Starting phenix.real_space_refine
on Sat Apr  4 23:33:33 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9p86_71366/04_2026/9p86_71366.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9p86_71366/04_2026/9p86_71366.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9p86_71366/04_2026/9p86_71366.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9p86_71366/04_2026/9p86_71366.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9p86_71366/04_2026/9p86_71366.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9p86_71366/04_2026/9p86_71366.map"
  }
  resolution = 2.9
  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=  -0.000 sd=   0.022
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      22      5.16       5
     C    3795      2.51       5
     N    1034      2.21       5
     O    1042      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5893
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "B"
      Number of atoms: 2271
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2271
          Classifications: {'peptide': 338}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 111}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 329
          Unresolved non-hydrogen angles: 410
          Unresolved non-hydrogen dihedrals: 250
          Unresolved non-hydrogen chiralities: 25
          Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 17, 'GLN:plan1': 8, 'ARG:plan': 11, 'ASN:plan1': 9, 'HIS:plan': 1, 'ASN%COO:plan1': 1}
          Unresolved non-hydrogen planarities: 205
    Chain: "G"
      Number of atoms: 318
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 318
          Classifications: {'peptide': 55}
          Incomplete info: {'truncation_to_alanine': 33}
          Link IDs: {'PTRANS': 4, 'TRANS': 50}
          Unresolved non-hydrogen bonds: 107
          Unresolved non-hydrogen angles: 130
          Unresolved non-hydrogen dihedrals: 86
          Unresolved non-hydrogen chiralities: 9
          Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 2, 'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 3, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 51
    Chain: "L"
      Number of atoms: 49
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 49
          Classifications: {'peptide': 6}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 1, 'TRANS': 4}
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 7
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "R"
      Number of atoms: 1836
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 290, 1836
          Classifications: {'peptide': 290}
          Incomplete info: {'truncation_to_alanine': 148}
          Link IDs: {'PTRANS': 10, 'TRANS': 279}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 482
          Unresolved non-hydrogen angles: 618
          Unresolved non-hydrogen dihedrals: 381
          Unresolved non-hydrogen chiralities: 69
          Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 6, 'ASN:plan1': 7, 'TYR:plan': 3, 'PHE:plan': 8, 'HIS:plan': 5, 'ARG:plan': 10, 'GLN:plan1': 5}
          Unresolved non-hydrogen planarities: 219
    Chain: "A"
      Number of atoms: 1419
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 220, 1419
          Classifications: {'peptide': 220}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 116}
          Link IDs: {'PTRANS': 5, 'TRANS': 214}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 413
          Unresolved non-hydrogen angles: 507
          Unresolved non-hydrogen dihedrals: 326
          Unresolved non-hydrogen chiralities: 27
          Planarities with less than four sites: {'GLU:plan': 17, 'ARG:plan': 15, 'ASN:plan1': 8, 'GLN:plan1': 7, 'ASP:plan': 13, 'HIS:plan': 2, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 251
  Time building chain proxies: 1.25, per 1000 atoms: 0.21
  Number of scatterers: 5893
  At special positions: 0
  Unit cell: (70.72, 97.344, 130.624, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      22     16.00
     O    1042      8.00
     N    1034      7.00
     C    3795      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 141 " - pdb=" SG  CYS R 224 " 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: 0.32
  Conformation dependent library (CDL) restraints added in 324.9 milliseconds
  

  1774 Ramachandran restraints generated.
    887 Oldfield, 0 Emsley, 887 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1724

