Starting phenix.real_space_refine
on Tue Mar  3 16:35:39 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8dl7_27498/03_2026/8dl7_27498_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8dl7_27498/03_2026/8dl7_27498.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8dl7_27498/03_2026/8dl7_27498.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8dl7_27498/03_2026/8dl7_27498.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8dl7_27498/03_2026/8dl7_27498_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8dl7_27498/03_2026/8dl7_27498_neut.cif"
  }
  resolution = 2.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.012 sd=   0.075
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     S      37      5.16       5
     C    4236      2.51       5
     N    1094      2.21       5
     O    1217      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6586
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "A"
      Number of atoms: 3547
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 467, 3536
          Classifications: {'peptide': 467}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 12, 'TRANS': 454}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 31
          Unresolved non-hydrogen angles: 37
          Unresolved non-hydrogen dihedrals: 27
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 20
      Conformer: "B"
        Number of residues, atoms: 467, 3536
          Classifications: {'peptide': 467}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 12, 'TRANS': 454}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 31
          Unresolved non-hydrogen angles: 37
          Unresolved non-hydrogen dihedrals: 27
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 20
          bond proxies already assigned to first conformer: 3596
    Chain: "C"
      Number of atoms: 1373
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 213, 1373
          Classifications: {'peptide': 213}
          Incomplete info: {'truncation_to_alanine': 91}
          Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 203}
          Unresolved chain link angles: 4
          Unresolved non-hydrogen bonds: 290
          Unresolved non-hydrogen angles: 372
          Unresolved non-hydrogen dihedrals: 242
          Unresolved non-hydrogen chiralities: 26
          Planarities with less than four sites: {'GLU:plan': 7, 'PHE:plan': 3, 'GLN:plan1': 3, 'ASN:plan1': 7, 'ASP:plan': 6, 'TRP:plan': 2, 'ARG:plan': 3, 'TYR:plan': 2, 'HIS:plan': 2}
          Unresolved non-hydrogen planarities: 154
    Chain: "D"
      Number of atoms: 1438
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 219, 1438
          Classifications: {'peptide': 219}
          Incomplete info: {'backbone_only': 5, 'truncation_to_alanine': 80}
          Link IDs: {'PTRANS': 14, 'TRANS': 204}
          Unresolved chain link angles: 9
          Unresolved non-hydrogen bonds: 251
          Unresolved non-hydrogen angles: 335
          Unresolved non-hydrogen dihedrals: 207
          Unresolved non-hydrogen chiralities: 40
          Planarities with less than four sites: {'TYR:plan': 3, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 2, 'TRP:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 2, 'GLN:plan1': 2}
          Unresolved non-hydrogen planarities: 91
    Chain: "F"
      Number of atoms: 8
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 8
          Classifications: {'peptide': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 1
          Planarities with less than four sites: {'SQ6:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "F"
      Number of atoms: 70
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 70
          Unusual residues: {'EOE': 1}
          Classifications: {'peptide': 6, 'undetermined': 1}
          Link IDs: {'TRANS': 4, None: 2}
            Not linked:
              pdbres="2GX F   4 "
              pdbres="EOE F   5 "
            Not linked:
              pdbres="EOE F   5 "
              pdbres="ARG F   6 "
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Planarities with less than four sites: {'2GX:plan-3': 1, 'EOE:plan-1': 1}
          Unresolved non-hydrogen planarities: 2
    Chain: "F"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 28
          Unusual residues: {'3FB': 1, 'ACA': 1}
          Classifications: {'peptide': 1, 'undetermined': 2}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 1
          Planarities with less than four sites: {'3FB:plan-2': 1, 'ACA:plan-1': 1, 'SOW:plan-2': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "F"
      Number of atoms: 17
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 17
          Unusual residues: {'SQI': 1}
          Classifications: {'undetermined': 1}
    Chain: "A"
      Number of atoms: 104
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 104
          Unusual residues: {'POV': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "D"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  APHE A 292 " occ=0.37
      ... (20 atoms not shown)
      pdb=" CZ BPHE A 292 " occ=0.63
  Time building chain proxies: 2.20, per 1000 atoms: 0.33
  Number of scatterers: 6586
  At special positions: 0
  Unit cell: (83.6, 74.8, 145.2, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      37     16.00
     P       2     15.00
     O    1217      8.00
     N    1094      7.00
     C    4236      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 326 " - pdb=" SG  CYS F   7 " distance=2.06
    Simple disulfide: pdb=" SG  CYS A 367 " - pdb=" SG  CYS A 553 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  43 " - pdb=" SG  CYS C 108 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  41 " - pdb=" SG  CYS D 115 " distance=2.03

  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 additional links: simple=1, symmetry=0
    Simple link:   pdb=" C   ARG F   8 " - pdb=" N   3FB F   9 "
  Number of custom bonds: simple=6, symmetry=0
  Number of additional bonds: simple=6, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.07
  Conformation dependent library (CDL) restraints added in 385.2 milliseconds
  

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
    Skipped
      Input residue is complicated and confusing
        pdb=" CB  3FB F   9 "
  Number of C-beta restraints generated:  1660

