Starting phenix.real_space_refine
on Tue Mar  3 20:16:40 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7e8f_31017/03_2026/7e8f_31017.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7e8f_31017/03_2026/7e8f_31017.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.18
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7e8f_31017/03_2026/7e8f_31017.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7e8f_31017/03_2026/7e8f_31017.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7e8f_31017/03_2026/7e8f_31017.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7e8f_31017/03_2026/7e8f_31017.map"
  }
  resolution = 3.18
  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=   0.001 sd=   0.009
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: 4
    Type Number    sf(0)   Gaussians
     S      37      5.16       5
     C    5569      2.51       5
     N    1468      2.21       5
     O    1694      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 26 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: 8768
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 2079
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 258, 2079
          Classifications: {'peptide': 258}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 14, 'TRANS': 243}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 18
          Unresolved non-hydrogen angles: 24
          Unresolved non-hydrogen dihedrals: 19
          Planarities with less than four sites: {'ARG:plan': 1, 'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 14
    Chain: "H"
      Number of atoms: 938
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 124, 938
          Classifications: {'peptide': 124}
          Link IDs: {'PTRANS': 2, 'TRANS': 121}
    Chain: "L"
      Number of atoms: 780
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 105, 780
          Classifications: {'peptide': 105}
          Link IDs: {'PTRANS': 7, 'TRANS': 97}
    Chain: "C"
      Number of atoms: 944
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 124, 944
          Classifications: {'peptide': 124}
          Link IDs: {'PTRANS': 2, 'TRANS': 121}
    Chain: "B"
      Number of atoms: 852
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 112, 852
          Classifications: {'peptide': 112}
          Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 103}
    Chain: "D"
      Number of atoms: 874
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 116, 874
          Classifications: {'peptide': 116}
          Link IDs: {'PTRANS': 3, 'TRANS': 112}
    Chain: "E"
      Number of atoms: 803
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 803
          Classifications: {'peptide': 106}
          Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100}
    Chain: "R"
      Number of atoms: 1498
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 189, 1498
          Classifications: {'peptide': 189}
          Link IDs: {'PTRANS': 9, 'TRANS': 179}
          Chain breaks: 1
  Time building chain proxies: 1.96, per 1000 atoms: 0.22
  Number of scatterers: 8768
  At special positions: 0
  Unit cell: (133.604, 78.9, 99.94, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      37     16.00
     O    1694      8.00
     N    1468      7.00
     C    5569      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=12, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  15 " - pdb=" SG  CYS A 136 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 131 " - pdb=" SG  CYS A 166 " distance=2.04
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  22 " - pdb=" SG  CYS L  87 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  96 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B  23 " - pdb=" SG  CYS B  93 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D  22 " - pdb=" SG  CYS D  95 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  23 " - pdb=" SG  CYS E  88 " distance=2.04
    Simple disulfide: pdb=" SG  CYS R 336 " - pdb=" SG  CYS R 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 379 " - pdb=" SG  CYS R 432 " distance=2.06
    Simple disulfide: pdb=" SG  CYS R 391 " - pdb=" SG  CYS R 525 " distance=2.04
    Simple disulfide: pdb=" SG  CYS R 480 " - pdb=" SG  CYS R 488 " 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 custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.54
  Conformation dependent library (CDL) restraints added in 293.7 milliseconds
  