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 9 sheets defined
      47.5% alpha, 18.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.19
  Creating SS restraints...
    Processing helix  chain 'B' and resid 2 through 26
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'B' and resid 35 through 37
      No H-bonds generated for 'chain 'B' and resid 35 through 37'
    Processing helix  chain 'G' and resid 9 through 24
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'G' and resid 45 through 48
      removed outlier: 3.750A  pdb=" N   ASP G  48 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'G' and resid 45 through 48'
    Processing helix  chain 'R' and resid 59 through 88
    Processing helix  chain 'R' and resid 101 through 127
      Proline residue:  R 121  - end of helix
    Processing helix  chain 'R' and resid 139 through 172
      removed outlier: 4.356A  pdb=" N   GLY R 143 " --> pdb=" O   ALA R 139 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 172 through 179
    Processing helix  chain 'R' and resid 181 through 206
      removed outlier: 3.736A  pdb=" N   ALA R 197 " --> pdb=" O   TRP R 193 " (cutoff:3.500A)
      Proline residue:  R 202  - end of helix
    Processing helix  chain 'R' and resid 229 through 245
    Processing helix  chain 'R' and resid 245 through 271
    Processing helix  chain 'R' and resid 281 through 329
      Proline residue:  R 318  - end of helix
    Processing helix  chain 'R' and resid 335 through 368
      removed outlier: 3.513A  pdb=" N   SER R 357 " --> pdb=" O   PHE R 353 " (cutoff:3.500A)
      Proline residue:  R 361  - end of helix
      removed outlier: 4.158A  pdb=" N   SER R 368 " --> pdb=" O   TYR R 364 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 368 through 374
    Processing helix  chain 'A' and resid 15 through 39
      removed outlier: 4.034A  pdb=" N   GLU A  39 " --> pdb=" O   ASP A  35 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 51 through 63
    Processing helix  chain 'A' and resid 212 through 221
      removed outlier: 3.510A  pdb=" N   LYS A 215 " --> pdb=" O   GLU A 212 " (cutoff:3.500A)
      removed outlier: 4.921A  pdb=" N   ILE A 217 " --> pdb=" O   ARG A 214 " (cutoff:3.500A)
      removed outlier: 5.582A  pdb=" N   HIS A 218 " --> pdb=" O   LYS A 215 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   GLU A 221 " --> pdb=" O   HIS A 218 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 235
      No H-bonds generated for 'chain 'A' and resid 233 through 235'
    Processing helix  chain 'A' and resid 246 through 260
      removed outlier: 3.718A  pdb=" N   GLU A 250 " --> pdb=" O   ASN A 246 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 275 through 286
    Processing helix  chain 'A' and resid 301 through 315
    Processing helix  chain 'A' and resid 335 through 354
    Processing sheet with id=AA1, first strand: chain 'B' and resid 46 through 51
      removed outlier: 6.918A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.694A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.738A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.538A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 3.900A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.871A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.199A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.839A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.436A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.594A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.178A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.253A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 5.908A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.142A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151
      removed outlier: 4.104A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 4.120A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.961A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.377A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.726A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.352A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.486A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 6.585A  pdb=" N   ALA B 208 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 4.526A  pdb=" N   THR B 221 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.754A  pdb=" N   LEU B 210 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.644A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.588A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.648A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.515A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.508A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 4.510A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 6.451A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'R' and resid 207 through 211
    Processing sheet with id=AA9, first strand: chain 'A' and resid 190 through 196
      removed outlier: 6.589A  pdb=" N   LEU A  40 " --> pdb=" O   ARG A 202 " (cutoff:3.500A)
      removed outlier: 7.659A  pdb=" N   VAL A 204 " --> pdb=" O   LEU A  40 " (cutoff:3.500A)
      removed outlier: 6.706A  pdb=" N   LEU A  42 " --> pdb=" O   VAL A 204 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   SER A 225 " --> pdb=" O   LYS A  41 " (cutoff:3.500A)
      removed outlier: 6.241A  pdb=" N   ILE A 226 " --> pdb=" O   ILE A 270 " (cutoff:3.500A)
      removed outlier: 7.113A  pdb=" N   PHE A 272 " --> pdb=" O   ILE A 226 " (cutoff:3.500A)
      removed outlier: 6.623A  pdb=" N   PHE A 228 " --> pdb=" O   PHE A 272 " (cutoff:3.500A)
      removed outlier: 7.478A  pdb=" N   ASN A 274 " --> pdb=" O   PHE A 228 " (cutoff:3.500A)
      removed outlier: 6.751A  pdb=" N   VAL A 230 " --> pdb=" O   ASN A 274 " (cutoff:3.500A)

    403 hydrogen bonds defined for protein.
    1182 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.83