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 10 sheets defined
      47.3% alpha, 19.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.16
  Creating SS restraints...
    Processing helix  chain 'A' and resid 13 through 21
      removed outlier: 3.632A  pdb=" N   LEU A  17 " --> pdb=" O   CYS A  13 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   ALA A  18 " --> pdb=" O   CYS A  14 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 23 through 54
      removed outlier: 3.762A  pdb=" N   TYR A  54 " --> pdb=" O   LEU A  50 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 57 through 84
      removed outlier: 4.386A  pdb=" N   THR A  61 " --> pdb=" O   SER A  57 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 87 through 116
      removed outlier: 3.758A  pdb=" N   VAL A  91 " --> pdb=" O   ALA A  87 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 117 through 123
    Processing helix  chain 'A' and resid 126 through 164
      removed outlier: 4.420A  pdb=" N   THR A 130 " --> pdb=" O   GLY A 126 " (cutoff:3.500A)
      removed outlier: 3.955A  pdb=" N   SER A 131 " --> pdb=" O   TRP A 127 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 167 through 198
      Proline residue:  A 189  - end of helix
    Processing helix  chain 'A' and resid 200 through 230
    Processing helix  chain 'A' and resid 231 through 234
      removed outlier: 3.665A  pdb=" N   ALA A 234 " --> pdb=" O   PRO A 231 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 231 through 234'
    Processing helix  chain 'A' and resid 285 through 304
      Proline residue:  A 291  - end of helix
    Processing helix  chain 'A' and resid 307 through 317
      removed outlier: 3.545A  pdb=" N   GLY A 311 " --> pdb=" O   VAL A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 325 through 336
    Processing helix  chain 'A' and resid 339 through 367
    Processing helix  chain 'A' and resid 369 through 390
      removed outlier: 3.833A  pdb=" N   SER A 390 " --> pdb=" O   LEU A 386 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 452 through 483
      removed outlier: 3.511A  pdb=" N   SER A 456 " --> pdb=" O   ILE A 452 " (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: 3.559A  pdb=" N   HIS A 507 " --> pdb=" O   LEU A 503 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 519 through 547
      removed outlier: 3.686A  pdb=" N   LEU A 523 " --> pdb=" O   ALA A 519 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   GLY A 547 " --> pdb=" O   GLN A 543 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 99 through 103
      removed outlier: 3.763A  pdb=" N   LEU C 103 " --> pdb=" O   SER C 100 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 141 through 147
    Processing helix  chain 'C' and resid 202 through 208
    Processing helix  chain 'D' and resid 47 through 51
    Processing helix  chain 'D' and resid 81 through 84
      removed outlier: 3.533A  pdb=" N   GLN D  84 " --> pdb=" O   PRO D  81 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 81 through 84'
    Processing helix  chain 'D' and resid 106 through 110
      removed outlier: 3.764A  pdb=" N   THR D 110 " --> pdb=" O   SER D 107 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'C' and resid 24 through 25
      removed outlier: 3.638A  pdb=" N   ASP C  90 " --> pdb=" O   SER C  87 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 30 through 32
      removed outlier: 6.312A  pdb=" N   MET C  31 " --> pdb=" O   GLU C 125 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'C' and resid 73 through 74
      removed outlier: 6.566A  pdb=" N   TRP C  55 " --> pdb=" O   LEU C  67 " (cutoff:3.500A)
      removed outlier: 4.981A  pdb=" N   TYR C  69 " --> pdb=" O   VAL C  53 " (cutoff:3.500A)
      removed outlier: 6.927A  pdb=" N   VAL C  53 " --> pdb=" O   TYR C  69 " (cutoff:3.500A)
      removed outlier: 4.287A  pdb=" N   THR C 117 " --> pdb=" O   GLN C 110 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 137 through 138
      removed outlier: 3.730A  pdb=" N   VAL C 153 " --> pdb=" O   PHE C 138 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   ASN C 158 " --> pdb=" O   TYR C 193 " (cutoff:3.500A)
      removed outlier: 6.105A  pdb=" N   TYR C 193 " --> pdb=" O   ASN C 158 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 165 through 170
      removed outlier: 6.320A  pdb=" N   HIS C 218 " --> pdb=" O   SER C 223 " (cutoff:3.500A)
      removed outlier: 6.382A  pdb=" N   SER C 223 " --> pdb=" O   HIS C 218 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 22 through 25
    Processing sheet with id=AA7, first strand: chain 'D' and resid 29 through 31
      removed outlier: 6.512A  pdb=" N   MET D  53 " --> pdb=" O   TRP D  69 " (cutoff:3.500A)
      removed outlier: 4.316A  pdb=" N   TRP D  69 " --> pdb=" O   MET D  53 " (cutoff:3.500A)
      removed outlier: 6.721A  pdb=" N   TRP D  55 " --> pdb=" O   ILE D  67 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 145 through 146
      removed outlier: 5.556A  pdb=" N   TYR D 200 " --> pdb=" O   GLY D 169 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 145 through 146
      removed outlier: 5.556A  pdb=" N   TYR D 200 " --> pdb=" O   GLY D 169 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 176 through 179
      removed outlier: 4.680A  pdb=" N   ILE D 218 " --> pdb=" O   ILE D 235 " (cutoff:3.500A)

    437 hydrogen bonds defined for protein.
    1239 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: 1.07

  Time building geometry restraints manager: 1.23 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 1172
        1.33 -     1.45: 1704
        1.45 -     1.57: 3763
        1.57 -     1.70: 4
        1.70 -     1.82: 58
  Bond restraints: 6701
  Sorted by residual:
  bond pdb=" N   SOW F  11 "
       pdb=" CB  SOW F  11 "
    ideal  model  delta    sigma   weight residual
    1.435  1.502 -0.067 2.00e-02 2.50e+03 1.11e+01
  bond pdb=" N   VAL A 484 "
       pdb=" CA  VAL A 484 "
    ideal  model  delta    sigma   weight residual
    1.459  1.497 -0.039 1.19e-02 7.06e+03 1.05e+01
  bond pdb=" N   ILE A 485 "
       pdb=" CA  ILE A 485 "
    ideal  model  delta    sigma   weight residual
    1.457  1.493 -0.036 1.19e-02 7.06e+03 9.22e+00
  bond pdb=" N   GLU A 488 "
       pdb=" CA  GLU A 488 "
    ideal  model  delta    sigma   weight residual
    1.459  1.486 -0.027 9.10e-03 1.21e+04 8.85e+00
  bond pdb=" N   VAL A 113 "
       pdb=" CA  VAL A 113 "
    ideal  model  delta    sigma   weight residual
    1.460  1.495 -0.035 1.19e-02 7.06e+03 8.77e+00
  ... (remaining 6696 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     6.96: 9092
        6.96 -    13.92: 5
       13.92 -    20.88: 0
       20.88 -    27.85: 0
       27.85 -    34.81: 1
  Bond angle restraints: 9098
  Sorted by residual:
  angle pdb=" N   SOW F  11 "
        pdb=" CA  SOW F  11 "
        pdb=" C   SOW F  11 "
      ideal   model   delta    sigma   weight residual
     112.87  147.68  -34.81 3.00e+00 1.11e-01 1.35e+02
  angle pdb=" CA  SOW F  11 "
        pdb=" N   SOW F  11 "
        pdb=" CB  SOW F  11 "
      ideal   model   delta    sigma   weight residual
     114.32  100.44   13.88 3.00e+00 1.11e-01 2.14e+01
  angle pdb=" C   CYS F   7 "
        pdb=" CA  CYS F   7 "
        pdb=" CB  CYS F   7 "
      ideal   model   delta    sigma   weight residual
     110.42  101.58    8.84 1.99e+00 2.53e-01 1.97e+01
  angle pdb=" C   ILE A 491 "
        pdb=" N   ILE A 492 "
        pdb=" CA  ILE A 492 "
      ideal   model   delta    sigma   weight residual
     120.56  115.55    5.01 1.26e+00 6.30e-01 1.58e+01
  angle pdb=" N   ALA D 111 "
        pdb=" CA  ALA D 111 "
        pdb=" C   ALA D 111 "
      ideal   model   delta    sigma   weight residual
     107.73  112.51   -4.78 1.34e+00 5.57e-01 1.27e+01
  ... (remaining 9093 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.94: 3500
       17.94 -    35.88: 296
       35.88 -    53.81: 110
       53.81 -    71.75: 21
       71.75 -    89.69: 7
  Dihedral angle restraints: 3934
    sinusoidal: 1340
      harmonic: 2594
  Sorted by residual:
  dihedral pdb=" C   SOW F  11 "
           pdb=" N   SOW F  11 "
           pdb=" CA  SOW F  11 "
           pdb=" CB  SOW F  11 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -149.11   26.51     0      2.50e+00 1.60e-01 1.12e+02
  dihedral pdb=" N   SOW F  11 "
           pdb=" C   SOW F  11 "
           pdb=" CA  SOW F  11 "
           pdb=" CB  SOW F  11 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  100.36   22.44     0      2.50e+00 1.60e-01 8.05e+01
  dihedral pdb=" C   CYS F   7 "
           pdb=" N   CYS F   7 "
           pdb=" CA  CYS F   7 "
           pdb=" CB  CYS F   7 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -109.34  -13.26     0      2.50e+00 1.60e-01 2.81e+01
  ... (remaining 3931 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.076: 940
       0.076 -    0.152: 114
       0.152 -    0.228: 8
       0.228 -    0.305: 0
       0.305 -    0.381: 1
  Chirality restraints: 1063
  Sorted by residual:
  chirality pdb=" CA  CYS F   7 "
            pdb=" N   CYS F   7 "
            pdb=" C   CYS F   7 "
            pdb=" CB  CYS F   7 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.89   -0.38 2.00e-01 2.50e+01 3.63e+00
  chirality pdb=" CB  ILE A 152 "
            pdb=" CA  ILE A 152 "
            pdb=" CG1 ILE A 152 "
            pdb=" CG2 ILE A 152 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.42    0.23 2.00e-01 2.50e+01 1.28e+00
  chirality pdb=" CA  ILE A 485 "
            pdb=" N   ILE A 485 "
            pdb=" C   ILE A 485 "
            pdb=" CB  ILE A 485 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.62   -0.19 2.00e-01 2.50e+01 9.05e-01
  ... (remaining 1060 not shown)

