER) cc_final: 0.7433 (ptm160)
REVERT: L   49 LYS cc_start: 0.9036 (ttmm) cc_final: 0.8797 (mttt)
REVERT: L  182 THR cc_start: 0.8086 (m) cc_final: 0.7620 (t)
REVERT: H   16 GLN cc_start: 0.8305 (mt0) cc_final: 0.7972 (mt0)
  outliers start: 30
  outliers final: 19
  residues processed: 121
  average time/residue: 1.1954
  time to fit residues: 152.6826
Evaluate side-chains
  117 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 96
  time to evaluate  : 0.961 
-------------------------------------------------------------------------------
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  361 THR
Chi-restraints excluded: chain A residue  364 ARG
Chi-restraints excluded: chain A residue  457 LEU
Chi-restraints excluded: chain A residue  474 LEU
Chi-restraints excluded: chain A residue  507 HIS
Chi-restraints excluded: chain L residue   18 ARG
Chi-restraints excluded: chain L residue   97 GLU
Chi-restraints excluded: chain L residue  136 VAL
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   54 SER
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 25 optimal weight:    0.9980
   chunk 45 optimal weight:   10.0000
   chunk 11 optimal weight:    0.6980
   chunk 32 optimal weight:    0.9980
   chunk 77 optimal weight:   10.0000
   chunk 48 optimal weight:    0.2980
   chunk 75 optimal weight:    0.9990
   chunk 60 optimal weight:    9.9990
   chunk 30 optimal weight:   10.0000
   chunk 58 optimal weight:    6.9990
   chunk 52 optimal weight:   10.0000
   overall best weight:    0.7982

-------------------------------------------------------------------------------
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 = 0.4068 r_free = 0.4068 target = 0.164608 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.114317 restraints weight = 16646.162|
|-----------------------------------------------------------------------------|
r_work (start): 0.3470 rms_B_bonded: 2.35
r_work: 0.3387 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3292 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.3292
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3274
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3274 r_free = 0.3274    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3274 r_free = 0.3274    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3274
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8777
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   0.042   7005  Z= 0.148
  Angle     :  0.533  10.431   9547  Z= 0.272
  Chirality :  0.040   0.186   1124
  Planarity :  0.004   0.046   1176
  Dihedral  :  9.330  69.746   1018
  Min Nonbonded Distance : 1.991

Molprobity Statistics.
  All-atom Clashscore : 5.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 17.31 %
    Favored  : 79.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.42 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.44 (0.29), residues: 879
  helix:  2.76 (0.26), residues: 393
  sheet:  1.58 (0.36), residues: 210
  loop : -0.07 (0.39), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP H  34 
 HIS   0.006   0.001   HIS L  94 
 PHE   0.010   0.001   PHE A 295 
 TYR   0.022   0.001   TYR H  78 
 ARG   0.002   0.000   ARG L 112 

*********************** 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
  125 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 101
  time to evaluate  : 0.791 
Fit side-chains
   revert: symmetry clash
REVERT: B   24 LYS cc_start: 0.8814 (mmtp) cc_final: 0.8446 (mttt)
REVERT: A  296 ARG cc_start: 0.8452 (mtm180) cc_final: 0.8052 (mtt-85)
REVERT: L   49 LYS cc_start: 0.8959 (ttmm) cc_final: 0.8394 (tptm)
REVERT: L  182 THR cc_start: 0.8122 (m) cc_final: 0.7646 (t)
REVERT: H   16 GLN cc_start: 0.8294 (mt0) cc_final: 0.7964 (mt0)
  outliers start: 24
  outliers final: 15
  residues processed: 119
  average time/residue: 1.2143
  time to fit residues: 152.8349
Evaluate side-chains
  113 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 98
  time to evaluate  : 0.822 
-------------------------------------------------------------------------------
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  367 CYS
Chi-restraints excluded: chain A residue  457 LEU
Chi-restraints excluded: chain A residue  485 ILE
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   13 LYS
Chi-restraints excluded: chain H residue   83 ASN
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 55 optimal weight:   20.0000
   chunk 69 optimal weight:    2.9990
   chunk 35 optimal weight:    0.6980
   chunk 60 optimal weight:    6.9990
   chunk 76 optimal weight:    8.9990
   chunk 31 optimal weight:    0.6980
   chunk 19 optimal weight:    4.9990
   chunk 45 optimal weight:    2.9990
   chunk 41 optimal weight:    4.9990
   chunk 63 optimal weight:    8.9990
   chunk 61 optimal weight:    6.9990
   overall best weight:    2.4786

-------------------------------------------------------------------------------
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 = 0.4021 r_free = 0.4021 target = 0.160460 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.110842 restraints weight = 10584.463|
|-----------------------------------------------------------------------------|
r_work (start): 0.3431 rms_B_bonded: 1.92
r_work: 0.3350 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3256 rms_B_bonded: 3.67 restraints_weight: 0.2500
r_work (final): 0.3256
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3224
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3224 r_free = 0.3224    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3224 r_free = 0.3224    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3224
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8829
moved from start:          0.2303