  Time building geometry restraints manager: 0.47 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1494
        1.33 -     1.45: 1246
        1.45 -     1.58: 3250
        1.58 -     1.70: 0
        1.70 -     1.82: 28
  Bond restraints: 6018
  Sorted by residual:
  bond pdb=" N   ILE L  12 "
       pdb=" CA  ILE L  12 "
    ideal  model  delta    sigma   weight residual
    1.457  1.494 -0.037 1.22e-02 6.72e+03 9.05e+00
  bond pdb=" N   ILE A 323 "
       pdb=" CA  ILE A 323 "
    ideal  model  delta    sigma   weight residual
    1.459  1.493 -0.035 1.19e-02 7.06e+03 8.59e+00
  bond pdb=" N   VAL A 314 "
       pdb=" CA  VAL A 314 "
    ideal  model  delta    sigma   weight residual
    1.459  1.495 -0.036 1.25e-02 6.40e+03 8.41e+00
  bond pdb=" N   ILE A 324 "
       pdb=" CA  ILE A 324 "
    ideal  model  delta    sigma   weight residual
    1.459  1.495 -0.036 1.25e-02 6.40e+03 8.08e+00
  bond pdb=" N   TYR A 356 "
       pdb=" CA  TYR A 356 "
    ideal  model  delta    sigma   weight residual
    1.457  1.488 -0.031 1.16e-02 7.43e+03 7.19e+00
  ... (remaining 6013 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.49: 8012
        1.49 -     2.99: 227
        2.99 -     4.48: 38
        4.48 -     5.97: 14
        5.97 -     7.47: 3
  Bond angle restraints: 8294
  Sorted by residual:
  angle pdb=" N   VAL A 314 "
        pdb=" CA  VAL A 314 "
        pdb=" C   VAL A 314 "
      ideal   model   delta    sigma   weight residual
     113.00  108.12    4.88 1.30e+00 5.92e-01 1.41e+01
  angle pdb=" C   ILE A 259 "
        pdb=" CA  ILE A 259 "
        pdb=" CB  ILE A 259 "
      ideal   model   delta    sigma   weight residual
     112.22  107.17    5.05 1.38e+00 5.25e-01 1.34e+01
  angle pdb=" CA  GLY B 272 "
        pdb=" C   GLY B 272 "
        pdb=" O   GLY B 272 "
      ideal   model   delta    sigma   weight residual
     121.90  118.12    3.78 1.08e+00 8.57e-01 1.22e+01
  angle pdb=" CA  LYS A 322 "
        pdb=" C   LYS A 322 "
        pdb=" O   LYS A 322 "
      ideal   model   delta    sigma   weight residual
     121.87  118.10    3.77 1.16e+00 7.43e-01 1.06e+01
  angle pdb=" N   LEU A 316 "
        pdb=" CA  LEU A 316 "
        pdb=" C   LEU A 316 "
      ideal   model   delta    sigma   weight residual
     112.86  108.97    3.89 1.22e+00 6.72e-01 1.02e+01
  ... (remaining 8289 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.63: 3170
       17.63 -    35.26: 203
       35.26 -    52.90: 41
       52.90 -    70.53: 9
       70.53 -    88.16: 3
  Dihedral angle restraints: 3426
    sinusoidal: 775
      harmonic: 2651
  Sorted by residual:
  dihedral pdb=" CA  ASP B  76 "
           pdb=" CB  ASP B  76 "
           pdb=" CG  ASP B  76 "
           pdb=" OD1 ASP B  76 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -87.25   57.25     1      2.00e+01 2.50e-03 1.10e+01
  dihedral pdb=" CA  LYS B  78 "
           pdb=" C   LYS B  78 "
           pdb=" N   LEU B  79 "
           pdb=" CA  LEU B  79 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.99   16.01     0      5.00e+00 4.00e-02 1.03e+01
  dihedral pdb=" SG  CYS R 141 "
           pdb=" CB  CYS R 224 "
           pdb=" SG  CYS R 224 "
           pdb=" CA  CYS R 224 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -73.00  -18.74  -54.26     1      2.00e+01 2.50e-03 9.98e+00
  ... (remaining 3423 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 670
       0.037 -    0.075: 234
       0.075 -    0.112: 79
       0.112 -    0.150: 17
       0.150 -    0.187: 10
  Chirality restraints: 1010
  Sorted by residual:
  chirality pdb=" CA  ILE A 323 "
            pdb=" N   ILE A 323 "
            pdb=" C   ILE A 323 "
            pdb=" CB  ILE A 323 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.62   -0.19 2.00e-01 2.50e+01 8.73e-01
  chirality pdb=" CA  PHE B 235 "
            pdb=" N   PHE B 235 "
            pdb=" C   PHE B 235 "
            pdb=" CB  PHE B 235 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.69   -0.18 2.00e-01 2.50e+01 8.17e-01
  chirality pdb=" CA  LEU A 358 "
            pdb=" N   LEU A 358 "
            pdb=" C   LEU A 358 "
            pdb=" CB  LEU A 358 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.69   -0.18 2.00e-01 2.50e+01 7.76e-01
  ... (remaining 1007 not shown)

  Planarity restraints: 1082
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A 192 "    0.052 5.00e-02 4.00e+02   7.91e-02 1.00e+01
        pdb=" N   PRO A 193 "   -0.137 5.00e-02 4.00e+02
        pdb=" CA  PRO A 193 "    0.042 5.00e-02 4.00e+02
        pdb=" CD  PRO A 193 "    0.043 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN R 360 "   -0.042 5.00e-02 4.00e+02   6.25e-02 6.26e+00
        pdb=" N   PRO R 361 "    0.108 5.00e-02 4.00e+02
        pdb=" CA  PRO R 361 "   -0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO R 361 "   -0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS A 311 "    0.009 2.00e-02 2.50e+03   1.74e-02 3.04e+00
        pdb=" C   LYS A 311 "   -0.030 2.00e-02 2.50e+03
        pdb=" O   LYS A 311 "    0.011 2.00e-02 2.50e+03
        pdb=" N   MET A 312 "    0.010 2.00e-02 2.50e+03
  ... (remaining 1079 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1215
        2.78 -     3.31: 5473
        3.31 -     3.84: 9932
        3.84 -     4.37: 10559
        4.37 -     4.90: 19066
  Nonbonded interactions: 46245
  Sorted by model distance:
  nonbonded pdb=" O   ILE B  58 "
            pdb=" OG  SER B 316 "
     model   vdw
     2.247 3.040
  nonbonded pdb=" O   CYS B 149 "
            pdb=" NH1 ARG B 150 "
     model   vdw
     2.302 3.120
  nonbonded pdb=" OG1 THR B 274 "
            pdb=" O   VAL B 315 "
     model   vdw
     2.316 3.040
  nonbonded pdb=" NE  ARG B 137 "
            pdb=" O   ILE B 171 "
     model   vdw
     2.319 3.120
  nonbonded pdb=" OG  SER R 107 "
            pdb=" OD1 ASN R 158 "
     model   vdw
     2.336 3.040
  ... (remaining 46240 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.440
  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:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.100
  Find NCS groups from input model:        0.030
  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:6.710
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.430
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6892
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      :  0.004   0.055   6019  Z= 0.240
  Angle     :  0.628   7.466   8296  Z= 0.388
  Chirality :  0.046   0.187   1010
  Planarity :  0.004   0.079   1082
  Dihedral  : 13.146  88.162   1699
  Min Nonbonded Distance : 2.247