  Planarity restraints: 1145
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN A 155 "   -0.010 2.00e-02 2.50e+03   1.91e-02 3.66e+00
        pdb=" C   GLN A 155 "    0.033 2.00e-02 2.50e+03
        pdb=" O   GLN A 155 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   ARG A 156 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG D  59 "   -0.160 9.50e-02 1.11e+02   7.16e-02 3.15e+00
        pdb=" NE  ARG D  59 "    0.009 2.00e-02 2.50e+03
        pdb=" CZ  ARG D  59 "    0.002 2.00e-02 2.50e+03
        pdb=" NH1 ARG D  59 "    0.002 2.00e-02 2.50e+03
        pdb=" NH2 ARG D  59 "   -0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP D  80 "    0.025 5.00e-02 4.00e+02   3.85e-02 2.38e+00
        pdb=" N   PRO D  81 "   -0.067 5.00e-02 4.00e+02
        pdb=" CA  PRO D  81 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO D  81 "    0.021 5.00e-02 4.00e+02
  ... (remaining 1142 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1200
        2.77 -     3.30: 6177
        3.30 -     3.84: 10308
        3.84 -     4.37: 10967
        4.37 -     4.90: 19837
  Nonbonded interactions: 48489
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A 504 "
            pdb=" CAH 2GX F   4 "
     model   vdw
     2.238 3.340
  nonbonded pdb=" OG  SER C  70 "
            pdb=" OD1 ASN C  73 "
     model   vdw
     2.281 3.040
  nonbonded pdb=" OE1 GLU A 165 "
            pdb=" OH  TYR D  51 "
     model   vdw
     2.282 3.040
  nonbonded pdb=" O   SER D  26 "
            pdb=" OG1 THR D 133 "
     model   vdw
     2.299 3.040
  nonbonded pdb=" OE1 GLU C 125 "
            pdb=" N   ILE C 126 "
     model   vdw
     2.315 3.120
  ... (remaining 48484 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=0.37 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:             0.550
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.260
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:7.200
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.210
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8252
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   0.102   6712  Z= 0.415
  Angle     :  0.818  34.807   9109  Z= 0.465
  Chirality :  0.050   0.381   1063
  Planarity :  0.004   0.072   1144
  Dihedral  : 16.202  89.691   2259
  Min Nonbonded Distance : 2.238

Molprobity Statistics.
  All-atom Clashscore : 7.18
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  4.49 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 27.13 %
    Favored  : 69.97 %
  Cbeta Deviations :  0.36 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.47 (0.29), residues: 893
  helix:  2.03 (0.27), residues: 401
  sheet:  1.39 (0.38), residues: 214
  loop : -0.97 (0.35), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D  32 
 TYR   0.008   0.001   TYR C 160 
 PHE   0.010   0.001   PHE A 308 
 TRP   0.008   0.001   TRP A 299 
 HIS   0.005   0.001   HIS A 535 

Details of bonding type rmsd
  covalent geometry    : bond        0.00497 ( 6701)
  covalent geometry    : angle       0.80392 ( 9098)
  SS BOND              : bond        0.01573 (    4)
  SS BOND              : angle       5.21673 (    8)
  hydrogen bonds       : bond        0.11962 (  428)
  hydrogen bonds       : angle       5.76789 ( 1239)
  Misc. bond           : bond        0.09215 (    6)
  link_TRANS           : bond        0.00010 (    1)
  link_TRANS           : angle       0.43694 (    3)

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

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

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 46
  time to evaluate  : 0.234 
Fit side-chains
REVERT: A  112 MET cc_start: 0.7950 (OUTLIER) cc_final: 0.7711 (tmm)
REVERT: A  194 GLN cc_start: 0.8501 (OUTLIER) cc_final: 0.8258 (tm-30)
REVERT: A  198 PHE cc_start: 0.8182 (OUTLIER) cc_final: 0.7862 (t80)
REVERT: C  125 GLU cc_start: 0.6373 (tp30) cc_final: 0.6036 (tp30)
REVERT: D  108 GLU cc_start: 0.8735 (tm-30) cc_final: 0.8466 (tm-30)
  outliers start: 17
  outliers final: 11
  residues processed: 62
  average time/residue: 0.5982
  time to fit residues: 38.8671
Evaluate side-chains
  59 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 45
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   51 VAL
Chi-restraints excluded: chain A residue  112 MET
Chi-restraints excluded: chain A residue  186 ILE
Chi-restraints excluded: chain A residue  194 GLN
Chi-restraints excluded: chain A residue  198 PHE
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  381 LEU
Chi-restraints excluded: chain A residue  455 VAL
Chi-restraints excluded: chain A residue  507 HIS
Chi-restraints excluded: chain C residue   33 THR
Chi-restraints excluded: chain C residue   51 THR
Chi-restraints excluded: chain D residue  136 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 49 optimal weight:   40.0000
   chunk 53 optimal weight:    6.9990
   chunk 5 optimal weight:    7.9990
   chunk 33 optimal weight:    0.0770
   chunk 65 optimal weight:   50.0000
   chunk 62 optimal weight:   30.0000
   chunk 51 optimal weight:    0.0670
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:   50.0000
   chunk 45 optimal weight:    4.9990
   chunk 74 optimal weight:   10.0000
   overall best weight:    3.2282