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2052

  Finding SS restraints...
    Secondary structure from input PDB file:
      12 helices and 26 sheets defined
      5.7% alpha, 42.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.36
  Creating SS restraints...
    Processing helix  chain 'H' and resid 27 through 32
      removed outlier: 3.546A  pdb=" N   SER H  30 " --> pdb=" O   PHE H  27 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 87 through 91
    Processing helix  chain 'H' and resid 103 through 108
      removed outlier: 4.672A  pdb=" N   SER H 108 " --> pdb=" O   SER H 104 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 26 through 30
      removed outlier: 3.582A  pdb=" N   ASP L  29 " --> pdb=" O   LYS L  26 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 78 through 82
      removed outlier: 3.900A  pdb=" N   GLU L  82 " --> pdb=" O   ALA L  79 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 28 through 32
    Processing helix  chain 'D' and resid 86 through 90
      removed outlier: 3.783A  pdb=" N   THR D  90 " --> pdb=" O   ALA D  87 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 50 through 52
      No H-bonds generated for 'chain 'E' and resid 50 through 52'
    Processing helix  chain 'R' and resid 365 through 370
      removed outlier: 3.797A  pdb=" N   ASN R 370 " --> pdb=" O   SER R 366 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 405 through 410
      removed outlier: 4.567A  pdb=" N   ARG R 408 " --> pdb=" O   ASP R 405 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 416 through 422
    Processing helix  chain 'R' and resid 438 through 443
      removed outlier: 3.526A  pdb=" N   SER R 443 " --> pdb=" O   ASN R 439 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31
      removed outlier: 4.458A  pdb=" N   ALA A  27 " --> pdb=" O   TRP A  64 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   SER A  60 " --> pdb=" O   SER A  31 " (cutoff:3.500A)
      removed outlier: 8.509A  pdb=" N   ASN A  61 " --> pdb=" O   TYR A 269 " (cutoff:3.500A)
      removed outlier: 6.496A  pdb=" N   TYR A 269 " --> pdb=" O   ASN A  61 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   THR A  63 " --> pdb=" O   VAL A 267 " (cutoff:3.500A)
      removed outlier: 5.770A  pdb=" N   PHE A 201 " --> pdb=" O   ASP A 228 " (cutoff:3.500A)
      removed outlier: 4.311A  pdb=" N   ASP A 228 " --> pdb=" O   PHE A 201 " (cutoff:3.500A)
      removed outlier: 7.012A  pdb=" N   ILE A 203 " --> pdb=" O   LEU A 226 " (cutoff:3.500A)
      removed outlier: 7.540A  pdb=" N   HIS A 207 " --> pdb=" O   ALA A 222 " (cutoff:3.500A)
      removed outlier: 9.392A  pdb=" N   ALA A 222 " --> pdb=" O   HIS A 207 " (cutoff:3.500A)
      removed outlier: 6.514A  pdb=" N   VAL A  36 " --> pdb=" O   LEU A 223 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55
      removed outlier: 7.004A  pdb=" N   LYS A 278 " --> pdb=" O   THR A 286 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85
    Processing sheet with id=AA4, first strand: chain 'A' and resid 154 through 160
      removed outlier: 9.840A  pdb=" N   SER A 155 " --> pdb=" O   PHE A 140 " (cutoff:3.500A)
      removed outlier: 11.101A  pdb=" N   PHE A 140 " --> pdb=" O   SER A 155 " (cutoff:3.500A)
      removed outlier: 10.282A  pdb=" N   PHE A 157 " --> pdb=" O   ASP A 138 " (cutoff:3.500A)
      removed outlier: 11.113A  pdb=" N   ASP A 138 " --> pdb=" O   PHE A 157 " (cutoff:3.500A)
      removed outlier: 7.368A  pdb=" N   VAL A 159 " --> pdb=" O   CYS A 136 " (cutoff:3.500A)
      removed outlier: 9.241A  pdb=" N   THR A 240 " --> pdb=" O   ASN A 137 " (cutoff:3.500A)
      removed outlier: 4.416A  pdb=" N   LEU A 242 " --> pdb=" O   PRO A 139 " (cutoff:3.500A)
      removed outlier: 4.745A  pdb=" N   ARG A 246 " --> pdb=" O   VAL A 143 " (cutoff:3.500A)
      removed outlier: 6.191A  pdb=" N   LEU A 241 " --> pdb=" O   ARG A 102 " (cutoff:3.500A)
      removed outlier: 6.155A  pdb=" N   ARG A 102 " --> pdb=" O   ASN A 121 " (cutoff:3.500A)
      removed outlier: 4.252A  pdb=" N   PHE A 168 " --> pdb=" O   VAL A 130 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 154 through 160
      removed outlier: 9.840A  pdb=" N   SER A 155 " --> pdb=" O   PHE A 140 " (cutoff:3.500A)
      removed outlier: 11.101A  pdb=" N   PHE A 140 " --> pdb=" O   SER A 155 " (cutoff:3.500A)
      removed outlier: 10.282A  pdb=" N   PHE A 157 " --> pdb=" O   ASP A 138 " (cutoff:3.500A)
      removed outlier: 11.113A  pdb=" N   ASP A 138 " --> pdb=" O   PHE A 157 " (cutoff:3.500A)
      removed outlier: 7.368A  pdb=" N   VAL A 159 " --> pdb=" O   CYS A 136 " (cutoff:3.500A)
      removed outlier: 9.241A  pdb=" N   THR A 240 " --> pdb=" O   ASN A 137 " (cutoff:3.500A)
      removed outlier: 4.416A  pdb=" N   LEU A 242 " --> pdb=" O   PRO A 139 " (cutoff:3.500A)
      removed outlier: 4.745A  pdb=" N   ARG A 246 " --> pdb=" O   VAL A 143 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'H' and resid 4 through 7
    Processing sheet with id=AA7, first strand: chain 'H' and resid 11 through 12
      removed outlier: 6.664A  pdb=" N   MET H  34 " --> pdb=" O   SER H  50 " (cutoff:3.500A)
      removed outlier: 4.448A  pdb=" N   SER H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 6.660A  pdb=" N   TRP H  36 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'H' and resid 11 through 12
      removed outlier: 4.039A  pdb=" N   VAL H 114 " --> pdb=" O   THR H  98 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'L' and resid 9 through 12
      removed outlier: 6.838A  pdb=" N   VAL L  10 " --> pdb=" O   THR L 104 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   ALA L  83 " --> pdb=" O   LEU L 103 " (cutoff:3.500A)
      removed outlier: 6.072A  pdb=" N   GLN L  36 " --> pdb=" O   LEU L  45 " (cutoff:3.500A)
      removed outlier: 5.462A  pdb=" N   LEU L  45 " --> pdb=" O   GLN L  36 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'L' and resid 9 through 12
      removed outlier: 6.838A  pdb=" N   VAL L  10 " --> pdb=" O   THR L 104 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   ALA L  83 " --> pdb=" O   LEU L 103 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'L' and resid 18 through 23
    Processing sheet with id=AB3, first strand: chain 'C' and resid 3 through 7
      removed outlier: 3.587A  pdb=" N   SER C  21 " --> pdb=" O   SER C   7 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 11 through 12
      removed outlier: 5.871A  pdb=" N   ARG C  38 " --> pdb=" O   TRP C  47 " (cutoff:3.500A)
      removed outlier: 5.313A  pdb=" N   TRP C  47 " --> pdb=" O   ARG C  38 " (cutoff:3.500A)
      removed outlier: 7.600A  pdb=" N   ALA C  40 " --> pdb=" O   LEU C  45 " (cutoff:3.500A)
      removed outlier: 6.659A  pdb=" N   LEU C  45 " --> pdb=" O   ALA C  40 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 11 through 12
      removed outlier: 6.807A  pdb=" N   CYS C  96 " --> pdb=" O   TRP C 115 " (cutoff:3.500A)
      removed outlier: 4.610A  pdb=" N   TRP C 115 " --> pdb=" O   CYS C  96 " (cutoff:3.500A)
      removed outlier: 6.691A  pdb=" N   LYS C  98 " --> pdb=" O   ASP C 113 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'B' and resid 4 through 7
    Processing sheet with id=AB7, first strand: chain 'B' and resid 10 through 13
      removed outlier: 3.514A  pdb=" N   GLU B 110 " --> pdb=" O   LEU B  11 " (cutoff:3.500A)
      removed outlier: 6.468A  pdb=" N   LEU B  38 " --> pdb=" O   TYR B  54 " (cutoff:3.500A)
      removed outlier: 4.650A  pdb=" N   TYR B  54 " --> pdb=" O   LEU B  38 " (cutoff:3.500A)
      removed outlier: 6.532A  pdb=" N   TRP B  40 " --> pdb=" O   LEU B  52 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'D' and resid 3 through 7
    Processing sheet with id=AB9, first strand: chain 'D' and resid 11 through 12
    Processing sheet with id=AC1, first strand: chain 'D' and resid 57 through 59
      removed outlier: 6.496A  pdb=" N   TRP D  36 " --> pdb=" O   VAL D  48 " (cutoff:3.500A)
      removed outlier: 4.482A  pdb=" N   VAL D  50 " --> pdb=" O   MET D  34 " (cutoff:3.500A)
      removed outlier: 6.761A  pdb=" N   MET D  34 " --> pdb=" O   VAL D  50 " (cutoff:3.500A)
      removed outlier: 4.040A  pdb=" N   TYR D  33 " --> pdb=" O   ASP D  98 " (cutoff:3.500A)
      removed outlier: 4.423A  pdb=" N   VAL D 106 " --> pdb=" O   ARG D  97 " (cutoff:3.500A)
      removed outlier: 7.264A  pdb=" N   LEU D  99 " --> pdb=" O   MET D 104 " (cutoff:3.500A)
      removed outlier: 7.611A  pdb=" N   MET D 104 " --> pdb=" O   LEU D  99 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'D' and resid 57 through 59
      removed outlier: 6.496A  pdb=" N   TRP D  36 " --> pdb=" O   VAL D  48 " (cutoff:3.500A)
      removed outlier: 4.482A  pdb=" N   VAL D  50 " --> pdb=" O   MET D  34 " (cutoff:3.500A)
      removed outlier: 6.761A  pdb=" N   MET D  34 " --> pdb=" O   VAL D  50 " (cutoff:3.500A)
      removed outlier: 4.040A  pdb=" N   TYR D  33 " --> pdb=" O   ASP D  98 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'E' and resid 5 through 7
    Processing sheet with id=AC4, first strand: chain 'E' and resid 10 through 13
      removed outlier: 3.578A  pdb=" N   LEU E  11 " --> pdb=" O   LYS E 103 " (cutoff:3.500A)
      removed outlier: 7.074A  pdb=" N   LEU E  33 " --> pdb=" O   TYR E  49 " (cutoff:3.500A)
      removed outlier: 5.107A  pdb=" N   TYR E  49 " --> pdb=" O   LEU E  33 " (cutoff:3.500A)
      removed outlier: 6.469A  pdb=" N   TRP E  35 " --> pdb=" O   LEU E  47 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'R' and resid 354 through 358
      removed outlier: 3.515A  pdb=" N   LYS R 378 " --> pdb=" O   VAL R 433 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'R' and resid 361 through 362
      removed outlier: 6.707A  pdb=" N   CYS R 361 " --> pdb=" O   CYS R 525 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AC6
    Processing sheet with id=AC7, first strand: chain 'R' and resid 452 through 454
    Processing sheet with id=AC8, first strand: chain 'R' and resid 473 through 474

    326 hydrogen bonds defined for protein.
    801 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: 1.32

