Starting phenix.real_space_refine
on Tue Feb  3 23:10:58 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9uym_64618/02_2026/9uym_64618.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9uym_64618/02_2026/9uym_64618.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9uym_64618/02_2026/9uym_64618.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9uym_64618/02_2026/9uym_64618.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9uym_64618/02_2026/9uym_64618.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9uym_64618/02_2026/9uym_64618.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.009 sd=   0.043
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       6      5.49       5
     S      26      5.16       5
     C    4948      2.51       5
     N    1267      2.21       5
     O    1334      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7581
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "L"
      Number of atoms: 565
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 85, 565
          Classifications: {'peptide': 85}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 31}
          Link IDs: {'PTRANS': 3, 'TRANS': 81}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 119
          Unresolved non-hydrogen angles: 147
          Unresolved non-hydrogen dihedrals: 97
          Unresolved non-hydrogen chiralities: 10
          Planarities with less than four sites: {'GLU:plan': 4, 'GLN:plan1': 3, 'ARG:plan': 4, 'HIS:plan': 2, 'ASP:plan': 1, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 67
    Chain: "B"
      Number of atoms: 703
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 703
          Classifications: {'peptide': 98}
          Incomplete info: {'truncation_to_alanine': 18}
          Link IDs: {'PTRANS': 2, 'TRANS': 95}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 56
          Unresolved non-hydrogen angles: 69
          Unresolved non-hydrogen dihedrals: 43
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 3, 'ASP:plan': 4}
          Unresolved non-hydrogen planarities: 36
    Chain: "C"
      Number of atoms: 1573
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 217, 1573
          Classifications: {'peptide': 217}
          Incomplete info: {'truncation_to_alanine': 34}
          Link IDs: {'PTRANS': 7, 'TRANS': 209}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 105
          Unresolved non-hydrogen angles: 126
          Unresolved non-hydrogen dihedrals: 89
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 2, 'GLU:plan': 2, 'PHE:plan': 1, 'ASN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 59
    Chain: "A"
      Number of atoms: 2341
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 315, 2341
          Classifications: {'peptide': 315}
          Incomplete info: {'truncation_to_alanine': 47}
          Link IDs: {'PTRANS': 23, 'TRANS': 291}
          Chain breaks: 6
          Unresolved non-hydrogen bonds: 185
          Unresolved non-hydrogen angles: 222
          Unresolved non-hydrogen dihedrals: 154
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ASP:plan': 11, 'ARG:plan': 5, 'GLU:plan': 8, 'GLN:plan1': 4, 'HIS:plan': 3, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 124
    Chain: "R"
      Number of atoms: 2364
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 299, 2364
          Classifications: {'peptide': 299}
          Incomplete info: {'truncation_to_alanine': 29}
          Link IDs: {'PTRANS': 10, 'TRANS': 288}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 123
          Unresolved non-hydrogen angles: 151
          Unresolved non-hydrogen dihedrals: 106
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 3, 'PHE:plan': 1, 'GLN:plan1': 2, 'ARG:plan': 3, 'HIS:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 1, 'TPO:plan-1': 2}
          Unresolved non-hydrogen planarities: 73
    Chain: "A"
      Number of atoms: 35
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 35
          Unusual residues: {'Y01': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.51, per 1000 atoms: 0.20
  Number of scatterers: 7581
  At special positions: 0
  Unit cell: (71.757, 112.455, 167.076, 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      26     16.00
     P       6     15.00
     O    1334      8.00
     N    1267      7.00
     C    4948      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS L  98 " - pdb=" SG  CYS L 117 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L 101 " - pdb=" SG  CYS L 135 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  95 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  24 " - pdb=" SG  CYS C  89 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 146 " - pdb=" SG  CYS C 220 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 110 " - pdb=" SG  CYS R 187 " 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: 0.72
  Conformation dependent library (CDL) restraints added in 270.0 milliseconds
  