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

Flipped N/Q/H residues before XYZ refinement:
A 194 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.072845 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2922 r_free = 0.2922 target = 0.048596 restraints weight = 61827.390|
|-----------------------------------------------------------------------------|
r_work (start): 0.2838 rms_B_bonded: 5.38
r_work (final): 0.2838
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2838
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2838 r_free = 0.2838    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2837 r_free = 0.2837    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2837
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8295
moved from start:          0.0966

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   6712  Z= 0.207
  Angle     :  0.745  41.593   9109  Z= 0.345
  Chirality :  0.042   0.176   1063
  Planarity :  0.004   0.044   1144
  Dihedral  :  9.202  81.751   1104
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 4.50
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.71 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  4.27 %
    Allowed  : 24.40 %
    Favored  : 71.33 %
  Cbeta Deviations :  0.24 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.15 (0.29), residues: 893
  helix:  2.82 (0.26), residues: 402
  sheet:  1.54 (0.38), residues: 214
  loop : -0.88 (0.36), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG F   8 
 TYR   0.010   0.001   TYR C  69 
 PHE   0.012   0.002   PHE A 508 
 TRP   0.010   0.001   TRP D  69 
 HIS   0.006   0.001   HIS A 535 

Details of bonding type rmsd
  covalent geometry    : bond        0.00473 ( 6701)
  covalent geometry    : angle       0.74528 ( 9098)
  SS BOND              : bond        0.00391 (    4)
  SS BOND              : angle       0.94281 (    8)
  hydrogen bonds       : bond        0.07679 (  428)
  hydrogen bonds       : angle       4.45982 ( 1239)
  Misc. bond           : bond        0.00033 (    6)
  link_TRANS           : bond        0.00000 (    1)
  link_TRANS           : angle       0.70758 (    3)

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

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

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 43
  time to evaluate  : 0.189 
Fit side-chains
REVERT: A  112 MET cc_start: 0.7972 (ttm) cc_final: 0.7692 (tmm)
REVERT: C   98 MET cc_start: 0.8712 (ppp) cc_final: 0.8507 (ppp)
REVERT: D   22 GLN cc_start: 0.8880 (OUTLIER) cc_final: 0.8647 (tt0)
REVERT: D  108 GLU cc_start: 0.8823 (tm-30) cc_final: 0.8485 (tm-30)
REVERT: D  118 LYS cc_start: 0.8751 (OUTLIER) cc_final: 0.8392 (tptp)
  outliers start: 25
  outliers final: 7
  residues processed: 64
  average time/residue: 0.5891
  time to fit residues: 39.5391
Evaluate side-chains
  50 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 41
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 MET
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   50 LEU
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  381 LEU
Chi-restraints excluded: chain A residue  389 ILE
Chi-restraints excluded: chain A residue  507 HIS
Chi-restraints excluded: chain D residue   22 GLN
Chi-restraints excluded: chain D residue  118 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 45 optimal weight:    4.9990
   chunk 32 optimal weight:    0.7980
   chunk 64 optimal weight:   20.0000
   chunk 1 optimal weight:    0.9980
   chunk 66 optimal weight:   50.0000
   chunk 8 optimal weight:    0.9980
   chunk 84 optimal weight:   10.0000
   chunk 53 optimal weight:    8.9990
   chunk 14 optimal weight:    0.8980
   chunk 73 optimal weight:    0.0570
   chunk 58 optimal weight:   30.0000
   overall best weight:    0.7498

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

Flipped N/Q/H residues before XYZ refinement:
C  26 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.076630 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3046 r_free = 0.3046 target = 0.053527 restraints weight = 44350.642|
|-----------------------------------------------------------------------------|
r_work (start): 0.2976 rms_B_bonded: 4.79
r_work (final): 0.2976
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2974
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2974 r_free = 0.2974    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2974 r_free = 0.2974    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2974
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8167
moved from start:          0.1273

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   6712  Z= 0.110
  Angle     :  0.690  41.894   9109  Z= 0.307
  Chirality :  0.040   0.213   1063
  Planarity :  0.003   0.048   1144
  Dihedral  :  8.202  83.467   1088
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 3.79
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.71 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 26.62 %
    Favored  : 70.99 %
  Cbeta Deviations :  0.24 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.47 (0.29), residues: 893
  helix:  3.28 (0.26), residues: 403
  sheet:  1.59 (0.38), residues: 208
  loop : -0.93 (0.35), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG F   8 
 TYR   0.008   0.001   TYR A  64 
 PHE   0.009   0.001   PHE A  49 
 TRP   0.010   0.001   TRP D  69 
 HIS   0.004   0.001   HIS A 535 

Details of bonding type rmsd
  covalent geometry    : bond        0.00208 ( 6701)
  covalent geometry    : angle       0.69063 ( 9098)
  SS BOND              : bond        0.00280 (    4)
  SS BOND              : angle       0.49456 (    8)
  hydrogen bonds       : bond        0.05017 (  428)
  hydrogen bonds       : angle       3.89411 ( 1239)
  Misc. bond           : bond        0.00021 (    6)
  link_TRANS           : bond        0.00008 (    1)
  link_TRANS           : angle       0.48391 (    3)