  Time building geometry restraints manager: 0.76 seconds

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

  Histogram of bond lengths:
        1.22 -     1.35: 2807
        1.35 -     1.48: 2512
        1.48 -     1.61: 3611
        1.61 -     1.74: 0
        1.74 -     1.87: 49
  Bond restraints: 8979
  Sorted by residual:
  bond pdb=" CB  CYS R 379 "
       pdb=" SG  CYS R 379 "
    ideal  model  delta    sigma   weight residual
    1.808  1.873 -0.065 3.30e-02 9.18e+02 3.84e+00
  bond pdb=" CA  CYS A 166 "
       pdb=" CB  CYS A 166 "
    ideal  model  delta    sigma   weight residual
    1.536  1.500  0.036 2.08e-02 2.31e+03 3.03e+00
  bond pdb=" CB  PRO L   8 "
       pdb=" CG  PRO L   8 "
    ideal  model  delta    sigma   weight residual
    1.492  1.579 -0.087 5.00e-02 4.00e+02 3.01e+00
  bond pdb=" C   GLN B  47 "
       pdb=" N   SER B  48 "
    ideal  model  delta    sigma   weight residual
    1.340  1.258  0.082 5.87e-02 2.90e+02 1.95e+00
  bond pdb=" CG  LEU R 461 "
       pdb=" CD1 LEU R 461 "
    ideal  model  delta    sigma   weight residual
    1.521  1.476  0.045 3.30e-02 9.18e+02 1.86e+00
  ... (remaining 8974 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.22: 12007
        2.22 -     4.44: 168
        4.44 -     6.65: 17
        6.65 -     8.87: 3
        8.87 -    11.09: 2
  Bond angle restraints: 12197
  Sorted by residual:
  angle pdb=" CA  CYS R 432 "
        pdb=" CB  CYS R 432 "
        pdb=" SG  CYS R 432 "
      ideal   model   delta    sigma   weight residual
     114.40  125.49  -11.09 2.30e+00 1.89e-01 2.32e+01
  angle pdb=" CA  PRO L   8 "
        pdb=" N   PRO L   8 "
        pdb=" CD  PRO L   8 "
      ideal   model   delta    sigma   weight residual
     112.00  105.50    6.50 1.40e+00 5.10e-01 2.16e+01
  angle pdb=" CA  CYS A 166 "
        pdb=" CB  CYS A 166 "
        pdb=" SG  CYS A 166 "
      ideal   model   delta    sigma   weight residual
     114.40  124.20   -9.80 2.30e+00 1.89e-01 1.82e+01
  angle pdb=" C   ILE E  29 "
        pdb=" N   SER E  30 "
        pdb=" CA  SER E  30 "
      ideal   model   delta    sigma   weight residual
     121.54  128.44   -6.90 1.91e+00 2.74e-01 1.31e+01
  angle pdb=" N   SER E  30 "
        pdb=" CA  SER E  30 "
        pdb=" C   SER E  30 "
      ideal   model   delta    sigma   weight residual
     110.80  118.40   -7.60 2.13e+00 2.20e-01 1.27e+01
  ... (remaining 12192 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.09: 4761
       18.09 -    36.19: 418
       36.19 -    54.28: 64
       54.28 -    72.38: 9
       72.38 -    90.47: 7
  Dihedral angle restraints: 5259
    sinusoidal: 2015
      harmonic: 3244
  Sorted by residual:
  dihedral pdb=" CA  HIS B  31 "
           pdb=" C   HIS B  31 "
           pdb=" N   SER B  32 "
           pdb=" CA  SER B  32 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  143.72   36.28     0      5.00e+00 4.00e-02 5.27e+01
  dihedral pdb=" CB  CYS R 379 "
           pdb=" SG  CYS R 379 "
           pdb=" SG  CYS R 432 "
           pdb=" CB  CYS R 432 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   42.44   50.56     1      1.00e+01 1.00e-02 3.50e+01
  dihedral pdb=" CB  CYS A 131 "
           pdb=" SG  CYS A 131 "
           pdb=" SG  CYS A 166 "
           pdb=" CB  CYS A 166 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   45.01   47.99     1      1.00e+01 1.00e-02 3.17e+01
  ... (remaining 5256 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 958
       0.045 -    0.089: 273
       0.089 -    0.134: 92
       0.134 -    0.178: 3
       0.178 -    0.223: 3
  Chirality restraints: 1329
  Sorted by residual:
  chirality pdb=" CA  CYS A 166 "
            pdb=" N   CYS A 166 "
            pdb=" C   CYS A 166 "
            pdb=" CB  CYS A 166 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.24e+00
  chirality pdb=" CA  CYS R 432 "
            pdb=" N   CYS R 432 "
            pdb=" C   CYS R 432 "
            pdb=" CB  CYS R 432 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.07e+00
  chirality pdb=" CA  THR B  99 "
            pdb=" N   THR B  99 "
            pdb=" C   THR B  99 "
            pdb=" CB  THR B  99 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.35    0.18 2.00e-01 2.50e+01 8.03e-01
  ... (remaining 1326 not shown)

  Planarity restraints: 1569
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO L   7 "   -0.085 5.00e-02 4.00e+02   1.26e-01 2.54e+01
        pdb=" N   PRO L   8 "    0.218 5.00e-02 4.00e+02
        pdb=" CA  PRO L   8 "   -0.066 5.00e-02 4.00e+02
        pdb=" CD  PRO L   8 "   -0.066 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR B  14 "   -0.046 5.00e-02 4.00e+02   6.92e-02 7.65e+00
        pdb=" N   PRO B  15 "    0.120 5.00e-02 4.00e+02
        pdb=" CA  PRO B  15 "   -0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO B  15 "   -0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE R 347 "    0.017 2.00e-02 2.50e+03   1.72e-02 5.15e+00
        pdb=" CG  PHE R 347 "   -0.039 2.00e-02 2.50e+03
        pdb=" CD1 PHE R 347 "    0.013 2.00e-02 2.50e+03
        pdb=" CD2 PHE R 347 "    0.002 2.00e-02 2.50e+03
        pdb=" CE1 PHE R 347 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 PHE R 347 "    0.008 2.00e-02 2.50e+03
        pdb=" CZ  PHE R 347 "    0.001 2.00e-02 2.50e+03
  ... (remaining 1566 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 313
        2.71 -     3.25: 8172
        3.25 -     3.80: 13819
        3.80 -     4.35: 18791
        4.35 -     4.90: 31839
  Nonbonded interactions: 72934
  Sorted by model distance:
  nonbonded pdb=" OH  TYR C 107 "
            pdb=" OG  SER B  32 "
     model   vdw
     2.157 3.040
  nonbonded pdb=" OG  SER E  30 "
            pdb=" OE1 GLN R 498 "
     model   vdw
     2.170 3.040
  nonbonded pdb=" OE1 GLN L  36 "
            pdb=" OH  TYR L  85 "
     model   vdw
     2.186 3.040
  nonbonded pdb=" OH  TYR A  37 "
            pdb=" O   LEU A  54 "
     model   vdw
     2.205 3.040
  nonbonded pdb=" OH  TYR A 144 "
            pdb=" OE2 GLU A 156 "
     model   vdw
     2.207 3.040
  ... (remaining 72929 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=1.00 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:             0.360
  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:          0.130
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     8.780
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  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:1.080
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.450
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7798
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      :  0.005   0.087   8991  Z= 0.210
  Angle     :  0.689  11.089  12221  Z= 0.380
  Chirality :  0.046   0.223   1329
  Planarity :  0.005   0.126   1569
  Dihedral  : 13.858  90.470   3171
  Min Nonbonded Distance : 2.157