Molprobity Statistics.
  All-atom Clashscore : 5.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  0.54 %
    Allowed  : 21.98 %
    Favored  : 77.48 %
  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:  1.63 (0.29), residues: 887
  helix:  3.07 (0.25), residues: 406
  sheet:  0.30 (0.43), residues: 150
  loop : -1.18 (0.32), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG L   9 
 TYR   0.030   0.002   TYR R 153 
 PHE   0.019   0.001   PHE R 326 
 TRP   0.023   0.001   TRP R 134 
 HIS   0.002   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00380 ( 6018)
  covalent geometry    : angle       0.62707 ( 8294)
  SS BOND              : bond        0.00414 (    1)
  SS BOND              : angle       2.17118 (    2)
  hydrogen bonds       : bond        0.11296 (  403)
  hydrogen bonds       : angle       4.79818 ( 1182)

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

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

  1774 Ramachandran restraints generated.
    887 Oldfield, 0 Emsley, 887 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1774 Ramachandran restraints generated.
    887 Oldfield, 0 Emsley, 887 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 86
  time to evaluate  : 0.203 
Fit side-chains
REVERT: R  100 THR cc_start: 0.6687 (m) cc_final: 0.6217 (t)
REVERT: R  148 ARG cc_start: 0.7313 (mmm-85) cc_final: 0.7011 (ttm-80)
  outliers start: 2
  outliers final: 1
  residues processed: 88
  average time/residue: 0.2318
  time to fit residues: 22.4419
Evaluate side-chains
  78 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 77
  time to evaluate  : 0.168 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  356 TYR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 53 optimal weight:   40.0000
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    0.6980
   chunk 38 optimal weight:   20.0000
   chunk 61 optimal weight:    4.9990
   chunk 45 optimal weight:    0.0570
   chunk 74 optimal weight:    6.9990
   overall best weight:    1.7504

-------------------------------------------------------------------------------
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 = 0.4544 r_free = 0.4544 target = 0.218733 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.168517 restraints weight = 6706.958|
|-----------------------------------------------------------------------------|
r_work (start): 0.4014 rms_B_bonded: 2.31
r_work: 0.3826 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.3696 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.3696
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7475
moved from start:          0.1012

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   6019  Z= 0.196
  Angle     :  0.598  10.534   8296  Z= 0.311
  Chirality :  0.044   0.142   1010
  Planarity :  0.004   0.066   1082
  Dihedral  :  4.276  42.769    950
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 4.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 20.64 %
    Favored  : 76.14 %
  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:  1.59 (0.29), residues: 887
  helix:  3.10 (0.25), residues: 407
  sheet: -0.14 (0.39), residues: 168
  loop : -1.13 (0.33), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 150 
 TYR   0.016   0.002   TYR R 145 
 PHE   0.015   0.002   PHE B 151 
 TRP   0.013   0.002   TRP R 134 
 HIS   0.003   0.001   HIS A 218 

Details of bonding type rmsd
  covalent geometry    : bond        0.00455 ( 6018)
  covalent geometry    : angle       0.59730 ( 8294)
  SS BOND              : bond        0.00571 (    1)
  SS BOND              : angle       2.31548 (    2)
  hydrogen bonds       : bond        0.04425 (  403)
  hydrogen bonds       : angle       4.22706 ( 1182)

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

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

  1774 Ramachandran restraints generated.
    887 Oldfield, 0 Emsley, 887 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1774 Ramachandran restraints generated.
    887 Oldfield, 0 Emsley, 887 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 79
  time to evaluate  : 0.151 
Fit side-chains
REVERT: R  100 THR cc_start: 0.7340 (m) cc_final: 0.6753 (t)
  outliers start: 12
  outliers final: 4
  residues processed: 89
  average time/residue: 0.2454
  time to fit residues: 24.2456
Evaluate side-chains
  80 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 76
  time to evaluate  : 0.201 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  105 TYR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain R residue  241 THR
Chi-restraints excluded: chain A residue  356 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 46 optimal weight:    0.9980
   chunk 12 optimal weight:    0.9980
   chunk 40 optimal weight:    3.9990
   chunk 19 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9990
   chunk 22 optimal weight:    0.9980
   chunk 43 optimal weight:    0.5980
   chunk 57 optimal weight:    0.9990
   chunk 10 optimal weight:    0.8980
   chunk 47 optimal weight:    0.7980
   chunk 34 optimal weight:    5.9990
   overall best weight:    0.8580

-------------------------------------------------------------------------------
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 = 0.4570 r_free = 0.4570 target = 0.221809 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4131 r_free = 0.4131 target = 0.173029 restraints weight = 6688.966|
|-----------------------------------------------------------------------------|
r_work (start): 0.4068 rms_B_bonded: 2.21
r_work: 0.3862 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.3736 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.3736
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7430
moved from start:          0.1187