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

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

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 48
  time to evaluate  : 0.236 
Fit side-chains
REVERT: A  112 MET cc_start: 0.7882 (ttm) cc_final: 0.7680 (tmm)
REVERT: C   98 MET cc_start: 0.8949 (ppp) cc_final: 0.8680 (ppp)
REVERT: D  108 GLU cc_start: 0.8811 (tm-30) cc_final: 0.8471 (tm-30)
REVERT: F    6 ARG cc_start: 0.7026 (mmm160) cc_final: 0.6766 (mmm-85)
  outliers start: 14
  outliers final: 8
  residues processed: 59
  average time/residue: 0.6280
  time to fit residues: 38.8319
Evaluate side-chains
  53 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 45
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 MET
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  381 LEU
Chi-restraints excluded: chain A residue  385 ILE
Chi-restraints excluded: chain A residue  507 HIS
Chi-restraints excluded: chain D residue   78 ILE
Chi-restraints excluded: chain D residue  136 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 81 optimal weight:   30.0000
   chunk 23 optimal weight:    6.9990
   chunk 16 optimal weight:    0.7980
   chunk 73 optimal weight:    4.9990
   chunk 86 optimal weight:   30.0000
   chunk 37 optimal weight:    3.9990
   chunk 18 optimal weight:   10.0000
   chunk 36 optimal weight:    4.9990
   chunk 78 optimal weight:    5.9990
   chunk 7 optimal weight:    6.9990
   chunk 24 optimal weight:    3.9990
   overall best weight:    3.7588

-------------------------------------------------------------------------------
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 = 0.3503 r_free = 0.3503 target = 0.072131 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2910 r_free = 0.2910 target = 0.048305 restraints weight = 44428.361|
|-----------------------------------------------------------------------------|
r_work (start): 0.2833 rms_B_bonded: 4.62
r_work: 0.2662 rms_B_bonded: 4.95 restraints_weight: 0.5000
r_work (final): 0.2662
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2663
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2663 r_free = 0.2663    target_work(ls_wunit_k1) = 0.041         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2663 r_free = 0.2663    target_work(ls_wunit_k1) = 0.041         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2663
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8394
moved from start:          0.1317

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053   6712  Z= 0.232
  Angle     :  0.754  41.818   9109  Z= 0.353
  Chirality :  0.043   0.180   1063
  Planarity :  0.004   0.047   1144
  Dihedral  :  8.588  84.393   1087
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 3.94
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.82 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  4.78 %
    Allowed  : 24.74 %
    Favored  : 70.48 %
  Cbeta Deviations :  0.24 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.28 (0.29), residues: 893
  helix:  3.00 (0.26), residues: 403
  sheet:  1.46 (0.38), residues: 214
  loop : -0.85 (0.36), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG F   8 
 TYR   0.010   0.001   TYR C 160 
 PHE   0.013   0.002   PHE A 459 
 TRP   0.009   0.001   TRP D  69 
 HIS   0.005   0.001   HIS A 535 

Details of bonding type rmsd
  covalent geometry    : bond        0.00537 ( 6701)
  covalent geometry    : angle       0.75430 ( 9098)
  SS BOND              : bond        0.00379 (    4)
  SS BOND              : angle       0.85321 (    8)
  hydrogen bonds       : bond        0.08186 (  428)
  hydrogen bonds       : angle       4.35755 ( 1239)
  Misc. bond           : bond        0.00031 (    6)
  link_TRANS           : bond        0.00027 (    1)
  link_TRANS           : angle       0.53145 (    3)

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

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

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 49
  time to evaluate  : 0.249 
Fit side-chains
REVERT: A  112 MET cc_start: 0.8013 (ttm) cc_final: 0.7609 (tmm)
REVERT: A  312 MET cc_start: 0.9402 (mmm) cc_final: 0.9161 (mmm)
REVERT: C   98 MET cc_start: 0.9273 (ppp) cc_final: 0.8994 (ppp)
REVERT: D  108 GLU cc_start: 0.9156 (tm-30) cc_final: 0.8782 (tm-30)
REVERT: D  118 LYS cc_start: 0.8968 (OUTLIER) cc_final: 0.8665 (tptp)
  outliers start: 28
  outliers final: 10
  residues processed: 69
  average time/residue: 0.6307
  time to fit residues: 45.5050
Evaluate side-chains
  58 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 47
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 MET
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  381 LEU
Chi-restraints excluded: chain A residue  385 ILE
Chi-restraints excluded: chain A residue  389 ILE
Chi-restraints excluded: chain A residue  507 HIS
Chi-restraints excluded: chain C residue   25 THR
Chi-restraints excluded: chain D residue  118 LYS
Chi-restraints excluded: chain D residue  136 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 33 optimal weight:    0.0870
   chunk 60 optimal weight:    9.9990
   chunk 31 optimal weight:    0.9990
   chunk 38 optimal weight:    2.9990
   chunk 36 optimal weight:    7.9990
   chunk 22 optimal weight:    0.9980
   chunk 6 optimal weight:    2.9990
   chunk 20 optimal weight:    0.8980
   chunk 21 optimal weight:    3.9990
   chunk 72 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9990
   overall best weight:    0.7962

-------------------------------------------------------------------------------
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 = 0.3571 r_free = 0.3571 target = 0.075633 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3013 r_free = 0.3013 target = 0.052236 restraints weight = 47685.918|
|-----------------------------------------------------------------------------|
r_work (start): 0.2938 rms_B_bonded: 4.90
r_work (final): 0.2938
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2940
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2940 r_free = 0.2940    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2940 r_free = 0.2940    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2940
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8200
moved from start:          0.1403

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   6712  Z= 0.118
  Angle     :  0.714  41.859   9109  Z= 0.319
  Chirality :  0.040   0.223   1063
  Planarity :  0.003   0.047   1144
  Dihedral  :  8.094  80.900   1087
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 4.10
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.93 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 26.28 %
    Favored  : 71.16 %
  Cbeta Deviations :  0.24 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.45 (0.30), residues: 893
  helix:  3.25 (0.26), residues: 403
  sheet:  1.50 (0.38), residues: 208
  loop : -0.84 (0.36), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG F   8 
 TYR   0.008   0.001   TYR C 160 
 PHE   0.009   0.001   PHE A 295 
 TRP   0.010   0.001   TRP D  69 
 HIS   0.004   0.001   HIS A 535 

Details of bonding type rmsd
  covalent geometry    : bond        0.00225 ( 6701)
  covalent geometry    : angle       0.71428 ( 9098)
  SS BOND              : bond        0.00688 (    4)
  SS BOND              : angle       0.67995 (    8)
  hydrogen bonds       : bond        0.05431 (  428)
  hydrogen bonds       : angle       3.88921 ( 1239)
  Misc. bond           : bond        0.00034 (    6)
  link_TRANS           : bond        0.00092 (    1)
  link_TRANS           : angle       0.54823 (    3)