Molprobity Statistics.
  All-atom Clashscore : 8.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.55 %
    Favored  : 92.45 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.52 %
    Favored  : 99.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -1.64 (0.24), residues: 1112
  helix: -4.20 (0.58), residues: 27
  sheet: -0.58 (0.25), residues: 419
  loop : -1.30 (0.23), residues: 666

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG R 357 
 TYR   0.014   0.002   TYR R 505 
 PHE   0.039   0.002   PHE R 347 
 TRP   0.013   0.002   TRP C  47 
 HIS   0.005   0.001   HIS B  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00509 ( 8979)
  covalent geometry    : angle       0.68175 (12197)
  SS BOND              : bond        0.00959 (   12)
  SS BOND              : angle       2.36864 (   24)
  hydrogen bonds       : bond        0.23546 (  297)
  hydrogen bonds       : angle      10.09327 (  801)

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

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

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 164
  time to evaluate  : 0.317 
Fit side-chains
REVERT: H   56 SER cc_start: 0.8477 (p) cc_final: 0.8251 (p)
REVERT: D   19 ARG cc_start: 0.7236 (ttp-170) cc_final: 0.6939 (ttp-170)
REVERT: D   61 ASP cc_start: 0.7102 (m-30) cc_final: 0.6892 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 164
  average time/residue: 0.1002
  time to fit residues: 22.3650
Evaluate side-chains
  142 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 142
  time to evaluate  : 0.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 108 optimal weight:    6.9990
   chunk 49 optimal weight:    4.9990
   chunk 97 optimal weight:    3.9990
   chunk 53 optimal weight:    8.9990
   chunk 5 optimal weight:    7.9990
   chunk 33 optimal weight:    7.9990
   chunk 65 optimal weight:   10.0000
   chunk 62 optimal weight:    7.9990
   chunk 51 optimal weight:    0.9990
   chunk 100 optimal weight:    4.9990
   chunk 106 optimal weight:    4.9990
   overall best weight:    3.9990

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

Flipped N/Q/H residues before XYZ refinement:
A 207 HIS
H  99 ASN
E  90 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.114948 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2946 r_free = 0.2946 target = 0.095765 restraints weight = 10775.674|
|-----------------------------------------------------------------------------|
r_work (start): 0.2951 rms_B_bonded: 1.53
r_work: 0.2837 rms_B_bonded: 1.89 restraints_weight: 0.5000
r_work: 0.2708 rms_B_bonded: 3.13 restraints_weight: 0.2500
r_work (final): 0.2708
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7926
moved from start:          0.0889

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.099   8991  Z= 0.263
  Angle     :  0.734  12.020  12221  Z= 0.389
  Chirality :  0.048   0.216   1329
  Planarity :  0.005   0.079   1569
  Dihedral  :  5.998  39.914   1241
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 7.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.27 %
    Favored  : 91.73 %
  Rotamer:
    Outliers :  0.84 %
    Allowed  :  7.32 %
    Favored  : 91.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -1.53 (0.25), residues: 1112
  helix: -4.49 (0.42), residues: 33
  sheet: -0.47 (0.24), residues: 453
  loop : -1.21 (0.24), residues: 626

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C  72 
 TYR   0.017   0.002   TYR R 505 
 PHE   0.036   0.002   PHE A  79 
 TRP   0.016   0.002   TRP C  47 
 HIS   0.005   0.002   HIS A 207 

Details of bonding type rmsd
  covalent geometry    : bond        0.00633 ( 8979)
  covalent geometry    : angle       0.72785 (12197)
  SS BOND              : bond        0.00915 (   12)
  SS BOND              : angle       2.25689 (   24)
  hydrogen bonds       : bond        0.04976 (  297)
  hydrogen bonds       : angle       6.87372 (  801)

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

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

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 148
  time to evaluate  : 0.317 
Fit side-chains
REVERT: D   19 ARG cc_start: 0.7359 (ttp-170) cc_final: 0.7003 (ttp-170)
REVERT: D   61 ASP cc_start: 0.7998 (m-30) cc_final: 0.7489 (p0)
REVERT: R  444 LYS cc_start: 0.8226 (ttmt) cc_final: 0.7853 (ttmt)
  outliers start: 8
  outliers final: 5
  residues processed: 154
  average time/residue: 0.0920
  time to fit residues: 19.2396
Evaluate side-chains
  146 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 141
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue  100 ILE
Chi-restraints excluded: chain A residue  172 SER
Chi-restraints excluded: chain L residue  104 THR
Chi-restraints excluded: chain C residue   69 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 55 optimal weight:    0.9990
   chunk 13 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 92 optimal weight:    0.5980
   chunk 62 optimal weight:    7.9990
   chunk 39 optimal weight:    3.9990
   chunk 34 optimal weight:    9.9990
   chunk 49 optimal weight:    2.9990
   chunk 77 optimal weight:    1.9990
   chunk 35 optimal weight:    0.8980
   chunk 74 optimal weight:    0.8980
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
B   6 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.118907 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3006 r_free = 0.3006 target = 0.099969 restraints weight = 10671.750|
|-----------------------------------------------------------------------------|
r_work (start): 0.3014 rms_B_bonded: 1.54
r_work: 0.2896 rms_B_bonded: 1.95 restraints_weight: 0.5000
r_work: 0.2764 rms_B_bonded: 3.23 restraints_weight: 0.2500
r_work (final): 0.2764
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7862
moved from start:          0.1339

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8991  Z= 0.120
  Angle     :  0.581  10.132  12221  Z= 0.309
  Chirality :  0.044   0.201   1329
  Planarity :  0.004   0.065   1569
  Dihedral  :  5.252  36.210   1241
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 7.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.21 %
    Favored  : 93.79 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  : 10.46 %
    Favored  : 88.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -1.13 (0.25), residues: 1112
  helix: -5.18 (0.18), residues: 26
  sheet: -0.06 (0.25), residues: 440
  loop : -1.04 (0.24), residues: 646

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C  19 
 TYR   0.013   0.001   TYR A 265 
 PHE   0.017   0.001   PHE A  79 
 TRP   0.011   0.001   TRP C  47 
 HIS   0.004   0.001   HIS B  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 8979)
  covalent geometry    : angle       0.57520 (12197)
  SS BOND              : bond        0.00630 (   12)
  SS BOND              : angle       1.90240 (   24)
  hydrogen bonds       : bond        0.03457 (  297)
  hydrogen bonds       : angle       5.93564 (  801)

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

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

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 170
  time to evaluate  : 0.306 
Fit side-chains
REVERT: C   77 ASN cc_start: 0.8321 (m110) cc_final: 0.8044 (m110)
REVERT: D   12 ILE cc_start: 0.6658 (tp) cc_final: 0.6341 (mt)
REVERT: D   19 ARG cc_start: 0.7378 (ttp-170) cc_final: 0.6974 (ttp-170)
REVERT: E   31 SER cc_start: 0.7951 (m) cc_final: 0.7433 (p)
REVERT: R  444 LYS cc_start: 0.8237 (ttmt) cc_final: 0.7853 (ttmt)
  outliers start: 10
  outliers final: 5
  residues processed: 178
  average time/residue: 0.0909
  time to fit residues: 22.0393
Evaluate side-chains
  158 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 153
  time to evaluate  : 0.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue  104 THR
Chi-restraints excluded: chain C residue    7 SER
Chi-restraints excluded: chain C residue   69 THR
Chi-restraints excluded: chain E residue    7 SER
Chi-restraints excluded: chain R residue  382 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 42 optimal weight:    8.9990
   chunk 38 optimal weight:    7.9990
   chunk 28 optimal weight:    9.9990
   chunk 56 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 1 optimal weight:    8.9990
   chunk 72 optimal weight:    2.9990
   chunk 74 optimal weight:    0.7980
   chunk 32 optimal weight:    6.9990
   chunk 57 optimal weight:    0.9980
   chunk 48 optimal weight:    0.4980
   overall best weight:    2.4584