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   6019  Z= 0.124
  Angle     :  0.512   7.589   8296  Z= 0.268
  Chirality :  0.042   0.135   1010
  Planarity :  0.004   0.058   1082
  Dihedral  :  3.971  41.336    950
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 4.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 21.98 %
    Favored  : 74.80 %
  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:  1.75 (0.29), residues: 887
  helix:  3.25 (0.25), residues: 407
  sheet:  0.05 (0.40), residues: 163
  loop : -1.13 (0.33), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 314 
 TYR   0.014   0.001   TYR R 145 
 PHE   0.019   0.001   PHE R 326 
 TRP   0.013   0.001   TRP R 134 
 HIS   0.002   0.001   HIS B  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 6018)
  covalent geometry    : angle       0.51028 ( 8294)
  SS BOND              : bond        0.00178 (    1)
  SS BOND              : angle       2.36170 (    2)
  hydrogen bonds       : bond        0.03782 (  403)
  hydrogen bonds       : angle       4.02749 ( 1182)

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

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

  1774 Ramachandran restraints generated.
    887 Oldfield, 0 Emsley, 887 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1774 Ramachandran restraints generated.
    887 Oldfield, 0 Emsley, 887 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 80
  time to evaluate  : 0.149 
Fit side-chains
REVERT: R  100 THR cc_start: 0.7264 (m) cc_final: 0.6719 (t)
  outliers start: 12
  outliers final: 3
  residues processed: 88
  average time/residue: 0.2589
  time to fit residues: 25.0150
Evaluate side-chains
  80 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 77
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain A residue  356 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 22 optimal weight:    0.8980
   chunk 56 optimal weight:    4.9990
   chunk 26 optimal weight:    0.0040
   chunk 63 optimal weight:    0.0770
   chunk 16 optimal weight:    4.9990
   chunk 54 optimal weight:    9.9990
   chunk 38 optimal weight:   30.0000
   chunk 64 optimal weight:    2.9990
   chunk 7 optimal weight:    0.3980
   chunk 59 optimal weight:    1.9990
   chunk 21 optimal weight:    3.9990
   overall best weight:    0.6752

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

Flipped N/Q/H residues before XYZ refinement:
** R 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4579 r_free = 0.4579 target = 0.222562 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.168493 restraints weight = 6618.336|
|-----------------------------------------------------------------------------|
r_work (start): 0.4015 rms_B_bonded: 2.11
r_work: 0.3886 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3754 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.3754
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7403
moved from start:          0.1370

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042   6019  Z= 0.111
  Angle     :  0.487   6.698   8296  Z= 0.256
  Chirality :  0.041   0.135   1010
  Planarity :  0.003   0.047   1082
  Dihedral  :  3.773  38.734    950
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 3.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 23.32 %
    Favored  : 73.73 %
  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:  1.86 (0.29), residues: 887
  helix:  3.34 (0.25), residues: 408
  sheet:  0.07 (0.40), residues: 165
  loop : -1.08 (0.33), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 150 
 TYR   0.022   0.001   TYR R 144 
 PHE   0.022   0.001   PHE R 326 
 TRP   0.016   0.001   TRP R 134 
 HIS   0.001   0.000   HIS A 327 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 ( 6018)
  covalent geometry    : angle       0.48559 ( 8294)
  SS BOND              : bond        0.00536 (    1)
  SS BOND              : angle       2.23418 (    2)
  hydrogen bonds       : bond        0.03500 (  403)
  hydrogen bonds       : angle       3.88884 ( 1182)

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

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

  1774 Ramachandran restraints generated.
    887 Oldfield, 0 Emsley, 887 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1774 Ramachandran restraints generated.
    887 Oldfield, 0 Emsley, 887 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 82
  time to evaluate  : 0.153 
Fit side-chains
REVERT: R  100 THR cc_start: 0.7284 (m) cc_final: 0.6749 (t)
REVERT: R  171 CYS cc_start: 0.8217 (m) cc_final: 0.7969 (m)
REVERT: A  259 ILE cc_start: 0.7437 (OUTLIER) cc_final: 0.7022 (mt)
  outliers start: 11
  outliers final: 7
  residues processed: 90
  average time/residue: 0.2125
  time to fit residues: 21.3081
Evaluate side-chains
  84 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 76
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   91 HIS
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  105 TYR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain R residue  127 PHE
Chi-restraints excluded: chain A residue  259 ILE
Chi-restraints excluded: chain A residue  356 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 46 optimal weight:    0.9990
   chunk 36 optimal weight:    3.9990
   chunk 1 optimal weight:    7.9990
   chunk 60 optimal weight:    3.9990
   chunk 48 optimal weight:    0.8980
   chunk 4 optimal weight:    0.1980
   chunk 3 optimal weight:    7.9990
   chunk 77 optimal weight:    4.9990
   chunk 6 optimal weight:    4.9990
   chunk 30 optimal weight:    8.9990
   chunk 35 optimal weight:    5.9990
   overall best weight:    2.0186