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

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

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 52
  time to evaluate  : 0.150 
Fit side-chains
REVERT: A  111 MET cc_start: 0.8130 (ttt) cc_final: 0.7784 (ttt)
REVERT: A  112 MET cc_start: 0.7704 (ttm) cc_final: 0.7427 (tmm)
REVERT: A  486 GLU cc_start: 0.8469 (pt0) cc_final: 0.8240 (pp20)
REVERT: D  108 GLU cc_start: 0.8885 (tm-30) cc_final: 0.8547 (tm-30)
  outliers start: 15
  outliers final: 7
  residues processed: 62
  average time/residue: 0.6625
  time to fit residues: 42.8558
Evaluate side-chains
  54 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 47
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 MET
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  381 LEU
Chi-restraints excluded: chain A residue  385 ILE
Chi-restraints excluded: chain A residue  507 HIS
Chi-restraints excluded: chain D residue  136 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 30 optimal weight:    0.9980
   chunk 64 optimal weight:   20.0000
   chunk 12 optimal weight:    2.9990
   chunk 76 optimal weight:    4.9990
   chunk 46 optimal weight:    0.0470
   chunk 69 optimal weight:    8.9990
   chunk 70 optimal weight:    1.9990
   chunk 15 optimal weight:    2.9990
   chunk 54 optimal weight:    5.9990
   chunk 9 optimal weight:    2.9990
   chunk 81 optimal weight:   30.0000
   overall best weight:    1.8084

-------------------------------------------------------------------------------
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 = 0.3549 r_free = 0.3549 target = 0.074341 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2972 r_free = 0.2972 target = 0.050566 restraints weight = 59544.382|
|-----------------------------------------------------------------------------|
r_work (start): 0.2899 rms_B_bonded: 5.39
r_work (final): 0.2899
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2897
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2897 r_free = 0.2897    target_work(ls_wunit_k1) = 0.049         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2897 r_free = 0.2897    target_work(ls_wunit_k1) = 0.049         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2897
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8233
moved from start:          0.1385

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6712  Z= 0.145
  Angle     :  0.755  41.835   9109  Z= 0.335
  Chirality :  0.041   0.198   1063
  Planarity :  0.003   0.047   1144
  Dihedral  :  8.068  79.448   1087
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 4.10
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.03 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 26.28 %
    Favored  : 70.82 %
  Cbeta Deviations :  0.24 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.43 (0.30), residues: 893
  helix:  3.18 (0.26), residues: 403
  sheet:  1.51 (0.38), residues: 208
  loop : -0.78 (0.36), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F   6 
 TYR   0.008   0.001   TYR C 160 
 PHE   0.011   0.001   PHE A 308 
 TRP   0.008   0.001   TRP D  69 
 HIS   0.004   0.001   HIS A 535 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 6701)
  covalent geometry    : angle       0.75483 ( 9098)
  SS BOND              : bond        0.00295 (    4)
  SS BOND              : angle       0.85585 (    8)
  hydrogen bonds       : bond        0.06109 (  428)
  hydrogen bonds       : angle       3.93756 ( 1239)
  Misc. bond           : bond        0.00025 (    6)
  link_TRANS           : bond        0.00184 (    1)
  link_TRANS           : angle       0.84220 (    3)

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

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

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 49
  time to evaluate  : 0.222 
Fit side-chains
REVERT: A  111 MET cc_start: 0.8203 (OUTLIER) cc_final: 0.8002 (ttt)
REVERT: A  112 MET cc_start: 0.7673 (ttm) cc_final: 0.7411 (tmm)
REVERT: A  486 GLU cc_start: 0.8492 (pt0) cc_final: 0.8217 (pp20)
REVERT: D   22 GLN cc_start: 0.8888 (OUTLIER) cc_final: 0.8621 (tt0)
REVERT: D  108 GLU cc_start: 0.8924 (tm-30) cc_final: 0.8550 (tm-30)
  outliers start: 17
  outliers final: 7
  residues processed: 62
  average time/residue: 0.5937
  time to fit residues: 38.6678
Evaluate side-chains
  55 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 46
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 MET
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue  111 MET
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  381 LEU
Chi-restraints excluded: chain A residue  385 ILE
Chi-restraints excluded: chain A residue  507 HIS
Chi-restraints excluded: chain D residue   22 GLN
Chi-restraints excluded: chain D residue  136 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 48 optimal weight:    7.9990
   chunk 18 optimal weight:    8.9990
   chunk 75 optimal weight:    1.9990
   chunk 13 optimal weight:    5.9990
   chunk 52 optimal weight:   10.0000
   chunk 73 optimal weight:    0.7980
   chunk 14 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9990
   chunk 19 optimal weight:    3.9990
   chunk 4 optimal weight:    9.9990
   chunk 22 optimal weight:    0.7980
   overall best weight:    1.1186

-------------------------------------------------------------------------------
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 = 0.3568 r_free = 0.3568 target = 0.075398 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.051881 restraints weight = 60934.232|
|-----------------------------------------------------------------------------|
r_work (start): 0.2930 rms_B_bonded: 5.46
r_work (final): 0.2930
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2929
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2929 r_free = 0.2929    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2929 r_free = 0.2929    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2929
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8202
moved from start:          0.1496

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6712  Z= 0.123
  Angle     :  0.741  41.848   9109  Z= 0.328
  Chirality :  0.040   0.212   1063
  Planarity :  0.003   0.049   1144
  Dihedral  :  7.878  77.999   1086
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 3.87
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.82 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 26.62 %
    Favored  : 70.99 %
  Cbeta Deviations :  0.24 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.49 (0.30), residues: 893
  helix:  3.25 (0.26), residues: 403
  sheet:  1.52 (0.38), residues: 208
  loop : -0.76 (0.36), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F   8 
 TYR   0.007   0.001   TYR C 111 
 PHE   0.011   0.001   PHE A 308 
 TRP   0.009   0.001   TRP D  69 
 HIS   0.004   0.001   HIS A 535 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 6701)
  covalent geometry    : angle       0.74107 ( 9098)
  SS BOND              : bond        0.00284 (    4)
  SS BOND              : angle       0.63740 (    8)
  hydrogen bonds       : bond        0.05485 (  428)
  hydrogen bonds       : angle       3.82715 ( 1239)
  Misc. bond           : bond        0.00028 (    6)
  link_TRANS           : bond        0.00032 (    1)
  link_TRANS           : angle       0.71209 (    3)