  1912 Ramachandran restraints generated.
    956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1920

  Finding SS restraints...
    Secondary structure from input PDB file:
      17 helices and 15 sheets defined
      26.6% alpha, 26.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.26
  Creating SS restraints...
    Processing helix  chain 'L' and resid 24 through 40
      removed outlier: 3.632A  pdb=" N   HIS L  40 " --> pdb=" O   GLU L  36 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 134 through 141
      removed outlier: 3.627A  pdb=" N   VAL L 138 " --> pdb=" O   GLN L 134 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 80 through 84
      removed outlier: 4.342A  pdb=" N   PHE C  84 " --> pdb=" O   PRO C  81 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 211 through 215
      removed outlier: 4.090A  pdb=" N   THR C 215 " --> pdb=" O   ALA C 212 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 15 through 17
      No H-bonds generated for 'chain 'A' and resid 15 through 17'
    Processing helix  chain 'A' and resid 101 through 110
    Processing helix  chain 'R' and resid 36 through 65
      removed outlier: 3.719A  pdb=" N   SER R  41 " --> pdb=" O   VAL R  37 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   ILE R  53 " --> pdb=" O   PHE R  49 " (cutoff:3.500A)
      Proline residue:  R  54  - end of helix
    Processing helix  chain 'R' and resid 70 through 89
    Processing helix  chain 'R' and resid 89 through 98
      removed outlier: 3.819A  pdb=" N   TYR R  93 " --> pdb=" O   PHE R  89 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 109 through 141
    Processing helix  chain 'R' and resid 150 through 167
    Processing helix  chain 'R' and resid 168 through 173
      Proline residue:  R 171  - end of helix
      No H-bonds generated for 'chain 'R' and resid 168 through 173'
    Processing helix  chain 'R' and resid 197 through 215
      removed outlier: 3.853A  pdb=" N   ILE R 201 " --> pdb=" O   ASP R 197 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   HIS R 203 " --> pdb=" O   THR R 199 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 216 through 235
    Processing helix  chain 'R' and resid 242 through 275
      removed outlier: 3.516A  pdb=" N   TRP R 246 " --> pdb=" O   SER R 242 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   ILE R 248 " --> pdb=" O   HIS R 244 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   CYS R 258 " --> pdb=" O   ALA R 254 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   TRP R 259 " --> pdb=" O   PHE R 255 " (cutoff:3.500A)
      Proline residue:  R 261  - end of helix
      removed outlier: 4.133A  pdb=" N   LEU R 270 " --> pdb=" O   SER R 266 " (cutoff:3.500A)
      removed outlier: 4.014A  pdb=" N   THR R 271 " --> pdb=" O   ILE R 267 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   ILE R 272 " --> pdb=" O   TRP R 268 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   HIS R 273 " --> pdb=" O   GLU R 269 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 281 through 305
      removed outlier: 4.147A  pdb=" N   ILE R 286 " --> pdb=" O   MET R 282 " (cutoff:3.500A)
      Proline residue:  R 287  - end of helix
      Proline residue:  R 301  - end of helix
    Processing helix  chain 'R' and resid 312 through 318
      removed outlier: 3.642A  pdb=" N   ARG R 316 " --> pdb=" O   GLN R 312 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   SER R 317 " --> pdb=" O   ALA R 313 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'L' and resid 68 through 70
      removed outlier: 3.709A  pdb=" N   ALA L 100 " --> pdb=" O   LEU L  68 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 5 through 7
      removed outlier: 3.638A  pdb=" N   GLN B   5 " --> pdb=" O   VAL B  23 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   VAL B  23 " --> pdb=" O   GLN B   5 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 49 through 51
      removed outlier: 3.632A  pdb=" N   ALA B  49 " --> pdb=" O   TRP B  36 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 6 through 7
      removed outlier: 3.655A  pdb=" N   THR C   6 " --> pdb=" O   ARG C  25 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 54 through 55
      removed outlier: 3.630A  pdb=" N   TYR C  50 " --> pdb=" O   SER C  54 " (cutoff:3.500A)
      removed outlier: 5.523A  pdb=" N   LEU C  47 " --> pdb=" O   GLN C  38 " (cutoff:3.500A)
      removed outlier: 6.439A  pdb=" N   GLN C  38 " --> pdb=" O   LEU C  47 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   ILE C  49 " --> pdb=" O   TRP C  36 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 127 through 131
      removed outlier: 3.772A  pdb=" N   GLN C 127 " --> pdb=" O   SER C 149 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   SER C 149 " --> pdb=" O   GLN C 127 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   SER C 145 " --> pdb=" O   SER C 131 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   LEU C 144 " --> pdb=" O   LEU C 205 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 134 through 135
      removed outlier: 6.039A  pdb=" N   GLY C 134 " --> pdb=" O   THR C 241 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'C' and resid 181 through 184
      removed outlier: 6.963A  pdb=" N   TRP C 160 " --> pdb=" O   VAL C 172 " (cutoff:3.500A)
      removed outlier: 4.628A  pdb=" N   SER C 174 " --> pdb=" O   ILE C 158 " (cutoff:3.500A)
      removed outlier: 7.025A  pdb=" N   ILE C 158 " --> pdb=" O   SER C 174 " (cutoff:3.500A)
      removed outlier: 6.683A  pdb=" N   SER C 176 " --> pdb=" O   SER C 156 " (cutoff:3.500A)
      removed outlier: 8.908A  pdb=" N   SER C 156 " --> pdb=" O   SER C 176 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   TYR C 233 " --> pdb=" O   ARG C 222 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 113 through 118
    Processing sheet with id=AB1, first strand: chain 'A' and resid 27 through 29
      removed outlier: 3.753A  pdb=" N   PHE A 145 " --> pdb=" O   ILE A 169 " (cutoff:3.500A)
      removed outlier: 7.428A  pdb=" N   LYS A 171 " --> pdb=" O   VAL A 143 " (cutoff:3.500A)
      removed outlier: 9.660A  pdb=" N   VAL A 143 " --> pdb=" O   LYS A 171 " (cutoff:3.500A)
      removed outlier: 4.153A  pdb=" N   PHE A  81 " --> pdb=" O   VAL A  60 " (cutoff:3.500A)
      removed outlier: 6.858A  pdb=" N   PHE A  62 " --> pdb=" O   ASP A  79 " (cutoff:3.500A)
      removed outlier: 5.794A  pdb=" N   ASP A  79 " --> pdb=" O   PHE A  62 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 27 through 29
      removed outlier: 3.753A  pdb=" N   PHE A 145 " --> pdb=" O   ILE A 169 " (cutoff:3.500A)
      removed outlier: 7.428A  pdb=" N   LYS A 171 " --> pdb=" O   VAL A 143 " (cutoff:3.500A)
      removed outlier: 9.660A  pdb=" N   VAL A 143 " --> pdb=" O   LYS A 171 " (cutoff:3.500A)
      removed outlier: 4.007A  pdb=" N   LEU A 141 " --> pdb=" O   LEU A 130 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 185 through 187
      removed outlier: 3.852A  pdb=" N   ASN A 218 " --> pdb=" O   SER A 203 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   PHE A 269 " --> pdb=" O   VAL A 221 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 208 through 209
      removed outlier: 3.900A  pdb=" N   VAL A 336 " --> pdb=" O   LEU A 328 " (cutoff:3.500A)
      removed outlier: 4.079A  pdb=" N   TYR A 322 " --> pdb=" O   PHE A 342 " (cutoff:3.500A)
      removed outlier: 7.377A  pdb=" N   LEU A 344 " --> pdb=" O   VAL A 320 " (cutoff:3.500A)
      removed outlier: 9.230A  pdb=" N   VAL A 320 " --> pdb=" O   LEU A 344 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'A' and resid 208 through 209
      removed outlier: 3.900A  pdb=" N   VAL A 336 " --> pdb=" O   LEU A 328 " (cutoff:3.500A)
      removed outlier: 4.079A  pdb=" N   TYR A 322 " --> pdb=" O   PHE A 342 " (cutoff:3.500A)
      removed outlier: 7.377A  pdb=" N   LEU A 344 " --> pdb=" O   VAL A 320 " (cutoff:3.500A)
      removed outlier: 9.230A  pdb=" N   VAL A 320 " --> pdb=" O   LEU A 344 " (cutoff:3.500A)
      removed outlier: 6.695A  pdb=" N   ILE A 232 " --> pdb=" O   GLU A 258 " (cutoff:3.500A)
      removed outlier: 4.671A  pdb=" N   GLU A 258 " --> pdb=" O   ILE A 232 " (cutoff:3.500A)
      removed outlier: 7.048A  pdb=" N   VAL A 234 " --> pdb=" O   GLN A 256 " (cutoff:3.500A)
      removed outlier: 4.914A  pdb=" N   GLN A 256 " --> pdb=" O   VAL A 234 " (cutoff:3.500A)
      removed outlier: 6.709A  pdb=" N   VAL A 236 " --> pdb=" O   VAL A 254 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   VAL A 252 " --> pdb=" O   GLN A 238 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'R' and resid 177 through 180

    344 hydrogen bonds defined for protein.
    957 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: 1.02