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

Flipped N/Q/H residues before XYZ refinement:
** R 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4477 r_free = 0.4477 target = 0.211771 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.156669 restraints weight = 6748.327|
|-----------------------------------------------------------------------------|
r_work (start): 0.3897 rms_B_bonded: 2.15
r_work: 0.3777 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.3646 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.3646
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7503
moved from start:          0.1780

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.063   6019  Z= 0.217
  Angle     :  0.596  10.743   8296  Z= 0.314
  Chirality :  0.045   0.146   1010
  Planarity :  0.004   0.049   1082
  Dihedral  :  4.258  34.538    950
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 4.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  3.75 %
    Allowed  : 23.59 %
    Favored  : 72.65 %
  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:  1.52 (0.29), residues: 887
  helix:  3.06 (0.25), residues: 408
  sheet: -0.34 (0.39), residues: 169
  loop : -1.08 (0.34), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 150 
 TYR   0.025   0.002   TYR R 153 
 PHE   0.022   0.002   PHE R 326 
 TRP   0.013   0.002   TRP R 134 
 HIS   0.003   0.001   HIS A 218 

Details of bonding type rmsd
  covalent geometry    : bond        0.00516 ( 6018)
  covalent geometry    : angle       0.59455 ( 8294)
  SS BOND              : bond        0.00177 (    1)
  SS BOND              : angle       2.26330 (    2)
  hydrogen bonds       : bond        0.04470 (  403)
  hydrogen bonds       : angle       4.16830 ( 1182)

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

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

  1774 Ramachandran restraints generated.
    887 Oldfield, 0 Emsley, 887 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1774 Ramachandran restraints generated.
    887 Oldfield, 0 Emsley, 887 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 80
  time to evaluate  : 0.146 
Fit side-chains
REVERT: B  298 ASP cc_start: 0.7573 (OUTLIER) cc_final: 0.7156 (p0)
REVERT: R  100 THR cc_start: 0.7622 (m) cc_final: 0.7109 (t)
REVERT: A  259 ILE cc_start: 0.7562 (OUTLIER) cc_final: 0.7050 (mt)
  outliers start: 14
  outliers final: 7
  residues processed: 89
  average time/residue: 0.2570
  time to fit residues: 24.9588
Evaluate side-chains
  86 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 77
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  105 TYR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  298 ASP
Chi-restraints excluded: chain R residue  127 PHE
Chi-restraints excluded: chain R residue  355 VAL
Chi-restraints excluded: chain A residue  259 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 86 optimal weight:    3.9990
   chunk 69 optimal weight:    3.9990
   chunk 55 optimal weight:    4.9990
   chunk 15 optimal weight:    0.7980
   chunk 62 optimal weight:    4.9990
   chunk 87 optimal weight:    0.6980
   chunk 9 optimal weight:    0.9990
   chunk 12 optimal weight:    0.0030
   chunk 52 optimal weight:    3.9990
   chunk 0 optimal weight:   60.0000
   chunk 47 optimal weight:    0.8980
   overall best weight:    0.6792

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4524 r_free = 0.4524 target = 0.217313 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4006 r_free = 0.4006 target = 0.162557 restraints weight = 6679.655|
|-----------------------------------------------------------------------------|
r_work (start): 0.3946 rms_B_bonded: 2.23
r_work: 0.3822 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3692 rms_B_bonded: 4.62 restraints_weight: 0.2500
r_work (final): 0.3692
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7351
moved from start:          0.1795

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   6019  Z= 0.112
  Angle     :  0.497   7.602   8296  Z= 0.264
  Chirality :  0.042   0.158   1010
  Planarity :  0.003   0.044   1082
  Dihedral  :  3.645  19.784    948
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 4.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  4.29 %
    Allowed  : 23.86 %
    Favored  : 71.85 %
  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:  1.74 (0.29), residues: 887
  helix:  3.27 (0.25), residues: 408
  sheet: -0.17 (0.40), residues: 163
  loop : -1.05 (0.34), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 314 
 TYR   0.027   0.002   TYR R 153 
 PHE   0.025   0.001   PHE R 326 
 TRP   0.017   0.001   TRP R 134 
 HIS   0.001   0.000   HIS R 320 

Details of bonding type rmsd
  covalent geometry    : bond        0.00237 ( 6018)
  covalent geometry    : angle       0.49592 ( 8294)
  SS BOND              : bond        0.00004 (    1)
  SS BOND              : angle       2.20700 (    2)
  hydrogen bonds       : bond        0.03585 (  403)
  hydrogen bonds       : angle       3.95688 ( 1182)