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

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

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 51
  time to evaluate  : 0.241 
Fit side-chains
REVERT: A  111 MET cc_start: 0.8028 (OUTLIER) cc_final: 0.7729 (ttt)
REVERT: A  486 GLU cc_start: 0.8422 (pt0) cc_final: 0.8198 (pp20)
REVERT: C  127 LYS cc_start: 0.9510 (mmmm) cc_final: 0.9125 (mmmm)
REVERT: D  108 GLU cc_start: 0.8890 (tm-30) cc_final: 0.8521 (tm-30)
REVERT: F    6 ARG cc_start: 0.6961 (tmt90) cc_final: 0.6680 (tmt90)
  outliers start: 14
  outliers final: 8
  residues processed: 62
  average time/residue: 0.6624
  time to fit residues: 42.9487
Evaluate side-chains
  56 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 47
  time to evaluate  : 0.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 MET
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue  109 ILE
Chi-restraints excluded: chain A residue  111 MET
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  381 LEU
Chi-restraints excluded: chain A residue  385 ILE
Chi-restraints excluded: chain A residue  507 HIS
Chi-restraints excluded: chain D residue  136 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 70 optimal weight:    6.9990
   chunk 42 optimal weight:    3.9990
   chunk 4 optimal weight:    0.0870
   chunk 52 optimal weight:   10.0000
   chunk 8 optimal weight:    5.9990
   chunk 57 optimal weight:   40.0000
   chunk 23 optimal weight:    3.9990
   chunk 26 optimal weight:    0.1980
   chunk 3 optimal weight:    0.9980
   chunk 85 optimal weight:   50.0000
   chunk 25 optimal weight:    2.9990
   overall best weight:    1.6562

-------------------------------------------------------------------------------
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 = 0.3556 r_free = 0.3556 target = 0.074514 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2994 r_free = 0.2994 target = 0.051479 restraints weight = 36989.383|
|-----------------------------------------------------------------------------|
r_work (start): 0.2930 rms_B_bonded: 4.34
r_work: 0.2771 rms_B_bonded: 4.74 restraints_weight: 0.5000
r_work (final): 0.2771
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2769
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2769 r_free = 0.2769    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2769 r_free = 0.2769    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2769
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8313
moved from start:          0.1505

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   6712  Z= 0.145
  Angle     :  0.782  41.847   9109  Z= 0.348
  Chirality :  0.041   0.207   1063
  Planarity :  0.003   0.049   1144
  Dihedral  :  7.985  77.700   1086
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 3.87
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.03 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 26.79 %
    Favored  : 70.65 %
  Cbeta Deviations :  0.24 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.44 (0.29), residues: 893
  helix:  3.17 (0.26), residues: 403
  sheet:  1.51 (0.38), residues: 208
  loop : -0.74 (0.36), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG F   8 
 TYR   0.008   0.001   TYR C  69 
 PHE   0.012   0.001   PHE A 324 
 TRP   0.008   0.001   TRP D  69 
 HIS   0.004   0.001   HIS A 535 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 6701)
  covalent geometry    : angle       0.77870 ( 9098)
  SS BOND              : bond        0.00293 (    4)
  SS BOND              : angle       2.42417 (    8)
  hydrogen bonds       : bond        0.05937 (  428)
  hydrogen bonds       : angle       3.90594 ( 1239)
  Misc. bond           : bond        0.00037 (    6)
  link_TRANS           : bond        0.00175 (    1)
  link_TRANS           : angle       0.73626 (    3)

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

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

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 49
  time to evaluate  : 0.248 
Fit side-chains
REVERT: A  111 MET cc_start: 0.8282 (OUTLIER) cc_final: 0.7966 (ttt)
REVERT: A  486 GLU cc_start: 0.8825 (OUTLIER) cc_final: 0.8452 (pp20)
REVERT: C  127 LYS cc_start: 0.9494 (mmmm) cc_final: 0.9090 (mmmm)
REVERT: D   22 GLN cc_start: 0.8937 (OUTLIER) cc_final: 0.8724 (tt0)
REVERT: D  108 GLU cc_start: 0.9123 (tm-30) cc_final: 0.8749 (tm-30)
  outliers start: 15
  outliers final: 9
  residues processed: 59
  average time/residue: 0.6526
  time to fit residues: 40.4121
Evaluate side-chains
  59 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 47
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 MET
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   50 LEU
Chi-restraints excluded: chain A residue  109 ILE
Chi-restraints excluded: chain A residue  111 MET
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  381 LEU
Chi-restraints excluded: chain A residue  385 ILE
Chi-restraints excluded: chain A residue  486 GLU
Chi-restraints excluded: chain A residue  507 HIS
Chi-restraints excluded: chain D residue   22 GLN
Chi-restraints excluded: chain D residue  136 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 57 optimal weight:   50.0000
   chunk 82 optimal weight:   40.0000
   chunk 5 optimal weight:    2.9990
   chunk 74 optimal weight:   10.0000
   chunk 53 optimal weight:    9.9990
   chunk 76 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9980
   chunk 4 optimal weight:    6.9990
   chunk 58 optimal weight:   20.0000
   chunk 46 optimal weight:    0.0170
   chunk 66 optimal weight:   50.0000
   overall best weight:    2.8024

-------------------------------------------------------------------------------
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 = 0.3519 r_free = 0.3519 target = 0.073077 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2933 r_free = 0.2933 target = 0.049040 restraints weight = 51540.983|
|-----------------------------------------------------------------------------|
r_work (start): 0.2851 rms_B_bonded: 4.96
r_work (final): 0.2851
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2852
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2852 r_free = 0.2852    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2852 r_free = 0.2852    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2852
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8310
moved from start:          0.1567

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   6712  Z= 0.192
  Angle     :  0.811  41.841   9109  Z= 0.367
  Chirality :  0.042   0.191   1063
  Planarity :  0.003   0.049   1144
  Dihedral  :  8.187  77.339   1086
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 4.10
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.71 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 27.13 %
    Favored  : 70.31 %
  Cbeta Deviations :  0.24 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.35 (0.29), residues: 893
  helix:  3.11 (0.26), residues: 402
  sheet:  1.42 (0.38), residues: 208
  loop : -0.75 (0.36), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG F   8 
 TYR   0.010   0.001   TYR C 160 
 PHE   0.011   0.001   PHE A 459 
 TRP   0.008   0.001   TRP A 299 
 HIS   0.006   0.001   HIS A 535 

Details of bonding type rmsd
  covalent geometry    : bond        0.00440 ( 6701)
  covalent geometry    : angle       0.80944 ( 9098)
  SS BOND              : bond        0.00328 (    4)
  SS BOND              : angle       1.90958 (    8)
  hydrogen bonds       : bond        0.07274 (  428)
  hydrogen bonds       : angle       4.14259 ( 1239)
  Misc. bond           : bond        0.00052 (    6)
  link_TRANS           : bond        0.00096 (    1)
  link_TRANS           : angle       0.86416 (    3)