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

Flipped N/Q/H residues before XYZ refinement:
A 207 HIS
A 218 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.117431 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2979 r_free = 0.2979 target = 0.098072 restraints weight = 10880.896|
|-----------------------------------------------------------------------------|
r_work (start): 0.3004 rms_B_bonded: 1.58
r_work: 0.2892 rms_B_bonded: 1.94 restraints_weight: 0.5000
r_work: 0.2756 rms_B_bonded: 3.28 restraints_weight: 0.2500
r_work (final): 0.2756
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7916
moved from start:          0.1381

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.064   8991  Z= 0.177
  Angle     :  0.638  12.505  12221  Z= 0.336
  Chirality :  0.045   0.244   1329
  Planarity :  0.004   0.061   1569
  Dihedral  :  5.366  36.993   1241
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 7.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.01 %
    Favored  : 92.99 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 12.24 %
    Favored  : 85.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -1.06 (0.25), residues: 1112
  helix: -4.66 (0.32), residues: 33
  sheet: -0.02 (0.25), residues: 443
  loop : -0.96 (0.25), residues: 636

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG R 346 
 TYR   0.015   0.002   TYR R 505 
 PHE   0.021   0.002   PHE H  29 
 TRP   0.013   0.002   TRP C  47 
 HIS   0.005   0.001   HIS A 207 

Details of bonding type rmsd
  covalent geometry    : bond        0.00420 ( 8979)
  covalent geometry    : angle       0.62575 (12197)
  SS BOND              : bond        0.00651 (   12)
  SS BOND              : angle       2.85368 (   24)
  hydrogen bonds       : bond        0.03526 (  297)
  hydrogen bonds       : angle       5.87038 (  801)

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

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

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 155
  time to evaluate  : 0.325 
Fit side-chains
REVERT: H   89 GLU cc_start: 0.7049 (pm20) cc_final: 0.6840 (pm20)
REVERT: D   19 ARG cc_start: 0.7168 (ttp-170) cc_final: 0.6910 (ttp-170)
REVERT: E   31 SER cc_start: 0.7930 (m) cc_final: 0.7375 (p)
REVERT: R  408 ARG cc_start: 0.7851 (ttp80) cc_final: 0.7573 (ptm-80)
REVERT: R  444 LYS cc_start: 0.8257 (ttmt) cc_final: 0.7852 (ttmt)
  outliers start: 19
  outliers final: 12
  residues processed: 168
  average time/residue: 0.0952
  time to fit residues: 21.9313
Evaluate side-chains
  164 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 152
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue  100 ILE
Chi-restraints excluded: chain A residue  172 SER
Chi-restraints excluded: chain L residue  104 THR
Chi-restraints excluded: chain C residue    7 SER
Chi-restraints excluded: chain C residue   69 THR
Chi-restraints excluded: chain D residue   21 SER
Chi-restraints excluded: chain D residue   35 THR
Chi-restraints excluded: chain E residue    7 SER
Chi-restraints excluded: chain E residue   95 LEU
Chi-restraints excluded: chain R residue  382 VAL
Chi-restraints excluded: chain R residue  503 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 34 optimal weight:    5.9990
   chunk 76 optimal weight:    4.9990
   chunk 52 optimal weight:    0.7980
   chunk 53 optimal weight:    0.8980
   chunk 88 optimal weight:    7.9990
   chunk 91 optimal weight:   10.0000
   chunk 58 optimal weight:    5.9990
   chunk 48 optimal weight:    6.9990
   chunk 95 optimal weight:    5.9990
   chunk 8 optimal weight:    6.9990
   overall best weight:    3.3386

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

Flipped N/Q/H residues before XYZ refinement:
A 207 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.115786 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2957 r_free = 0.2957 target = 0.096388 restraints weight = 10866.158|
|-----------------------------------------------------------------------------|
r_work (start): 0.3005 rms_B_bonded: 1.57
r_work: 0.2894 rms_B_bonded: 1.92 restraints_weight: 0.5000
r_work: 0.2758 rms_B_bonded: 3.24 restraints_weight: 0.2500
r_work (final): 0.2758
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7942
moved from start:          0.1408

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.084   8991  Z= 0.221
  Angle     :  0.680  11.915  12221  Z= 0.356
  Chirality :  0.047   0.266   1329
  Planarity :  0.004   0.059   1569
  Dihedral  :  5.615  37.783   1241
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 6.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.01 %
    Favored  : 92.99 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 12.87 %
    Favored  : 84.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -1.14 (0.25), residues: 1112
  helix: -4.66 (0.34), residues: 33
  sheet: -0.11 (0.25), residues: 444
  loop : -0.99 (0.24), residues: 635

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG R 346 
 TYR   0.015   0.002   TYR B  37 
 PHE   0.024   0.002   PHE A  79 
 TRP   0.015   0.002   TRP C  47 
 HIS   0.006   0.001   HIS A 207 

Details of bonding type rmsd
  covalent geometry    : bond        0.00531 ( 8979)
  covalent geometry    : angle       0.66818 (12197)
  SS BOND              : bond        0.00806 (   12)
  SS BOND              : angle       2.87819 (   24)
  hydrogen bonds       : bond        0.03678 (  297)
  hydrogen bonds       : angle       5.97222 (  801)

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

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

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 149
  time to evaluate  : 0.336 
Fit side-chains
REVERT: A  290 ASP cc_start: 0.5855 (OUTLIER) cc_final: 0.5314 (t0)
REVERT: H   46 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7980 (tt0)
REVERT: H   89 GLU cc_start: 0.7194 (pm20) cc_final: 0.6988 (pm20)
REVERT: D   61 ASP cc_start: 0.7967 (m-30) cc_final: 0.7469 (p0)
REVERT: E   31 SER cc_start: 0.8141 (m) cc_final: 0.7550 (p)
REVERT: R  408 ARG cc_start: 0.7901 (ttp80) cc_final: 0.7626 (ptm-80)
REVERT: R  444 LYS cc_start: 0.8170 (ttmt) cc_final: 0.7756 (ttmt)
  outliers start: 25
  outliers final: 13
  residues processed: 166
  average time/residue: 0.0937
  time to fit residues: 21.4101
Evaluate side-chains
  159 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 144
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue   47 VAL
Chi-restraints excluded: chain A residue  100 ILE
Chi-restraints excluded: chain A residue  172 SER
Chi-restraints excluded: chain A residue  290 ASP
Chi-restraints excluded: chain H residue   46 GLU
Chi-restraints excluded: chain L residue  104 THR
Chi-restraints excluded: chain C residue    7 SER
Chi-restraints excluded: chain C residue   69 THR
Chi-restraints excluded: chain D residue   35 THR
Chi-restraints excluded: chain D residue  102 TYR
Chi-restraints excluded: chain E residue    7 SER
Chi-restraints excluded: chain E residue   33 LEU
Chi-restraints excluded: chain R residue  382 VAL
Chi-restraints excluded: chain R residue  503 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 57 optimal weight:    7.9990
   chunk 19 optimal weight:    0.9980
   chunk 86 optimal weight:    3.9990
   chunk 71 optimal weight:    3.9990
   chunk 12 optimal weight:    0.7980
   chunk 1 optimal weight:    8.9990
   chunk 53 optimal weight:    8.9990
   chunk 5 optimal weight:    6.9990
   chunk 92 optimal weight:    0.9980
   chunk 97 optimal weight:    0.9980
   chunk 45 optimal weight:    8.9990
   overall best weight:    1.5582