  Time building geometry restraints manager: 0.92 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1131
        1.31 -     1.43: 2226
        1.43 -     1.56: 4343
        1.56 -     1.68: 31
        1.68 -     1.81: 37
  Bond restraints: 7768
  Sorted by residual:
  bond pdb=" CAI Y01 A 401 "
       pdb=" CAZ Y01 A 401 "
    ideal  model  delta    sigma   weight residual
    1.332  1.686 -0.354 2.00e-02 2.50e+03 3.14e+02
  bond pdb=" CAP Y01 A 401 "
       pdb=" CAQ Y01 A 401 "
    ideal  model  delta    sigma   weight residual
    1.541  1.726 -0.185 2.00e-02 2.50e+03 8.51e+01
  bond pdb=" CBF Y01 A 401 "
       pdb=" CBH Y01 A 401 "
    ideal  model  delta    sigma   weight residual
    1.550  1.686 -0.136 2.00e-02 2.50e+03 4.60e+01
  bond pdb=" CAS Y01 A 401 "
       pdb=" CAU Y01 A 401 "
    ideal  model  delta    sigma   weight residual
    1.530  1.656 -0.126 2.00e-02 2.50e+03 3.96e+01
  bond pdb=" CAQ Y01 A 401 "
       pdb=" CBG Y01 A 401 "
    ideal  model  delta    sigma   weight residual
    1.523  1.645 -0.122 2.00e-02 2.50e+03 3.72e+01
  ... (remaining 7763 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.48: 10448
        2.48 -     4.95: 147
        4.95 -     7.43: 22
        7.43 -     9.91: 5
        9.91 -    12.38: 3
  Bond angle restraints: 10625
  Sorted by residual:
  angle pdb=" N   PHE R 101 "
        pdb=" CA  PHE R 101 "
        pdb=" C   PHE R 101 "
      ideal   model   delta    sigma   weight residual
     110.91  116.67   -5.76 1.17e+00 7.31e-01 2.42e+01
  angle pdb=" N   TYR A  48 "
        pdb=" CA  TYR A  48 "
        pdb=" C   TYR A  48 "
      ideal   model   delta    sigma   weight residual
     114.09  107.14    6.95 1.55e+00 4.16e-01 2.01e+01
  angle pdb=" CB  TPO R1359 "
        pdb=" OG1 TPO R1359 "
        pdb=" P   TPO R1359 "
      ideal   model   delta    sigma   weight residual
     119.31  106.93   12.38 3.00e+00 1.11e-01 1.70e+01
  angle pdb=" CB  TPO R1360 "
        pdb=" OG1 TPO R1360 "
        pdb=" P   TPO R1360 "
      ideal   model   delta    sigma   weight residual
     119.31  107.01   12.30 3.00e+00 1.11e-01 1.68e+01
  angle pdb=" CA  LEU R 144 "
        pdb=" CB  LEU R 144 "
        pdb=" CG  LEU R 144 "
      ideal   model   delta    sigma   weight residual
     116.30  127.70  -11.40 3.50e+00 8.16e-02 1.06e+01
  ... (remaining 10620 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.00: 4057
       16.00 -    32.00: 358
       32.00 -    48.00: 93
       48.00 -    63.99: 12
       63.99 -    79.99: 7
  Dihedral angle restraints: 4527
    sinusoidal: 1573
      harmonic: 2954
  Sorted by residual:
  dihedral pdb=" CB  CYS B  22 "
           pdb=" SG  CYS B  22 "
           pdb=" SG  CYS B  95 "
           pdb=" CB  CYS B  95 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -11.43  -74.57     1      1.00e+01 1.00e-02 7.05e+01
  dihedral pdb=" CA  LEU R 167 "
           pdb=" C   LEU R 167 "
           pdb=" N   ILE R 168 "
           pdb=" CA  ILE R 168 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.29   19.71     0      5.00e+00 4.00e-02 1.55e+01
  dihedral pdb=" CG  ARG R 202 "
           pdb=" CD  ARG R 202 "
           pdb=" NE  ARG R 202 "
           pdb=" CZ  ARG R 202 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00 -135.04  -44.96     2      1.50e+01 4.44e-03 1.07e+01
  ... (remaining 4524 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.113: 1244
       0.113 -    0.225: 19
       0.225 -    0.338: 1
       0.338 -    0.451: 0
       0.451 -    0.563: 1
  Chirality restraints: 1265
  Sorted by residual:
  chirality pdb=" CBI Y01 A 401 "
            pdb=" CAU Y01 A 401 "
            pdb=" CBE Y01 A 401 "
            pdb=" CBG Y01 A 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.94    2.37    0.56 2.00e-01 2.50e+01 7.93e+00
  chirality pdb=" CBF Y01 A 401 "
            pdb=" CAS Y01 A 401 "
            pdb=" CBD Y01 A 401 "
            pdb=" CBH Y01 A 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.45   -2.69    0.25 2.00e-01 2.50e+01 1.55e+00
  chirality pdb=" CBB Y01 A 401 "
            pdb=" CAC Y01 A 401 "
            pdb=" CAO Y01 A 401 "
            pdb=" CBE Y01 A 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.58    2.77   -0.20 2.00e-01 2.50e+01 9.78e-01
  ... (remaining 1262 not shown)

  Planarity restraints: 1300
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL B  78 "   -0.016 2.00e-02 2.50e+03   3.18e-02 1.01e+01
        pdb=" C   VAL B  78 "    0.055 2.00e-02 2.50e+03
        pdb=" O   VAL B  78 "   -0.021 2.00e-02 2.50e+03
        pdb=" N   TYR B  79 "   -0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 264 "   -0.039 5.00e-02 4.00e+02   5.86e-02 5.50e+00
        pdb=" N   PRO A 265 "    0.101 5.00e-02 4.00e+02
        pdb=" CA  PRO A 265 "   -0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO A 265 "   -0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A 178 "    0.036 5.00e-02 4.00e+02   5.52e-02 4.87e+00
        pdb=" N   PRO A 179 "   -0.095 5.00e-02 4.00e+02
        pdb=" CA  PRO A 179 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO A 179 "    0.031 5.00e-02 4.00e+02
  ... (remaining 1297 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.69: 136
        2.69 -     3.24: 6912
        3.24 -     3.80: 11085
        3.80 -     4.35: 14311
        4.35 -     4.90: 24492
  Nonbonded interactions: 56936
  Sorted by model distance:
  nonbonded pdb=" OH  TYR R 215 "
            pdb=" OG1 THR R 260 "
     model   vdw
     2.140 3.040
  nonbonded pdb=" OH  TYR L 149 "
            pdb=" OE1 GLU R 269 "
     model   vdw
     2.149 3.040
  nonbonded pdb=" OD1 ASP A 205 "
            pdb=" OH  TYR A 209 "
     model   vdw
     2.196 3.040
  nonbonded pdb=" O   VAL R  59 "
            pdb=" OG1 THR R  63 "
     model   vdw
     2.315 3.040
  nonbonded pdb=" O   HIS R 102 "
            pdb=" ND1 HIS R 102 "
     model   vdw
     2.342 3.120
  ... (remaining 56931 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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.010
  Normalize map: mean=0, sd=1:             1.500
  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:                     7.220
  Find NCS groups from input model:        0.020
  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:1.070
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.980
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7308
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      :  0.007   0.354   7774  Z= 0.367
  Angle     :  0.700  12.382  10637  Z= 0.352
  Chirality :  0.046   0.563   1265
  Planarity :  0.005   0.059   1300
  Dihedral  : 13.179  79.993   2589
  Min Nonbonded Distance : 2.140

Molprobity Statistics.
  All-atom Clashscore : 6.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.07 %
    Favored  : 93.93 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.14 %
    Favored  : 99.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.30 (0.29), residues: 956
  helix:  2.45 (0.35), residues: 226
  sheet:  1.52 (0.35), residues: 258
  loop : -1.86 (0.28), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG C 191 
 TYR   0.018   0.001   TYR R  22 
 PHE   0.027   0.001   PHE R  86 
 TRP   0.016   0.001   TRP C 227 
 HIS   0.003   0.000   HIS R 135 

Details of bonding type rmsd
  covalent geometry    : bond        0.00717 ( 7768)
  covalent geometry    : angle       0.70077 (10625)
  SS BOND              : bond        0.00051 (    6)
  SS BOND              : angle       0.30432 (   12)
  hydrogen bonds       : bond        0.21687 (  318)
  hydrogen bonds       : angle       7.91682 (  957)

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

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

  1912 Ramachandran restraints generated.
    956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1912 Ramachandran restraints generated.
    956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 129
  time to evaluate  : 0.269 
Fit side-chains
REVERT: R   99 MET cc_start: 0.8805 (ptm) cc_final: 0.8600 (ptm)
REVERT: R  310 LYS cc_start: 0.7095 (tmmt) cc_final: 0.6673 (tttt)
  outliers start: 0
  outliers final: 0
  residues processed: 129
  average time/residue: 0.0607
  time to fit residues: 10.9226
Evaluate side-chains
  115 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 0.173 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 97 optimal weight:    2.9990
   chunk 53 optimal weight:    6.9990
   chunk 5 optimal weight:    8.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    5.9990
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    6.9990
   chunk 45 optimal weight:    0.9980
   overall best weight:    1.3784