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056   7005  Z= 0.298
  Angle     :  0.621  10.806   9547  Z= 0.322
  Chirality :  0.044   0.227   1124
  Planarity :  0.005   0.049   1176
  Dihedral  :  9.037  66.858   1010
  Min Nonbonded Distance : 1.927

Molprobity Statistics.
  All-atom Clashscore : 4.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 17.18 %
    Favored  : 79.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.42 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.09 (0.28), residues: 879
  helix:  2.39 (0.25), residues: 393
  sheet:  1.58 (0.35), residues: 212
  loop : -0.29 (0.38), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP H  34 
 HIS   0.005   0.001   HIS L  94 
 PHE   0.013   0.002   PHE A 295 
 TYR   0.026   0.002   TYR H  78 
 ARG   0.003   0.001   ARG L 112 

*********************** 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
  129 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 102
  time to evaluate  : 0.811 
Fit side-chains
   revert: symmetry clash
REVERT: B   24 LYS cc_start: 0.8867 (mmtp) cc_final: 0.8459 (mttt)
REVERT: A  296 ARG cc_start: 0.8432 (mtm180) cc_final: 0.8026 (mtt-85)
REVERT: L   18 ARG cc_start: 0.7918 (OUTLIER) cc_final: 0.7447 (ptm160)
REVERT: L   43 LYS cc_start: 0.8665 (OUTLIER) cc_final: 0.8392 (mttt)
REVERT: L   49 LYS cc_start: 0.9016 (ttmm) cc_final: 0.8467 (tptm)
REVERT: H   16 GLN cc_start: 0.8325 (mt0) cc_final: 0.8013 (mt0)
  outliers start: 27
  outliers final: 21
  residues processed: 120
  average time/residue: 1.1985
  time to fit residues: 151.7533
Evaluate side-chains
  122 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 99
  time to evaluate  : 0.802 
-------------------------------------------------------------------------------
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  321 VAL
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  457 LEU
Chi-restraints excluded: chain A residue  485 ILE
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  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   83 ASN
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 71 optimal weight:    2.9990
   chunk 45 optimal weight:    9.9990
   chunk 44 optimal weight:    5.9990
   chunk 51 optimal weight:    0.9980
   chunk 47 optimal weight:    5.9990
   chunk 73 optimal weight:    0.9990
   chunk 58 optimal weight:    0.0470
   chunk 37 optimal weight:    0.5980
   chunk 20 optimal weight:    0.9990
   chunk 61 optimal weight:    3.9990
   chunk 78 optimal weight:   20.0000
   overall best weight:    0.7282

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

Flipped N/Q/H residues before XYZ refinement:
L 128 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4067 r_free = 0.4067 target = 0.164528 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.114437 restraints weight = 16697.964|
|-----------------------------------------------------------------------------|
r_work (start): 0.3466 rms_B_bonded: 2.70
r_work: 0.3378 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.3282 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.3282
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3290
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3290 r_free = 0.3290    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3290 r_free = 0.3290    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3290
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8780
moved from start:          0.2562

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041   7005  Z= 0.147
  Angle     :  0.535  10.953   9547  Z= 0.274
  Chirality :  0.040   0.173   1124
  Planarity :  0.004   0.046   1176
  Dihedral  :  8.302  59.322   1010
  Min Nonbonded Distance : 1.990

Molprobity Statistics.
  All-atom Clashscore : 5.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 18.11 %
    Favored  : 79.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.42 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.46 (0.29), residues: 879
  helix:  2.76 (0.26), residues: 393
  sheet:  1.67 (0.36), residues: 212
  loop : -0.11 (0.38), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP H  34 
 HIS   0.006   0.001   HIS L  94 
 PHE   0.010   0.001   PHE A 295 
 TYR   0.022   0.001   TYR H  78 
 ARG   0.002   0.000   ARG A 178 

*********************** 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
  119 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 98
  time to evaluate  : 0.795 
Fit side-chains
   revert: symmetry clash
REVERT: B   24 LYS cc_start: 0.8870 (mmtp) cc_final: 0.8453 (mttt)
REVERT: A  296 ARG cc_start: 0.8454 (mtm180) cc_final: 0.8040 (mtt-85)
REVERT: L   49 LYS cc_start: 0.8965 (ttmm) cc_final: 0.8391 (tptm)
REVERT: L  182 THR cc_start: 0.8087 (m) cc_final: 0.7599 (t)
REVERT: H   16 GLN cc_start: 0.8267 (mt0) cc_final: 0.7951 (mt0)
  outliers start: 21
  outliers final: 15
  residues processed: 114
  average time/residue: 1.2500
  time to fit residues: 150.1506
Evaluate side-chains
  111 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 96
  time to evaluate  : 0.766 
-------------------------------------------------------------------------------
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  352 THR
Chi-restraints excluded: chain A residue  361 THR
Chi-restraints excluded: chain A residue  367 CYS
Chi-restraints excluded: chain A residue  457 LEU
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 25 optimal weight:    0.8980
   chunk 0 optimal weight:   10.0000
   chunk 35 optimal weight:    0.9980
   chunk 70 optimal weight:    0.6980
   chunk 15 optimal weight:    3.9990
   chunk 75 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9980
   chunk 14 optimal weight:    0.8980
   chunk 69 optimal weight:    3.9990
   chunk 53 optimal weight:    1.9990
   overall best weight:    0.8980