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

Flipped N/Q/H residues before XYZ refinement:
A 207 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.118222 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2993 r_free = 0.2993 target = 0.098996 restraints weight = 10809.322|
|-----------------------------------------------------------------------------|
r_work (start): 0.3045 rms_B_bonded: 1.55
r_work: 0.2930 rms_B_bonded: 1.95 restraints_weight: 0.5000
r_work: 0.2796 rms_B_bonded: 3.27 restraints_weight: 0.2500
r_work (final): 0.2796
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7905
moved from start:          0.1597

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   8991  Z= 0.134
  Angle     :  0.606  12.939  12221  Z= 0.319
  Chirality :  0.044   0.282   1329
  Planarity :  0.004   0.055   1569
  Dihedral  :  5.242  35.947   1241
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 7.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.38 %
    Favored  : 93.62 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 14.23 %
    Favored  : 84.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.97 (0.25), residues: 1112
  helix: -5.05 (0.21), residues: 26
  sheet:  0.04 (0.25), residues: 444
  loop : -0.93 (0.24), residues: 642

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG R 357 
 TYR   0.013   0.001   TYR A 265 
 PHE   0.017   0.001   PHE H  29 
 TRP   0.012   0.001   TRP C  47 
 HIS   0.005   0.001   HIS A 207 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 8979)
  covalent geometry    : angle       0.59453 (12197)
  SS BOND              : bond        0.00678 (   12)
  SS BOND              : angle       2.66843 (   24)
  hydrogen bonds       : bond        0.03127 (  297)
  hydrogen bonds       : angle       5.65953 (  801)

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

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

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 151
  time to evaluate  : 0.316 
Fit side-chains
REVERT: H   89 GLU cc_start: 0.7191 (pm20) cc_final: 0.6983 (pm20)
REVERT: C   77 ASN cc_start: 0.8301 (m110) cc_final: 0.8050 (m110)
REVERT: D   19 ARG cc_start: 0.7014 (ttp-170) cc_final: 0.6774 (ttp-170)
REVERT: E   31 SER cc_start: 0.7768 (m) cc_final: 0.7221 (p)
REVERT: R  444 LYS cc_start: 0.8261 (ttmt) cc_final: 0.7851 (ttmt)
  outliers start: 17
  outliers final: 11
  residues processed: 163
  average time/residue: 0.0929
  time to fit residues: 20.8277
Evaluate side-chains
  157 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 146
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue  100 ILE
Chi-restraints excluded: chain A residue  172 SER
Chi-restraints excluded: chain L residue  104 THR
Chi-restraints excluded: chain C residue    7 SER
Chi-restraints excluded: chain C residue   69 THR
Chi-restraints excluded: chain D residue   35 THR
Chi-restraints excluded: chain D residue  102 TYR
Chi-restraints excluded: chain E residue    7 SER
Chi-restraints excluded: chain E residue   95 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 34 optimal weight:    9.9990
   chunk 56 optimal weight:    3.9990
   chunk 92 optimal weight:    2.9990
   chunk 43 optimal weight:    9.9990
   chunk 95 optimal weight:    6.9990
   chunk 7 optimal weight:    7.9990
   chunk 103 optimal weight:    1.9990
   chunk 77 optimal weight:    4.9990
   chunk 14 optimal weight:    8.9990
   chunk 20 optimal weight:    7.9990
   chunk 69 optimal weight:    0.3980
   overall best weight:    2.8788

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

Flipped N/Q/H residues before XYZ refinement:
A 207 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.116774 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2972 r_free = 0.2972 target = 0.097462 restraints weight = 10868.383|
|-----------------------------------------------------------------------------|
r_work (start): 0.3004 rms_B_bonded: 1.58
r_work: 0.2890 rms_B_bonded: 1.93 restraints_weight: 0.5000
r_work: 0.2754 rms_B_bonded: 3.26 restraints_weight: 0.2500
r_work (final): 0.2754
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7923
moved from start:          0.1578

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.073   8991  Z= 0.195
  Angle     :  0.655  12.924  12221  Z= 0.344
  Chirality :  0.046   0.296   1329
  Planarity :  0.004   0.035   1569
  Dihedral  :  5.466  37.087   1241
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 7.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.01 %
    Favored  : 92.99 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 14.02 %
    Favored  : 83.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -1.00 (0.25), residues: 1112
  helix: -5.06 (0.21), residues: 26
  sheet:  0.07 (0.25), residues: 436
  loop : -0.98 (0.24), residues: 650

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG R 346 
 TYR   0.016   0.002   TYR R 505 
 PHE   0.022   0.002   PHE H  29 
 TRP   0.013   0.002   TRP C  47 
 HIS   0.008   0.002   HIS A 207 

Details of bonding type rmsd
  covalent geometry    : bond        0.00465 ( 8979)
  covalent geometry    : angle       0.64007 (12197)
  SS BOND              : bond        0.00848 (   12)
  SS BOND              : angle       3.24800 (   24)
  hydrogen bonds       : bond        0.03413 (  297)
  hydrogen bonds       : angle       5.79751 (  801)

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

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

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 148
  time to evaluate  : 0.191 
Fit side-chains
REVERT: H   46 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7837 (tt0)
REVERT: H   89 GLU cc_start: 0.7205 (pm20) cc_final: 0.6992 (pm20)
REVERT: E   31 SER cc_start: 0.7840 (m) cc_final: 0.7251 (p)
REVERT: R  364 ASP cc_start: 0.7436 (OUTLIER) cc_final: 0.6924 (m-30)
REVERT: R  444 LYS cc_start: 0.8223 (ttmt) cc_final: 0.7817 (ttmt)
  outliers start: 28
  outliers final: 19
  residues processed: 169
  average time/residue: 0.0882
  time to fit residues: 20.5368
Evaluate side-chains
  167 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 146
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue   47 VAL
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue  100 ILE
Chi-restraints excluded: chain A residue  109 THR
Chi-restraints excluded: chain A residue  172 SER
Chi-restraints excluded: chain A residue  250 THR
Chi-restraints excluded: chain A residue  290 ASP
Chi-restraints excluded: chain H residue   46 GLU
Chi-restraints excluded: chain L residue  104 THR
Chi-restraints excluded: chain C residue    7 SER
Chi-restraints excluded: chain C residue   69 THR
Chi-restraints excluded: chain D residue   35 THR
Chi-restraints excluded: chain D residue  102 TYR
Chi-restraints excluded: chain E residue    7 SER
Chi-restraints excluded: chain E residue   30 SER
Chi-restraints excluded: chain E residue   33 LEU
Chi-restraints excluded: chain R residue  364 ASP
Chi-restraints excluded: chain R residue  382 VAL
Chi-restraints excluded: chain R residue  385 THR
Chi-restraints excluded: chain R residue  503 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 96 optimal weight:    6.9990
   chunk 57 optimal weight:    8.9990
   chunk 28 optimal weight:    4.9990
   chunk 69 optimal weight:    9.9990
   chunk 87 optimal weight:    8.9990
   chunk 107 optimal weight:    0.0870
   chunk 6 optimal weight:    2.9990
   chunk 18 optimal weight:    3.9990
   chunk 11 optimal weight:    3.9990
   chunk 81 optimal weight:    5.9990
   chunk 49 optimal weight:    5.9990
   overall best weight:    3.2166