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

Flipped N/Q/H residues before XYZ refinement:
B  44 HIS
C 159 HIS
C 163 GLN
A 199 HIS
A 223 ASN
A 249 GLN
A 282 ASN
** A 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R  56 ASN
R 102 HIS
** R 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.105298 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.085931 restraints weight = 15802.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.087894 restraints weight = 10078.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.089113 restraints weight = 7525.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.089836 restraints weight = 6271.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.090357 restraints weight = 5603.114|
|-----------------------------------------------------------------------------|
r_work (final): 0.3346
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7619
moved from start:          0.2189

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   7774  Z= 0.219
  Angle     :  0.662   5.879  10637  Z= 0.338
  Chirality :  0.045   0.191   1265
  Planarity :  0.005   0.049   1300
  Dihedral  :  5.690  53.547   1157
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 7.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.69 %
    Favored  : 93.31 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  :  8.61 %
    Favored  : 90.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.07 (0.28), residues: 956
  helix:  2.34 (0.35), residues: 227
  sheet:  1.35 (0.33), residues: 254
  loop : -2.01 (0.27), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C 222 
 TYR   0.016   0.002   TYR A 250 
 PHE   0.031   0.002   PHE C 226 
 TRP   0.015   0.002   TRP C 171 
 HIS   0.007   0.002   HIS R 263 

Details of bonding type rmsd
  covalent geometry    : bond        0.00518 ( 7768)
  covalent geometry    : angle       0.66149 (10625)
  SS BOND              : bond        0.00411 (    6)
  SS BOND              : angle       1.27245 (   12)
  hydrogen bonds       : bond        0.04130 (  318)
  hydrogen bonds       : angle       5.12773 (  957)

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

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

  1912 Ramachandran restraints generated.
    956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1912 Ramachandran restraints generated.
    956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 119
  time to evaluate  : 0.250 
Fit side-chains
REVERT: C  191 ARG cc_start: 0.8177 (mtm110) cc_final: 0.7806 (ttp-110)
REVERT: R  288 LEU cc_start: 0.8035 (tp) cc_final: 0.7806 (tt)
REVERT: R  310 LYS cc_start: 0.7372 (tmmt) cc_final: 0.6931 (tttt)
  outliers start: 9
  outliers final: 5
  residues processed: 124
  average time/residue: 0.0638
  time to fit residues: 11.0326
Evaluate side-chains
  114 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 109
  time to evaluate  : 0.200 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   48 VAL
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain R residue  163 LEU
Chi-restraints excluded: chain R residue  185 THR
Chi-restraints excluded: chain R residue  274 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 0 optimal weight:   20.0000
   chunk 43 optimal weight:    1.9990
   chunk 97 optimal weight:    3.9990
   chunk 44 optimal weight:    3.9990
   chunk 58 optimal weight:    0.6980
   chunk 19 optimal weight:    2.9990
   chunk 68 optimal weight:    2.9990
   chunk 35 optimal weight:    4.9990
   chunk 6 optimal weight:    5.9990
   chunk 8 optimal weight:   20.0000
   chunk 57 optimal weight:    5.9990
   overall best weight:    2.5388

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

Flipped N/Q/H residues before XYZ refinement:
L  74 GLN
C  39 GLN
A 182 GLN
A 199 HIS
A 249 GLN
** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 138 HIS
R 203 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.097945 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.079454 restraints weight = 15566.930|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.079744 restraints weight = 9998.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.080536 restraints weight = 8740.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.080711 restraints weight = 8219.332|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.080853 restraints weight = 7507.305|
|-----------------------------------------------------------------------------|
r_work (final): 0.3157
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7847
moved from start:          0.3993

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.058   7774  Z= 0.354
  Angle     :  0.784   8.535  10637  Z= 0.401
  Chirality :  0.050   0.179   1265
  Planarity :  0.006   0.046   1300
  Dihedral  :  7.050  53.941   1157
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 9.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.26 %
    Favored  : 91.74 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 14.21 %
    Favored  : 83.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.54 (0.27), residues: 956
  helix:  1.52 (0.33), residues: 226
  sheet:  1.01 (0.34), residues: 254
  loop : -2.22 (0.26), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 100 
 TYR   0.031   0.003   TYR A 250 
 PHE   0.039   0.003   PHE C 226 
 TRP   0.019   0.002   TRP C 171 
 HIS   0.009   0.002   HIS R 146 

Details of bonding type rmsd
  covalent geometry    : bond        0.00856 ( 7768)
  covalent geometry    : angle       0.78294 (10625)
  SS BOND              : bond        0.00514 (    6)
  SS BOND              : angle       1.50708 (   12)
  hydrogen bonds       : bond        0.05257 (  318)
  hydrogen bonds       : angle       5.41403 (  957)

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

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

  1912 Ramachandran restraints generated.
    956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1912 Ramachandran restraints generated.
    956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 114
  time to evaluate  : 0.266 
Fit side-chains
REVERT: C   28 GLN cc_start: 0.7492 (tm-30) cc_final: 0.6486 (tm-30)
REVERT: R  168 ILE cc_start: 0.8858 (tt) cc_final: 0.8643 (tt)
REVERT: R  288 LEU cc_start: 0.8197 (tp) cc_final: 0.7972 (tt)
REVERT: R  310 LYS cc_start: 0.8035 (tmmt) cc_final: 0.7283 (tttt)
  outliers start: 17
  outliers final: 14
  residues processed: 125
  average time/residue: 0.0633
  time to fit residues: 10.9765
Evaluate side-chains
  116 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 102
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue  115 VAL
Chi-restraints excluded: chain B residue   24 VAL
Chi-restraints excluded: chain B residue   48 VAL
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain A residue  242 ILE
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain A residue  358 VAL
Chi-restraints excluded: chain R residue  121 MET
Chi-restraints excluded: chain R residue  150 THR
Chi-restraints excluded: chain R residue  163 LEU
Chi-restraints excluded: chain R residue  184 HIS
Chi-restraints excluded: chain R residue  185 THR
Chi-restraints excluded: chain R residue  274 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 60 optimal weight:    0.9980
   chunk 21 optimal weight:    6.9990
   chunk 75 optimal weight:    0.6980
   chunk 73 optimal weight:    0.7980
   chunk 55 optimal weight:    0.7980
   chunk 80 optimal weight:    0.8980
   chunk 18 optimal weight:    1.9990
   chunk 78 optimal weight:    0.5980
   chunk 23 optimal weight:    0.8980
   chunk 22 optimal weight:    0.9980
   chunk 93 optimal weight:    1.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
L  74 GLN
B  44 HIS
B  81 GLN
C  39 GLN
A 199 HIS
A 282 ASN
A 361 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.100531 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.082457 restraints weight = 15885.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.082783 restraints weight = 9979.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.083360 restraints weight = 8905.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.083559 restraints weight = 8393.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.083732 restraints weight = 7549.965|
|-----------------------------------------------------------------------------|
r_work (final): 0.3213
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7780
moved from start:          0.3896