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

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

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 48
  time to evaluate  : 0.236 
Fit side-chains
REVERT: A  111 MET cc_start: 0.8143 (OUTLIER) cc_final: 0.7797 (ttt)
REVERT: A  312 MET cc_start: 0.9258 (tpp) cc_final: 0.8892 (mmm)
REVERT: C  127 LYS cc_start: 0.9485 (mmmm) cc_final: 0.9071 (mmmm)
REVERT: D   22 GLN cc_start: 0.8883 (OUTLIER) cc_final: 0.8626 (tt0)
REVERT: D  108 GLU cc_start: 0.8893 (tm-30) cc_final: 0.8541 (tm-30)
  outliers start: 15
  outliers final: 8
  residues processed: 56
  average time/residue: 0.7100
  time to fit residues: 41.5129
Evaluate side-chains
  55 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 45
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 MET
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue  111 MET
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  381 LEU
Chi-restraints excluded: chain A residue  385 ILE
Chi-restraints excluded: chain A residue  388 VAL
Chi-restraints excluded: chain A residue  507 HIS
Chi-restraints excluded: chain D residue   22 GLN
Chi-restraints excluded: chain D residue  136 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 46 optimal weight:    4.9990
   chunk 70 optimal weight:    7.9990
   chunk 21 optimal weight:    0.4980
   chunk 24 optimal weight:    5.9990
   chunk 43 optimal weight:    0.9980
   chunk 86 optimal weight:   50.0000
   chunk 59 optimal weight:    0.3980
   chunk 45 optimal weight:    0.3980
   chunk 37 optimal weight:    0.9980
   chunk 26 optimal weight:    2.9990
   chunk 22 optimal weight:    0.7980
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 = 0.3586 r_free = 0.3586 target = 0.076325 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.053020 restraints weight = 49920.083|
|-----------------------------------------------------------------------------|
r_work (start): 0.2964 rms_B_bonded: 5.03
r_work (final): 0.2964
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2963
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2963 r_free = 0.2963    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2963 r_free = 0.2963    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2963
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8176
moved from start:          0.1764

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   6712  Z= 0.121
  Angle     :  0.781  41.861   9109  Z= 0.344
  Chirality :  0.041   0.249   1063
  Planarity :  0.003   0.050   1144
  Dihedral  :  7.938  78.511   1086
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 3.94
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.60 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  : 28.50 %
    Favored  : 70.48 %
  Cbeta Deviations :  0.24 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.53 (0.30), residues: 893
  helix:  3.28 (0.26), residues: 403
  sheet:  1.53 (0.38), residues: 208
  loop : -0.73 (0.37), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG F   8 
 TYR   0.007   0.001   TYR A  64 
 PHE   0.010   0.001   PHE A 295 
 TRP   0.012   0.001   TRP D  69 
 HIS   0.003   0.001   HIS A 535 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 6701)
  covalent geometry    : angle       0.77969 ( 9098)
  SS BOND              : bond        0.00270 (    4)
  SS BOND              : angle       1.49929 (    8)
  hydrogen bonds       : bond        0.04980 (  428)
  hydrogen bonds       : angle       3.80839 ( 1239)
  Misc. bond           : bond        0.00056 (    6)
  link_TRANS           : bond        0.00059 (    1)
  link_TRANS           : angle       0.73099 (    3)

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

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

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 49
  time to evaluate  : 0.231 
Fit side-chains
REVERT: A  111 MET cc_start: 0.8113 (OUTLIER) cc_final: 0.7745 (ttt)
REVERT: A  486 GLU cc_start: 0.8464 (pt0) cc_final: 0.8264 (pp20)
REVERT: A  488 GLU cc_start: 0.8949 (mt-10) cc_final: 0.8350 (mp0)
REVERT: C  127 LYS cc_start: 0.9497 (mmmm) cc_final: 0.9098 (mmmm)
REVERT: D  108 GLU cc_start: 0.8891 (tm-30) cc_final: 0.8555 (tm-30)
  outliers start: 6
  outliers final: 6
  residues processed: 53
  average time/residue: 0.6886
  time to fit residues: 38.1498
Evaluate side-chains
  54 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 47
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 MET
Chi-restraints excluded: chain A residue  109 ILE
Chi-restraints excluded: chain A residue  111 MET
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  381 LEU
Chi-restraints excluded: chain A residue  385 ILE
Chi-restraints excluded: chain A residue  507 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 35 optimal weight:    0.0060
   chunk 68 optimal weight:    3.9990
   chunk 39 optimal weight:    5.9990
   chunk 61 optimal weight:   50.0000
   chunk 81 optimal weight:   20.0000
   chunk 2 optimal weight:    0.9980
   chunk 66 optimal weight:   50.0000
   chunk 34 optimal weight:   30.0000
   chunk 82 optimal weight:   40.0000
   chunk 79 optimal weight:    4.9990
   chunk 38 optimal weight:    0.3980
   overall best weight:    2.0800

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

Flipped N/Q/H residues before XYZ refinement:
A 100 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.074009 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2988 r_free = 0.2988 target = 0.051380 restraints weight = 27545.841|
|-----------------------------------------------------------------------------|
r_work (start): 0.2928 rms_B_bonded: 3.78
r_work: 0.2777 rms_B_bonded: 4.32 restraints_weight: 0.5000
r_work (final): 0.2777
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2776
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2776 r_free = 0.2776    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2776 r_free = 0.2776    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2776
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8319
moved from start:          0.1608

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   6712  Z= 0.160
  Angle     :  0.796  41.850   9109  Z= 0.356
  Chirality :  0.041   0.203   1063
  Planarity :  0.003   0.049   1144
  Dihedral  :  8.032  78.289   1086
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 4.10
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.26 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 27.65 %
    Favored  : 70.65 %
  Cbeta Deviations :  0.24 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.43 (0.30), residues: 893
  helix:  3.19 (0.26), residues: 403
  sheet:  1.31 (0.38), residues: 216
  loop : -0.68 (0.37), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG F   8 
 TYR   0.008   0.001   TYR C  69 
 PHE   0.010   0.001   PHE A 295 
 TRP   0.007   0.001   TRP D  69 
 HIS   0.004   0.001   HIS A 535 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 ( 6701)
  covalent geometry    : angle       0.79461 ( 9098)
  SS BOND              : bond        0.00292 (    4)
  SS BOND              : angle       1.59597 (    8)
  hydrogen bonds       : bond        0.06293 (  428)
  hydrogen bonds       : angle       3.96864 ( 1239)
  Misc. bond           : bond        0.00048 (    6)
  link_TRANS           : bond        0.00054 (    1)
  link_TRANS           : angle       0.68715 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2217.80 seconds
wall clock time: 38 minutes 22.82 seconds (2302.82 seconds total)