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

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

  1774 Ramachandran restraints generated.
    887 Oldfield, 0 Emsley, 887 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1774 Ramachandran restraints generated.
    887 Oldfield, 0 Emsley, 887 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 79
  time to evaluate  : 0.200 
Fit side-chains
REVERT: R  100 THR cc_start: 0.7379 (m) cc_final: 0.6872 (t)
REVERT: R  171 CYS cc_start: 0.8298 (m) cc_final: 0.8025 (m)
  outliers start: 16
  outliers final: 7
  residues processed: 89
  average time/residue: 0.2495
  time to fit residues: 24.3714
Evaluate side-chains
  83 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 76
  time to evaluate  : 0.206 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  105 TYR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  298 ASP
Chi-restraints excluded: chain R residue  127 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 35 optimal weight:   20.0000
   chunk 34 optimal weight:    9.9990
   chunk 66 optimal weight:    2.9990
   chunk 78 optimal weight:    1.9990
   chunk 55 optimal weight:    5.9990
   chunk 41 optimal weight:   30.0000
   chunk 49 optimal weight:    0.8980
   chunk 5 optimal weight:    0.8980
   chunk 20 optimal weight:    9.9990
   chunk 9 optimal weight:    0.6980
   chunk 10 optimal weight:    0.9980
   overall best weight:    1.0982

-------------------------------------------------------------------------------
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 = 0.4501 r_free = 0.4501 target = 0.214669 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.157276 restraints weight = 6756.816|
|-----------------------------------------------------------------------------|
r_work (start): 0.3918 rms_B_bonded: 2.27
r_work: 0.3797 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3663 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.3663
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7444
moved from start:          0.1921

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6019  Z= 0.139
  Angle     :  0.519   7.871   8296  Z= 0.276
  Chirality :  0.043   0.176   1010
  Planarity :  0.003   0.044   1082
  Dihedral  :  3.683  18.264    948
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 4.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 26.01 %
    Favored  : 71.31 %
  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:  1.72 (0.29), residues: 887
  helix:  3.26 (0.25), residues: 408
  sheet: -0.33 (0.39), residues: 170
  loop : -0.97 (0.35), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  68 
 TYR   0.020   0.002   TYR R 144 
 PHE   0.025   0.002   PHE R 326 
 TRP   0.017   0.001   TRP R 134 
 HIS   0.002   0.001   HIS A 218 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 6018)
  covalent geometry    : angle       0.51757 ( 8294)
  SS BOND              : bond        0.00424 (    1)
  SS BOND              : angle       2.24873 (    2)
  hydrogen bonds       : bond        0.03773 (  403)
  hydrogen bonds       : angle       3.98010 ( 1182)

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

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

  1774 Ramachandran restraints generated.
    887 Oldfield, 0 Emsley, 887 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1774 Ramachandran restraints generated.
    887 Oldfield, 0 Emsley, 887 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 78
  time to evaluate  : 0.201 
Fit side-chains
REVERT: R  100 THR cc_start: 0.7449 (m) cc_final: 0.6960 (t)
REVERT: R  171 CYS cc_start: 0.8350 (m) cc_final: 0.8084 (m)
REVERT: A  259 ILE cc_start: 0.7527 (OUTLIER) cc_final: 0.7053 (mt)
  outliers start: 10
  outliers final: 9
  residues processed: 85
  average time/residue: 0.2284
  time to fit residues: 21.5175
Evaluate side-chains
  87 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 77
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue   91 HIS
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  105 TYR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  298 ASP
Chi-restraints excluded: chain R residue  127 PHE
Chi-restraints excluded: chain R residue  241 THR
Chi-restraints excluded: chain A residue  259 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 42 optimal weight:    0.8980
   chunk 52 optimal weight:    8.9990
   chunk 84 optimal weight:    1.9990
   chunk 0 optimal weight:   60.0000
   chunk 1 optimal weight:    2.9990
   chunk 82 optimal weight:    0.0670
   chunk 60 optimal weight:    0.7980
   chunk 47 optimal weight:    0.8980
   chunk 74 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 53 optimal weight:    7.9990
   overall best weight:    0.9320

-------------------------------------------------------------------------------
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 = 0.4518 r_free = 0.4518 target = 0.216892 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.159873 restraints weight = 6755.101|
|-----------------------------------------------------------------------------|
r_work (start): 0.3919 rms_B_bonded: 2.33
r_work: 0.3800 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.3665 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.3665
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7384
moved from start:          0.1956

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6019  Z= 0.128
  Angle     :  0.514   7.823   8296  Z= 0.273
  Chirality :  0.043   0.189   1010
  Planarity :  0.003   0.042   1082
  Dihedral  :  3.632  17.307    948
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 4.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 25.20 %
    Favored  : 71.58 %
  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:  1.78 (0.29), residues: 887
  helix:  3.28 (0.25), residues: 408
  sheet: -0.14 (0.40), residues: 163
  loop : -0.99 (0.34), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  68 
 TYR   0.024   0.001   TYR R 144 
 PHE   0.026   0.002   PHE R 326 
 TRP   0.019   0.001   TRP R 134 
 HIS   0.002   0.001   HIS R 320 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 6018)
  covalent geometry    : angle       0.51247 ( 8294)
  SS BOND              : bond        0.00399 (    1)
  SS BOND              : angle       2.21816 (    2)
  hydrogen bonds       : bond        0.03674 (  403)
  hydrogen bonds       : angle       3.94177 ( 1182)