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7774  Z= 0.144
  Angle     :  0.588   8.859  10637  Z= 0.299
  Chirality :  0.042   0.151   1265
  Planarity :  0.004   0.043   1300
  Dihedral  :  6.245  53.064   1157
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 6.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.28 %
    Favored  : 93.72 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 17.08 %
    Favored  : 80.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.32 (0.27), residues: 956
  helix:  2.05 (0.34), residues: 226
  sheet:  0.92 (0.33), residues: 253
  loop : -2.13 (0.26), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 143 
 TYR   0.019   0.002   TYR A  64 
 PHE   0.019   0.002   PHE C 226 
 TRP   0.013   0.001   TRP C 171 
 HIS   0.005   0.001   HIS L  40 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 ( 7768)
  covalent geometry    : angle       0.58803 (10625)
  SS BOND              : bond        0.00296 (    6)
  SS BOND              : angle       0.79685 (   12)
  hydrogen bonds       : bond        0.03569 (  318)
  hydrogen bonds       : angle       4.81177 (  957)

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

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

  1912 Ramachandran restraints generated.
    956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1912 Ramachandran restraints generated.
    956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 105
  time to evaluate  : 0.269 
Fit side-chains
REVERT: C   28 GLN cc_start: 0.7434 (tm-30) cc_final: 0.6322 (tm-30)
REVERT: A  250 TYR cc_start: 0.6907 (m-10) cc_final: 0.6691 (m-10)
REVERT: A  358 VAL cc_start: 0.8052 (OUTLIER) cc_final: 0.7827 (t)
REVERT: R  223 SER cc_start: 0.7807 (t) cc_final: 0.7603 (m)
REVERT: R  281 VAL cc_start: 0.8662 (m) cc_final: 0.8416 (p)
REVERT: R  288 LEU cc_start: 0.8052 (tp) cc_final: 0.7701 (tt)
REVERT: R  294 PHE cc_start: 0.7781 (m-80) cc_final: 0.7458 (m-10)
REVERT: R  310 LYS cc_start: 0.7952 (tmmt) cc_final: 0.7224 (tttt)
  outliers start: 20
  outliers final: 15
  residues processed: 118
  average time/residue: 0.0695
  time to fit residues: 11.1252
Evaluate side-chains
  116 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 100
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue  138 VAL
Chi-restraints excluded: chain B residue   48 VAL
Chi-restraints excluded: chain C residue   95 VAL
Chi-restraints excluded: chain C residue  241 THR
Chi-restraints excluded: chain A residue   41 VAL
Chi-restraints excluded: chain A residue  151 VAL
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain A residue  298 ASP
Chi-restraints excluded: chain A residue  358 VAL
Chi-restraints excluded: chain R residue  121 MET
Chi-restraints excluded: chain R residue  150 THR
Chi-restraints excluded: chain R residue  163 LEU
Chi-restraints excluded: chain R residue  184 HIS
Chi-restraints excluded: chain R residue  185 THR
Chi-restraints excluded: chain R residue  257 VAL
Chi-restraints excluded: chain R residue  274 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 56 optimal weight:    5.9990
   chunk 25 optimal weight:    0.9990
   chunk 70 optimal weight:    0.9990
   chunk 85 optimal weight:    4.9990
   chunk 89 optimal weight:    0.7980
   chunk 79 optimal weight:    0.9990
   chunk 28 optimal weight:    0.0070
   chunk 46 optimal weight:    0.0270
   chunk 5 optimal weight:   10.0000
   chunk 44 optimal weight:    0.6980
   chunk 66 optimal weight:    2.9990
   overall best weight:    0.5058

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

Flipped N/Q/H residues before XYZ refinement:
A 361 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.101367 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.083142 restraints weight = 15713.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.083814 restraints weight = 10807.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.084579 restraints weight = 9397.228|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.084959 restraints weight = 7891.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.084923 restraints weight = 6857.925|
|-----------------------------------------------------------------------------|
r_work (final): 0.3234
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7749
moved from start:          0.3860

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7774  Z= 0.118
  Angle     :  0.564   8.847  10637  Z= 0.283
  Chirality :  0.041   0.143   1265
  Planarity :  0.004   0.042   1300
  Dihedral  :  5.837  50.974   1157
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 6.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.38 %
    Favored  : 93.62 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 17.49 %
    Favored  : 79.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.22 (0.28), residues: 956
  helix:  2.21 (0.34), residues: 228
  sheet:  0.72 (0.33), residues: 269
  loop : -2.06 (0.27), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 143 
 TYR   0.021   0.001   TYR A  64 
 PHE   0.016   0.001   PHE C 226 
 TRP   0.011   0.001   TRP R  75 
 HIS   0.005   0.001   HIS L  40 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 7768)
  covalent geometry    : angle       0.56396 (10625)
  SS BOND              : bond        0.00276 (    6)
  SS BOND              : angle       0.65609 (   12)
  hydrogen bonds       : bond        0.03148 (  318)
  hydrogen bonds       : angle       4.52198 (  957)

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

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

  1912 Ramachandran restraints generated.
    956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1912 Ramachandran restraints generated.
    956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 102
  time to evaluate  : 0.313 
Fit side-chains
REVERT: C   28 GLN cc_start: 0.7395 (tm-30) cc_final: 0.6232 (tm-30)
REVERT: A  358 VAL cc_start: 0.8047 (t) cc_final: 0.7817 (t)
REVERT: R   86 PHE cc_start: 0.8232 (t80) cc_final: 0.7908 (t80)
REVERT: R  281 VAL cc_start: 0.8648 (m) cc_final: 0.8413 (p)
REVERT: R  288 LEU cc_start: 0.7988 (tp) cc_final: 0.7630 (tt)
REVERT: R  294 PHE cc_start: 0.7772 (m-80) cc_final: 0.7526 (m-10)
REVERT: R  310 LYS cc_start: 0.7990 (tmmt) cc_final: 0.7294 (tttt)
  outliers start: 25
  outliers final: 15
  residues processed: 118
  average time/residue: 0.0934
  time to fit residues: 14.9164
Evaluate side-chains
  112 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 97
  time to evaluate  : 0.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue  138 VAL
Chi-restraints excluded: chain B residue   48 VAL
Chi-restraints excluded: chain C residue   95 VAL
Chi-restraints excluded: chain C residue  161 VAL
Chi-restraints excluded: chain C residue  241 THR
Chi-restraints excluded: chain A residue   41 VAL
Chi-restraints excluded: chain A residue   72 LEU
Chi-restraints excluded: chain A residue   74 LEU
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain A residue  242 ILE
Chi-restraints excluded: chain A residue  298 ASP
Chi-restraints excluded: chain R residue  150 THR
Chi-restraints excluded: chain R residue  185 THR
Chi-restraints excluded: chain R residue  257 VAL
Chi-restraints excluded: chain R residue  274 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 81 optimal weight:    0.0050
   chunk 25 optimal weight:    2.9990
   chunk 32 optimal weight:    2.9990
   chunk 2 optimal weight:   10.0000
   chunk 36 optimal weight:    3.9990
   chunk 13 optimal weight:    5.9990
   chunk 54 optimal weight:    6.9990
   chunk 19 optimal weight:    0.5980
   chunk 91 optimal weight:    1.9990
   chunk 66 optimal weight:    2.9990
   chunk 56 optimal weight:    2.9990
   overall best weight:    1.7200