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

Flipped N/Q/H residues before XYZ refinement:
A 173 GLN
A 207 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.116656 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2968 r_free = 0.2968 target = 0.097156 restraints weight = 10799.668|
|-----------------------------------------------------------------------------|
r_work (start): 0.3002 rms_B_bonded: 1.59
r_work: 0.2890 rms_B_bonded: 1.95 restraints_weight: 0.5000
r_work: 0.2756 rms_B_bonded: 3.27 restraints_weight: 0.2500
r_work (final): 0.2756
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7929
moved from start:          0.1595

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.081   8991  Z= 0.213
  Angle     :  0.681  13.938  12221  Z= 0.355
  Chirality :  0.047   0.317   1329
  Planarity :  0.004   0.035   1569
  Dihedral  :  5.641  37.433   1241
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 7.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.83 %
    Favored  : 93.17 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 14.12 %
    Favored  : 82.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -1.05 (0.25), residues: 1112
  helix: -5.07 (0.21), residues: 26
  sheet:  0.03 (0.25), residues: 445
  loop : -1.03 (0.24), residues: 641

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG R 346 
 TYR   0.017   0.002   TYR R 489 
 PHE   0.022   0.002   PHE H  29 
 TRP   0.013   0.002   TRP C  47 
 HIS   0.008   0.002   HIS A 207 

Details of bonding type rmsd
  covalent geometry    : bond        0.00512 ( 8979)
  covalent geometry    : angle       0.66833 (12197)
  SS BOND              : bond        0.00867 (   12)
  SS BOND              : angle       3.07742 (   24)
  hydrogen bonds       : bond        0.03483 (  297)
  hydrogen bonds       : angle       5.88482 (  801)

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

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

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 153
  time to evaluate  : 0.337 
Fit side-chains
REVERT: A  207 HIS cc_start: 0.7464 (m-70) cc_final: 0.7220 (m-70)
REVERT: H   46 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7812 (tt0)
REVERT: H   89 GLU cc_start: 0.7222 (pm20) cc_final: 0.6996 (pm20)
REVERT: C   76 LYS cc_start: 0.8375 (mtpt) cc_final: 0.8129 (mtpt)
REVERT: C   77 ASN cc_start: 0.8326 (m110) cc_final: 0.8056 (m110)
REVERT: B   22 SER cc_start: 0.7927 (t) cc_final: 0.7721 (m)
REVERT: D   61 ASP cc_start: 0.7989 (m-30) cc_final: 0.7479 (p0)
REVERT: E   31 SER cc_start: 0.7925 (m) cc_final: 0.7348 (p)
REVERT: R  364 ASP cc_start: 0.7395 (OUTLIER) cc_final: 0.6888 (m-30)
REVERT: R  444 LYS cc_start: 0.8145 (ttmt) cc_final: 0.7720 (ttmt)
REVERT: R  478 THR cc_start: 0.7673 (m) cc_final: 0.7170 (p)
  outliers start: 30
  outliers final: 21
  residues processed: 174
  average time/residue: 0.0867
  time to fit residues: 21.1256
Evaluate side-chains
  171 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 148
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue   47 VAL
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue  100 ILE
Chi-restraints excluded: chain A residue  109 THR
Chi-restraints excluded: chain A residue  172 SER
Chi-restraints excluded: chain A residue  250 THR
Chi-restraints excluded: chain A residue  290 ASP
Chi-restraints excluded: chain H residue   46 GLU
Chi-restraints excluded: chain H residue   53 SER
Chi-restraints excluded: chain L residue  104 THR
Chi-restraints excluded: chain C residue    7 SER
Chi-restraints excluded: chain C residue   69 THR
Chi-restraints excluded: chain D residue   35 THR
Chi-restraints excluded: chain D residue  102 TYR
Chi-restraints excluded: chain E residue    7 SER
Chi-restraints excluded: chain E residue   30 SER
Chi-restraints excluded: chain E residue   33 LEU
Chi-restraints excluded: chain R residue  347 PHE
Chi-restraints excluded: chain R residue  364 ASP
Chi-restraints excluded: chain R residue  382 VAL
Chi-restraints excluded: chain R residue  385 THR
Chi-restraints excluded: chain R residue  503 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 86 optimal weight:    6.9990
   chunk 15 optimal weight:    4.9990
   chunk 6 optimal weight:    3.9990
   chunk 51 optimal weight:    7.9990
   chunk 43 optimal weight:   10.0000
   chunk 89 optimal weight:    4.9990
   chunk 97 optimal weight:    6.9990
   chunk 20 optimal weight:    1.9990
   chunk 67 optimal weight:    7.9990
   chunk 108 optimal weight:    0.9990
   chunk 9 optimal weight:    1.9990
   overall best weight:    2.7990

-------------------------------------------------------------------------------
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 = 0.3233 r_free = 0.3233 target = 0.116907 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2973 r_free = 0.2973 target = 0.097491 restraints weight = 10784.876|
|-----------------------------------------------------------------------------|
r_work (start): 0.3020 rms_B_bonded: 1.59
r_work: 0.2906 rms_B_bonded: 1.95 restraints_weight: 0.5000
r_work: 0.2773 rms_B_bonded: 3.26 restraints_weight: 0.2500
r_work (final): 0.2773
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7923
moved from start:          0.1656

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.074   8991  Z= 0.193
  Angle     :  0.669  14.307  12221  Z= 0.349
  Chirality :  0.046   0.314   1329
  Planarity :  0.004   0.041   1569
  Dihedral  :  5.618  37.477   1241
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 7.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.83 %
    Favored  : 93.17 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 14.54 %
    Favored  : 82.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -1.04 (0.25), residues: 1112
  helix: -5.06 (0.21), residues: 26
  sheet:  0.04 (0.25), residues: 443
  loop : -1.02 (0.24), residues: 643

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG R 357 
 TYR   0.014   0.002   TYR R 505 
 PHE   0.021   0.002   PHE H  29 
 TRP   0.014   0.002   TRP C  47 
 HIS   0.005   0.001   HIS B  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00461 ( 8979)
  covalent geometry    : angle       0.65606 (12197)
  SS BOND              : bond        0.00845 (   12)
  SS BOND              : angle       3.05289 (   24)
  hydrogen bonds       : bond        0.03356 (  297)
  hydrogen bonds       : angle       5.85004 (  801)

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

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

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 150
  time to evaluate  : 0.330 
Fit side-chains
REVERT: H   89 GLU cc_start: 0.7226 (pm20) cc_final: 0.7006 (pm20)
REVERT: C   77 ASN cc_start: 0.8341 (m110) cc_final: 0.8071 (m110)
REVERT: B   22 SER cc_start: 0.7927 (t) cc_final: 0.7703 (m)
REVERT: E   31 SER cc_start: 0.7830 (m) cc_final: 0.7223 (p)
REVERT: R  364 ASP cc_start: 0.7391 (OUTLIER) cc_final: 0.6896 (m-30)
REVERT: R  444 LYS cc_start: 0.8245 (ttmt) cc_final: 0.7851 (ttmt)
REVERT: R  478 THR cc_start: 0.7702 (m) cc_final: 0.7286 (p)
  outliers start: 28
  outliers final: 22
  residues processed: 172
  average time/residue: 0.0840
  time to fit residues: 20.1614
Evaluate side-chains
  173 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 150
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue  100 ILE
Chi-restraints excluded: chain A residue  109 THR
Chi-restraints excluded: chain A residue  172 SER
Chi-restraints excluded: chain A residue  250 THR
Chi-restraints excluded: chain A residue  290 ASP
Chi-restraints excluded: chain H residue   53 SER
Chi-restraints excluded: chain L residue  104 THR
Chi-restraints excluded: chain C residue    7 SER
Chi-restraints excluded: chain C residue   69 THR
Chi-restraints excluded: chain D residue   35 THR
Chi-restraints excluded: chain D residue  102 TYR
Chi-restraints excluded: chain E residue    7 SER
Chi-restraints excluded: chain E residue   26 SER
Chi-restraints excluded: chain E residue   33 LEU
Chi-restraints excluded: chain E residue   95 LEU
Chi-restraints excluded: chain R residue  347 PHE
Chi-restraints excluded: chain R residue  364 ASP
Chi-restraints excluded: chain R residue  382 VAL
Chi-restraints excluded: chain R residue  385 THR
Chi-restraints excluded: chain R residue  432 CYS
Chi-restraints excluded: chain R residue  503 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 102 optimal weight:    3.9990
   chunk 101 optimal weight:   10.0000
   chunk 54 optimal weight:    4.9990
   chunk 25 optimal weight:    8.9990
   chunk 86 optimal weight:    0.8980
   chunk 63 optimal weight:    3.9990
   chunk 103 optimal weight:    2.9990
   chunk 90 optimal weight:    9.9990
   chunk 14 optimal weight:    2.9990
   chunk 30 optimal weight:    5.9990
   chunk 66 optimal weight:    8.9990
   overall best weight:    2.9788