-------------------------------------------------------------------------------
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 = 0.4063 r_free = 0.4063 target = 0.164218 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.116019 restraints weight = 8854.384|
|-----------------------------------------------------------------------------|
r_work (start): 0.3496 rms_B_bonded: 1.78
r_work: 0.3421 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.3330 rms_B_bonded: 3.47 restraints_weight: 0.2500
r_work (final): 0.3330
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3309
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3309 r_free = 0.3309    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3309 r_free = 0.3309    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3309
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8747
moved from start:          0.2569

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041   7005  Z= 0.157
  Angle     :  0.541  10.601   9547  Z= 0.277
  Chirality :  0.041   0.175   1124
  Planarity :  0.005   0.046   1176
  Dihedral  :  7.937  57.449   1010
  Min Nonbonded Distance : 1.985

Molprobity Statistics.
  All-atom Clashscore : 5.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 19.31 %
    Favored  : 78.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.42 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.52 (0.29), residues: 879
  helix:  2.76 (0.26), residues: 393
  sheet:  1.76 (0.36), residues: 212
  loop : -0.05 (0.39), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP H  34 
 HIS   0.006   0.001   HIS L  94 
 PHE   0.011   0.001   PHE A 295 
 TYR   0.022   0.001   TYR H  78 
 ARG   0.002   0.000   ARG L 112 

********************** 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
  112 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 97
  time to evaluate  : 0.702 
Fit side-chains
   revert: symmetry clash
REVERT: B   24 LYS cc_start: 0.8819 (mmtp) cc_final: 0.8427 (mttt)
REVERT: A  296 ARG cc_start: 0.8403 (mtm180) cc_final: 0.7993 (mtt-85)
REVERT: L   49 LYS cc_start: 0.8909 (ttmm) cc_final: 0.8346 (tptm)
REVERT: L  182 THR cc_start: 0.8088 (m) cc_final: 0.7612 (t)
REVERT: H   16 GLN cc_start: 0.8243 (mt0) cc_final: 0.7918 (mt0)
  outliers start: 15
  outliers final: 14
  residues processed: 108
  average time/residue: 1.2091
  time to fit residues: 137.8068
Evaluate side-chains
  111 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 97
  time to evaluate  : 0.810 
-------------------------------------------------------------------------------
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  352 THR
Chi-restraints excluded: chain A residue  361 THR
Chi-restraints excluded: chain A residue  367 CYS
Chi-restraints excluded: chain A residue  457 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  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 61 optimal weight:   10.0000
   chunk 67 optimal weight:   10.0000
   chunk 60 optimal weight:    6.9990
   chunk 38 optimal weight:    0.9980
   chunk 25 optimal weight:    0.8980
   chunk 19 optimal weight:    3.9990
   chunk 71 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9990
   chunk 29 optimal weight:    6.9990
   chunk 8 optimal weight:    1.9990
   overall best weight:    1.3786

-------------------------------------------------------------------------------
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 = 0.4046 r_free = 0.4046 target = 0.162711 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.111905 restraints weight = 16691.156|
|-----------------------------------------------------------------------------|
r_work (start): 0.3439 rms_B_bonded: 2.64
r_work: 0.3348 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3250 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.3250
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3256
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3256 r_free = 0.3256    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3256 r_free = 0.3256    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3256
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8819
moved from start:          0.2525

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7005  Z= 0.195
  Angle     :  0.570  10.674   9547  Z= 0.292
  Chirality :  0.042   0.182   1124
  Planarity :  0.005   0.045   1176
  Dihedral  :  7.926  58.186   1010
  Min Nonbonded Distance : 1.965

Molprobity Statistics.
  All-atom Clashscore : 5.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 18.38 %
    Favored  : 78.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.42 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.40 (0.29), residues: 879
  helix:  2.64 (0.26), residues: 393
  sheet:  1.72 (0.36), residues: 212
  loop : -0.09 (0.38), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP H  34 
 HIS   0.006   0.001   HIS L  94 
 PHE   0.011   0.001   PHE A 295 
 TYR   0.024   0.002   TYR H  78 
 ARG   0.002   0.000   ARG L 112 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8033.77 seconds
wall clock time: 142 minutes 16.44 seconds (8536.44 seconds total)