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

Flipped N/Q/H residues before XYZ refinement:
L  40 HIS
L  74 GLN
B  44 HIS
A 361 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.098163 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.079446 restraints weight = 15755.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.080658 restraints weight = 10706.279|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.080949 restraints weight = 8805.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.081225 restraints weight = 7904.596|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.081631 restraints weight = 6989.357|
|-----------------------------------------------------------------------------|
r_work (final): 0.3174
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7823
moved from start:          0.4283

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.043   7774  Z= 0.254
  Angle     :  0.669   9.316  10637  Z= 0.338
  Chirality :  0.045   0.173   1265
  Planarity :  0.005   0.040   1300
  Dihedral  :  6.129  50.778   1157
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 8.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.26 %
    Favored  : 91.74 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 18.17 %
    Favored  : 78.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.51 (0.27), residues: 956
  helix:  1.92 (0.34), residues: 229
  sheet:  0.69 (0.33), residues: 254
  loop : -2.22 (0.26), residues: 473

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 143 
 TYR   0.019   0.002   TYR C  92 
 PHE   0.028   0.002   PHE C 226 
 TRP   0.016   0.002   TRP C 171 
 HIS   0.006   0.001   HIS R 204 

Details of bonding type rmsd
  covalent geometry    : bond        0.00614 ( 7768)
  covalent geometry    : angle       0.66889 (10625)
  SS BOND              : bond        0.00442 (    6)
  SS BOND              : angle       0.89380 (   12)
  hydrogen bonds       : bond        0.04084 (  318)
  hydrogen bonds       : angle       4.84988 (  957)

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

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

  1912 Ramachandran restraints generated.
    956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1912 Ramachandran restraints generated.
    956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 102
  time to evaluate  : 0.316 
Fit side-chains
REVERT: B  110 VAL cc_start: 0.7923 (p) cc_final: 0.7722 (t)
REVERT: C   28 GLN cc_start: 0.7545 (tm-30) cc_final: 0.6327 (tm-30)
REVERT: C  233 TYR cc_start: 0.8060 (m-80) cc_final: 0.7697 (m-80)
REVERT: R  281 VAL cc_start: 0.8717 (m) cc_final: 0.8461 (p)
REVERT: R  288 LEU cc_start: 0.8121 (tp) cc_final: 0.7830 (tt)
REVERT: R  294 PHE cc_start: 0.7913 (m-80) cc_final: 0.7531 (m-80)
  outliers start: 26
  outliers final: 19
  residues processed: 122
  average time/residue: 0.0898
  time to fit residues: 15.0409
Evaluate side-chains
  118 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 99
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue  138 VAL
Chi-restraints excluded: chain B residue   27 PHE
Chi-restraints excluded: chain B residue   48 VAL
Chi-restraints excluded: chain C residue   95 VAL
Chi-restraints excluded: chain C residue  161 VAL
Chi-restraints excluded: chain C residue  241 THR
Chi-restraints excluded: chain A residue   41 VAL
Chi-restraints excluded: chain A residue   45 ASP
Chi-restraints excluded: chain A residue   72 LEU
Chi-restraints excluded: chain A residue   74 LEU
Chi-restraints excluded: chain A residue  165 VAL
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain A residue  242 ILE
Chi-restraints excluded: chain A residue  298 ASP
Chi-restraints excluded: chain R residue  150 THR
Chi-restraints excluded: chain R residue  184 HIS
Chi-restraints excluded: chain R residue  185 THR
Chi-restraints excluded: chain R residue  257 VAL
Chi-restraints excluded: chain R residue  274 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 42 optimal weight:    0.9980
   chunk 58 optimal weight:    1.9990
   chunk 48 optimal weight:    0.0970
   chunk 79 optimal weight:    0.5980
   chunk 73 optimal weight:    0.4980
   chunk 20 optimal weight:    1.9990
   chunk 86 optimal weight:    0.9990
   chunk 12 optimal weight:    5.9990
   chunk 74 optimal weight:    0.6980
   chunk 31 optimal weight:    0.6980
   chunk 13 optimal weight:    3.9990
   overall best weight:    0.5178

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

Flipped N/Q/H residues before XYZ refinement:
B  44 HIS
A 361 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.101109 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.082906 restraints weight = 15640.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.083808 restraints weight = 10545.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.084753 restraints weight = 8656.909|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.084872 restraints weight = 7288.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.084866 restraints weight = 6829.208|
|-----------------------------------------------------------------------------|
r_work (final): 0.3233
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7753
moved from start:          0.4126

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7774  Z= 0.118
  Angle     :  0.561   8.781  10637  Z= 0.281
  Chirality :  0.041   0.151   1265
  Planarity :  0.004   0.040   1300
  Dihedral  :  5.927  51.877   1157
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 7.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.07 %
    Favored  : 93.93 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 19.13 %
    Favored  : 78.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.30 (0.27), residues: 956
  helix:  2.23 (0.34), residues: 228
  sheet:  0.75 (0.33), residues: 252
  loop : -2.10 (0.26), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 143 
 TYR   0.025   0.001   TYR A  64 
 PHE   0.014   0.001   PHE C 226 
 TRP   0.012   0.001   TRP R  75 
 HIS   0.006   0.001   HIS R 204 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 7768)
  covalent geometry    : angle       0.56108 (10625)
  SS BOND              : bond        0.00331 (    6)
  SS BOND              : angle       0.62439 (   12)
  hydrogen bonds       : bond        0.03109 (  318)
  hydrogen bonds       : angle       4.49713 (  957)

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

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

  1912 Ramachandran restraints generated.
    956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1912 Ramachandran restraints generated.
    956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 102
  time to evaluate  : 0.372 
Fit side-chains
REVERT: C   28 GLN cc_start: 0.7430 (tm-30) cc_final: 0.6261 (tm-30)
REVERT: R   86 PHE cc_start: 0.8265 (t80) cc_final: 0.7973 (t80)
REVERT: R  288 LEU cc_start: 0.8003 (tp) cc_final: 0.7624 (tt)
REVERT: R  294 PHE cc_start: 0.7770 (m-80) cc_final: 0.7510 (m-10)
REVERT: R  310 LYS cc_start: 0.8001 (tmmt) cc_final: 0.7714 (tmmt)
  outliers start: 21
  outliers final: 20
  residues processed: 117
  average time/residue: 0.0913
  time to fit residues: 14.4547
Evaluate side-chains
  117 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 97
  time to evaluate  : 0.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue  138 VAL
Chi-restraints excluded: chain B residue   24 VAL
Chi-restraints excluded: chain B residue   27 PHE
Chi-restraints excluded: chain B residue   48 VAL
Chi-restraints excluded: chain C residue   95 VAL
Chi-restraints excluded: chain C residue  161 VAL
Chi-restraints excluded: chain C residue  241 THR
Chi-restraints excluded: chain A residue   45 ASP
Chi-restraints excluded: chain A residue   72 LEU
Chi-restraints excluded: chain A residue   74 LEU
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain A residue  242 ILE
Chi-restraints excluded: chain A residue  298 ASP
Chi-restraints excluded: chain A residue  337 SER
Chi-restraints excluded: chain A residue  358 VAL
Chi-restraints excluded: chain R residue  150 THR
Chi-restraints excluded: chain R residue  163 LEU
Chi-restraints excluded: chain R residue  184 HIS
Chi-restraints excluded: chain R residue  185 THR
Chi-restraints excluded: chain R residue  274 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 11 optimal weight:    0.0370
   chunk 16 optimal weight:    1.9990
   chunk 66 optimal weight:    2.9990
   chunk 17 optimal weight:    0.9990
   chunk 81 optimal weight:    3.9990
   chunk 69 optimal weight:    6.9990
   chunk 80 optimal weight:    0.1980
   chunk 26 optimal weight:    0.6980
   chunk 97 optimal weight:    3.9990
   chunk 60 optimal weight:    0.2980
   chunk 85 optimal weight:    3.9990
   overall best weight:    0.4460