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

Flipped N/Q/H residues before XYZ refinement:
** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.116826 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2971 r_free = 0.2971 target = 0.097439 restraints weight = 10717.802|
|-----------------------------------------------------------------------------|
r_work (start): 0.3014 rms_B_bonded: 1.57
r_work: 0.2902 rms_B_bonded: 1.94 restraints_weight: 0.5000
r_work: 0.2769 rms_B_bonded: 3.24 restraints_weight: 0.2500
r_work (final): 0.2769
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7926
moved from start:          0.1673

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.077   8991  Z= 0.203
  Angle     :  0.680  14.374  12221  Z= 0.355
  Chirality :  0.047   0.319   1329
  Planarity :  0.004   0.051   1569
  Dihedral  :  5.690  37.934   1241
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 7.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.92 %
    Favored  : 93.08 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 14.85 %
    Favored  : 82.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -1.06 (0.25), residues: 1112
  helix: -5.07 (0.21), residues: 26
  sheet:  0.01 (0.25), residues: 449
  loop : -1.04 (0.24), residues: 637

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B  24 
 TYR   0.015   0.002   TYR R 505 
 PHE   0.022   0.002   PHE H  29 
 TRP   0.013   0.002   TRP C  47 
 HIS   0.006   0.001   HIS A 207 

Details of bonding type rmsd
  covalent geometry    : bond        0.00485 ( 8979)
  covalent geometry    : angle       0.66645 (12197)
  SS BOND              : bond        0.00864 (   12)
  SS BOND              : angle       3.10293 (   24)
  hydrogen bonds       : bond        0.03426 (  297)
  hydrogen bonds       : angle       5.87501 (  801)

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

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

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 150
  time to evaluate  : 0.313 
Fit side-chains
REVERT: H   89 GLU cc_start: 0.7223 (pm20) cc_final: 0.6997 (pm20)
REVERT: C   77 ASN cc_start: 0.8350 (m110) cc_final: 0.8060 (m110)
REVERT: B   22 SER cc_start: 0.7945 (t) cc_final: 0.7715 (m)
REVERT: E    5 THR cc_start: 0.8277 (m) cc_final: 0.7874 (p)
REVERT: E   31 SER cc_start: 0.7870 (m) cc_final: 0.7314 (p)
REVERT: R  334 ASN cc_start: 0.5174 (t0) cc_final: 0.4967 (m110)
REVERT: R  364 ASP cc_start: 0.7402 (OUTLIER) cc_final: 0.6896 (m-30)
REVERT: R  444 LYS cc_start: 0.8238 (ttmt) cc_final: 0.7847 (ttmt)
REVERT: R  478 THR cc_start: 0.7786 (m) cc_final: 0.7385 (p)
  outliers start: 25
  outliers final: 23
  residues processed: 167
  average time/residue: 0.0886
  time to fit residues: 20.7875
Evaluate side-chains
  173 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 149
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue   47 VAL
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue  100 ILE
Chi-restraints excluded: chain A residue  109 THR
Chi-restraints excluded: chain A residue  172 SER
Chi-restraints excluded: chain A residue  250 THR
Chi-restraints excluded: chain A residue  290 ASP
Chi-restraints excluded: chain H residue   53 SER
Chi-restraints excluded: chain L residue   42 SER
Chi-restraints excluded: chain L residue  104 THR
Chi-restraints excluded: chain C residue    7 SER
Chi-restraints excluded: chain C residue   69 THR
Chi-restraints excluded: chain B residue   13 VAL
Chi-restraints excluded: chain D residue   35 THR
Chi-restraints excluded: chain D residue  102 TYR
Chi-restraints excluded: chain E residue    7 SER
Chi-restraints excluded: chain E residue   33 LEU
Chi-restraints excluded: chain E residue   95 LEU
Chi-restraints excluded: chain R residue  347 PHE
Chi-restraints excluded: chain R residue  364 ASP
Chi-restraints excluded: chain R residue  385 THR
Chi-restraints excluded: chain R residue  432 CYS
Chi-restraints excluded: chain R residue  503 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 60 optimal weight:    0.0970
   chunk 35 optimal weight:    1.9990
   chunk 51 optimal weight:    5.9990
   chunk 90 optimal weight:    9.9990
   chunk 30 optimal weight:    5.9990
   chunk 68 optimal weight:    5.9990
   chunk 31 optimal weight:    0.0670
   chunk 6 optimal weight:    0.9980
   chunk 98 optimal weight:    2.9990
   chunk 19 optimal weight:    0.7980
   chunk 55 optimal weight:    1.9990
   overall best weight:    0.7918

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

Flipped N/Q/H residues before XYZ refinement:
A 121 ASN
** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.121475 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3044 r_free = 0.3044 target = 0.102547 restraints weight = 10705.484|
|-----------------------------------------------------------------------------|
r_work (start): 0.3106 rms_B_bonded: 1.58
r_work: 0.3001 rms_B_bonded: 1.90 restraints_weight: 0.5000
r_work: 0.2871 rms_B_bonded: 3.23 restraints_weight: 0.2500
r_work (final): 0.2871
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7855
moved from start:          0.2057

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   8991  Z= 0.105
  Angle     :  0.580  13.331  12221  Z= 0.304
  Chirality :  0.044   0.268   1329
  Planarity :  0.004   0.048   1569
  Dihedral  :  5.039  33.663   1241
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 7.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.21 %
    Favored  : 93.79 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 15.79 %
    Favored  : 82.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.89 (0.25), residues: 1112
  helix: -4.95 (0.26), residues: 26
  sheet:  0.20 (0.25), residues: 433
  loop : -0.95 (0.24), residues: 653

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG R 357 
 TYR   0.013   0.001   TYR A 265 
 PHE   0.012   0.001   PHE A 106 
 TRP   0.012   0.001   TRP C  47 
 HIS   0.004   0.001   HIS A 207 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 ( 8979)
  covalent geometry    : angle       0.56794 (12197)
  SS BOND              : bond        0.00505 (   12)
  SS BOND              : angle       2.68884 (   24)
  hydrogen bonds       : bond        0.02846 (  297)
  hydrogen bonds       : angle       5.40280 (  801)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2076.60 seconds
wall clock time: 36 minutes 15.97 seconds (2175.97 seconds total)