-------------------------------------------------------------------------------
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 = 0.3532 r_free = 0.3532 target = 0.101484 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.083461 restraints weight = 15850.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.084072 restraints weight = 10915.827|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.084628 restraints weight = 9319.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.084989 restraints weight = 8345.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.085243 restraints weight = 7408.630|
|-----------------------------------------------------------------------------|
r_work (final): 0.3243
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7745
moved from start:          0.4100

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7774  Z= 0.112
  Angle     :  0.560   8.913  10637  Z= 0.279
  Chirality :  0.041   0.142   1265
  Planarity :  0.004   0.039   1300
  Dihedral  :  5.876  55.463   1157
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 7.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.01 %
    Favored  : 92.99 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 18.58 %
    Favored  : 78.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.18 (0.28), residues: 956
  helix:  2.39 (0.34), residues: 228
  sheet:  0.88 (0.33), residues: 250
  loop : -2.08 (0.26), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C 143 
 TYR   0.021   0.001   TYR A  64 
 PHE   0.014   0.001   PHE C 226 
 TRP   0.012   0.001   TRP R  75 
 HIS   0.006   0.001   HIS R 204 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 7768)
  covalent geometry    : angle       0.56002 (10625)
  SS BOND              : bond        0.00323 (    6)
  SS BOND              : angle       0.57651 (   12)
  hydrogen bonds       : bond        0.03047 (  318)
  hydrogen bonds       : angle       4.41867 (  957)

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

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

  1912 Ramachandran restraints generated.
    956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1912 Ramachandran restraints generated.
    956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 95
  time to evaluate  : 0.286 
Fit side-chains
REVERT: C   28 GLN cc_start: 0.7404 (tm-30) cc_final: 0.6218 (tm-30)
REVERT: A  250 TYR cc_start: 0.6952 (m-10) cc_final: 0.6612 (m-10)
REVERT: R   86 PHE cc_start: 0.8155 (t80) cc_final: 0.7879 (t80)
REVERT: R  288 LEU cc_start: 0.7987 (tp) cc_final: 0.7626 (tt)
REVERT: R  294 PHE cc_start: 0.7742 (m-80) cc_final: 0.7478 (m-10)
REVERT: R  310 LYS cc_start: 0.8023 (tmmt) cc_final: 0.7503 (tttt)
  outliers start: 24
  outliers final: 21
  residues processed: 113
  average time/residue: 0.0815
  time to fit residues: 12.7831
Evaluate side-chains
  116 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 95
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   50 THR
Chi-restraints excluded: chain L residue  138 VAL
Chi-restraints excluded: chain B residue   24 VAL
Chi-restraints excluded: chain B residue   27 PHE
Chi-restraints excluded: chain B residue   48 VAL
Chi-restraints excluded: chain C residue   95 VAL
Chi-restraints excluded: chain C residue  161 VAL
Chi-restraints excluded: chain C residue  241 THR
Chi-restraints excluded: chain A residue   41 VAL
Chi-restraints excluded: chain A residue   74 LEU
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain A residue  242 ILE
Chi-restraints excluded: chain A residue  243 VAL
Chi-restraints excluded: chain A residue  298 ASP
Chi-restraints excluded: chain A residue  358 VAL
Chi-restraints excluded: chain R residue  150 THR
Chi-restraints excluded: chain R residue  163 LEU
Chi-restraints excluded: chain R residue  184 HIS
Chi-restraints excluded: chain R residue  185 THR
Chi-restraints excluded: chain R residue  257 VAL
Chi-restraints excluded: chain R residue  274 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 35 optimal weight:    1.9990
   chunk 64 optimal weight:    2.9990
   chunk 37 optimal weight:    1.9990
   chunk 21 optimal weight:    0.3980
   chunk 43 optimal weight:    2.9990
   chunk 25 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 40 optimal weight:    0.0070
   chunk 78 optimal weight:    1.9990
   chunk 9 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9980
   overall best weight:    1.0802

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

Flipped N/Q/H residues before XYZ refinement:
B  44 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.099416 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.080984 restraints weight = 15697.777|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.082099 restraints weight = 10713.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.082932 restraints weight = 8697.061|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.083066 restraints weight = 7276.245|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.083066 restraints weight = 6878.180|
|-----------------------------------------------------------------------------|
r_work (final): 0.3198
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7787
moved from start:          0.4259

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   7774  Z= 0.174
  Angle     :  0.605   9.117  10637  Z= 0.303
  Chirality :  0.043   0.141   1265
  Planarity :  0.004   0.038   1300
  Dihedral  :  5.914  56.166   1157
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 7.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.32 %
    Favored  : 92.68 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 18.85 %
    Favored  : 77.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.34 (0.27), residues: 956
  helix:  2.21 (0.33), residues: 234
  sheet:  0.72 (0.33), residues: 254
  loop : -2.20 (0.26), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 143 
 TYR   0.020   0.002   TYR A  64 
 PHE   0.021   0.002   PHE C 226 
 TRP   0.016   0.001   TRP R  75 
 HIS   0.005   0.001   HIS R 204 

Details of bonding type rmsd
  covalent geometry    : bond        0.00420 ( 7768)
  covalent geometry    : angle       0.60537 (10625)
  SS BOND              : bond        0.00375 (    6)
  SS BOND              : angle       0.67614 (   12)
  hydrogen bonds       : bond        0.03524 (  318)
  hydrogen bonds       : angle       4.61064 (  957)

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

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

  1912 Ramachandran restraints generated.
    956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1912 Ramachandran restraints generated.
    956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 100
  time to evaluate  : 0.211 
Fit side-chains
REVERT: L  148 PHE cc_start: 0.7574 (t80) cc_final: 0.7370 (t80)
REVERT: C   28 GLN cc_start: 0.7510 (tm-30) cc_final: 0.6320 (tm-30)
REVERT: C  233 TYR cc_start: 0.8053 (m-80) cc_final: 0.7737 (m-80)
REVERT: A  250 TYR cc_start: 0.6932 (m-10) cc_final: 0.6542 (m-10)
REVERT: R   86 PHE cc_start: 0.8277 (t80) cc_final: 0.7982 (t80)
REVERT: R  288 LEU cc_start: 0.8085 (tp) cc_final: 0.7734 (tt)
REVERT: R  294 PHE cc_start: 0.7802 (m-80) cc_final: 0.7492 (m-10)
REVERT: R  310 LYS cc_start: 0.8001 (tmmt) cc_final: 0.7540 (tttt)
  outliers start: 26
  outliers final: 22
  residues processed: 119
  average time/residue: 0.0817
  time to fit residues: 13.3986
Evaluate side-chains
  121 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 99
  time to evaluate  : 0.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   50 THR
Chi-restraints excluded: chain L residue  115 VAL
Chi-restraints excluded: chain L residue  138 VAL
Chi-restraints excluded: chain B residue   24 VAL
Chi-restraints excluded: chain B residue   27 PHE
Chi-restraints excluded: chain B residue   48 VAL
Chi-restraints excluded: chain C residue   95 VAL
Chi-restraints excluded: chain C residue  161 VAL
Chi-restraints excluded: chain C residue  241 THR
Chi-restraints excluded: chain A residue   41 VAL
Chi-restraints excluded: chain A residue   45 ASP
Chi-restraints excluded: chain A residue   72 LEU
Chi-restraints excluded: chain A residue   74 LEU
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain A residue  242 ILE
Chi-restraints excluded: chain A residue  298 ASP
Chi-restraints excluded: chain A residue  358 VAL
Chi-restraints excluded: chain R residue  150 THR
Chi-restraints excluded: chain R residue  184 HIS
Chi-restraints excluded: chain R residue  185 THR
Chi-restraints excluded: chain R residue  257 VAL
Chi-restraints excluded: chain R residue  274 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 12 optimal weight:    7.9990
   chunk 23 optimal weight:    0.5980
   chunk 33 optimal weight:    0.9980
   chunk 95 optimal weight:    1.9990
   chunk 88 optimal weight:    2.9990
   chunk 71 optimal weight:    0.0010
   chunk 5 optimal weight:   10.0000
   chunk 94 optimal weight:    0.4980
   chunk 30 optimal weight:    1.9990
   chunk 73 optimal weight:    0.8980
   chunk 1 optimal weight:    0.0980
   overall best weight:    0.4186

-------------------------------------------------------------------------------
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 = 0.3530 r_free = 0.3530 target = 0.101461 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.083384 restraints weight = 15742.138|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.084042 restraints weight = 10870.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.084626 restraints weight = 9704.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.085009 restraints weight = 8244.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.085047 restraints weight = 7272.254|
|-----------------------------------------------------------------------------|
r_work (final): 0.3240
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7745
moved from start:          0.4192

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7774  Z= 0.108
  Angle     :  0.559   8.806  10637  Z= 0.277
  Chirality :  0.041   0.140   1265
  Planarity :  0.004   0.038   1300
  Dihedral  :  5.845  61.920   1157
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 7.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.90 %
    Favored  : 93.10 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 19.67 %
    Favored  : 77.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.21 (0.28), residues: 956
  helix:  2.41 (0.34), residues: 228
  sheet:  0.55 (0.33), residues: 268
  loop : -2.02 (0.27), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 143 
 TYR   0.019   0.001   TYR A  64 
 PHE   0.014   0.001   PHE C 226 
 TRP   0.012   0.001   TRP R  75 
 HIS   0.005   0.001   HIS R 204 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 7768)
  covalent geometry    : angle       0.55892 (10625)
  SS BOND              : bond        0.00317 (    6)
  SS BOND              : angle       0.56335 (   12)
  hydrogen bonds       : bond        0.03013 (  318)
  hydrogen bonds       : angle       4.40536 (  957)

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

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

  1912 Ramachandran restraints generated.
    956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1912 Ramachandran restraints generated.
    956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 104
  time to evaluate  : 0.294 
Fit side-chains
REVERT: C   28 GLN cc_start: 0.7397 (tm-30) cc_final: 0.6234 (tm-30)
REVERT: A  250 TYR cc_start: 0.6923 (m-10) cc_final: 0.6481 (m-10)
REVERT: R   86 PHE cc_start: 0.8131 (t80) cc_final: 0.7867 (t80)
REVERT: R  288 LEU cc_start: 0.7994 (tp) cc_final: 0.7612 (tt)
REVERT: R  294 PHE cc_start: 0.7735 (m-80) cc_final: 0.7465 (m-10)
REVERT: R  310 LYS cc_start: 0.7995 (tmmt) cc_final: 0.7541 (tttt)
  outliers start: 21
  outliers final: 21
  residues processed: 119
  average time/residue: 0.0894
  time to fit residues: 14.5675
Evaluate side-chains
  121 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 100
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   50 THR
Chi-restraints excluded: chain L residue  115 VAL
Chi-restraints excluded: chain L residue  138 VAL
Chi-restraints excluded: chain B residue   24 VAL
Chi-restraints excluded: chain B residue   27 PHE
Chi-restraints excluded: chain B residue   48 VAL
Chi-restraints excluded: chain C residue   95 VAL
Chi-restraints excluded: chain C residue  161 VAL
Chi-restraints excluded: chain C residue  241 THR
Chi-restraints excluded: chain A residue   41 VAL
Chi-restraints excluded: chain A residue   45 ASP
Chi-restraints excluded: chain A residue   72 LEU
Chi-restraints excluded: chain A residue   74 LEU
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain A residue  242 ILE
Chi-restraints excluded: chain A residue  298 ASP
Chi-restraints excluded: chain A residue  358 VAL
Chi-restraints excluded: chain R residue  150 THR
Chi-restraints excluded: chain R residue  184 HIS
Chi-restraints excluded: chain R residue  185 THR
Chi-restraints excluded: chain R residue  274 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 27 optimal weight:    1.9990
   chunk 48 optimal weight:    0.8980
   chunk 35 optimal weight:    6.9990
   chunk 79 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9980
   chunk 22 optimal weight:    3.9990
   chunk 12 optimal weight:    3.9990
   chunk 19 optimal weight:    0.0670
   chunk 0 optimal weight:   20.0000
   chunk 96 optimal weight:    0.8980
   chunk 92 optimal weight:    1.9990
   overall best weight:    0.7720

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

Flipped N/Q/H residues before XYZ refinement:
A 223 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.100373 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.082090 restraints weight = 15546.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.082712 restraints weight = 10754.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.083238 restraints weight = 9230.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.083631 restraints weight = 8046.255|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.084048 restraints weight = 7206.115|
|-----------------------------------------------------------------------------|
r_work (final): 0.3221
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7764
moved from start:          0.4245

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7774  Z= 0.140
  Angle     :  0.586   8.943  10637  Z= 0.291
  Chirality :  0.042   0.137   1265
  Planarity :  0.004   0.038   1300
  Dihedral  :  5.814  63.058   1157
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 6.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.80 %
    Favored  : 93.20 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 19.67 %
    Favored  : 77.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.19 (0.28), residues: 956
  helix:  2.38 (0.34), residues: 228
  sheet:  0.66 (0.33), residues: 259
  loop : -2.01 (0.27), residues: 469

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 143 
 TYR   0.021   0.001   TYR A  64 
 PHE   0.047   0.002   PHE L 148 
 TRP   0.014   0.001   TRP R  75 
 HIS   0.005   0.001   HIS R 204 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 ( 7768)
  covalent geometry    : angle       0.58629 (10625)
  SS BOND              : bond        0.00338 (    6)
  SS BOND              : angle       0.57954 (   12)
  hydrogen bonds       : bond        0.03235 (  318)
  hydrogen bonds       : angle       4.45957 (  957)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1199.02 seconds
wall clock time: 21 minutes 25.08 seconds (1285.08 seconds total)