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

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

  1774 Ramachandran restraints generated.
    887 Oldfield, 0 Emsley, 887 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1774 Ramachandran restraints generated.
    887 Oldfield, 0 Emsley, 887 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 80
  time to evaluate  : 0.217 
Fit side-chains
REVERT: R  100 THR cc_start: 0.7371 (m) cc_final: 0.6892 (t)
REVERT: R  171 CYS cc_start: 0.8331 (m) cc_final: 0.8039 (m)
REVERT: R  353 PHE cc_start: 0.8172 (t80) cc_final: 0.7803 (t80)
REVERT: A  259 ILE cc_start: 0.7474 (OUTLIER) cc_final: 0.7001 (mt)
  outliers start: 12
  outliers final: 6
  residues processed: 87
  average time/residue: 0.2452
  time to fit residues: 23.5420
Evaluate side-chains
  85 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 78
  time to evaluate  : 0.177 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  105 TYR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain R residue  241 THR
Chi-restraints excluded: chain A residue  259 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 15 optimal weight:    0.9980
   chunk 16 optimal weight:    0.9990
   chunk 41 optimal weight:   30.0000
   chunk 69 optimal weight:    0.0470
   chunk 87 optimal weight:    0.8980
   chunk 1 optimal weight:    8.9990
   chunk 37 optimal weight:    1.9990
   chunk 45 optimal weight:    3.9990
   chunk 55 optimal weight:    5.9990
   chunk 11 optimal weight:    2.9990
   chunk 75 optimal weight:    0.1980
   overall best weight:    0.6280

-------------------------------------------------------------------------------
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 = 0.4512 r_free = 0.4512 target = 0.215625 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4067 r_free = 0.4067 target = 0.165812 restraints weight = 6706.172|
|-----------------------------------------------------------------------------|
r_work (start): 0.4024 rms_B_bonded: 2.59
r_work: 0.3848 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3714 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.3714
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7381
moved from start:          0.2017

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.055   6019  Z= 0.110
  Angle     :  0.494   8.191   8296  Z= 0.262
  Chirality :  0.042   0.185   1010
  Planarity :  0.003   0.041   1082
  Dihedral  :  3.458  15.537    948
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 4.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 27.08 %
    Favored  : 70.51 %
  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:  1.85 (0.30), residues: 887
  helix:  3.33 (0.25), residues: 409
  sheet: -0.17 (0.40), residues: 165
  loop : -0.93 (0.35), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 150 
 TYR   0.024   0.001   TYR R 144 
 PHE   0.026   0.001   PHE R 326 
 TRP   0.022   0.001   TRP R 134 
 HIS   0.003   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00236 ( 6018)
  covalent geometry    : angle       0.49300 ( 8294)
  SS BOND              : bond        0.00433 (    1)
  SS BOND              : angle       2.17980 (    2)
  hydrogen bonds       : bond        0.03428 (  403)
  hydrogen bonds       : angle       3.87272 ( 1182)

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

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

  1774 Ramachandran restraints generated.
    887 Oldfield, 0 Emsley, 887 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1774 Ramachandran restraints generated.
    887 Oldfield, 0 Emsley, 887 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 77
  time to evaluate  : 0.208 
Fit side-chains
REVERT: B  283 ARG cc_start: 0.7822 (tpt-90) cc_final: 0.7555 (tpt170)
REVERT: R  100 THR cc_start: 0.7347 (m) cc_final: 0.6881 (t)
REVERT: R  171 CYS cc_start: 0.8227 (m) cc_final: 0.7967 (m)
REVERT: R  353 PHE cc_start: 0.8143 (t80) cc_final: 0.7802 (t80)
  outliers start: 9
  outliers final: 5
  residues processed: 83
  average time/residue: 0.2805
  time to fit residues: 25.3989
Evaluate side-chains
  78 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 73
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue   91 HIS
Chi-restraints excluded: chain B residue  105 TYR
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  317 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 70 optimal weight:    0.5980
   chunk 15 optimal weight:    0.8980
   chunk 22 optimal weight:    0.6980
   chunk 65 optimal weight:    0.9990
   chunk 18 optimal weight:    0.9990
   chunk 80 optimal weight:    0.1980
   chunk 20 optimal weight:    0.9980
   chunk 78 optimal weight:    0.6980
   chunk 11 optimal weight:    2.9990
   chunk 60 optimal weight:    2.9990
   chunk 76 optimal weight:    0.5980
   overall best weight:    0.5580

-------------------------------------------------------------------------------
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 = 0.4518 r_free = 0.4518 target = 0.216324 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 76)----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.159092 restraints weight = 6671.097|
|-----------------------------------------------------------------------------|
r_work (start): 0.3945 rms_B_bonded: 2.26
r_work: 0.3826 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.3692 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.3692
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7393
moved from start:          0.2076

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.051   6019  Z= 0.106
  Angle     :  0.498   9.720   8296  Z= 0.262
  Chirality :  0.042   0.203   1010
  Planarity :  0.003   0.040   1082
  Dihedral  :  3.402  15.061    948
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 4.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 27.61 %
    Favored  : 70.51 %
  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:  1.89 (0.30), residues: 887
  helix:  3.35 (0.25), residues: 409
  sheet: -0.10 (0.40), residues: 163
  loop : -0.92 (0.35), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 150 
 TYR   0.034   0.002   TYR R 153 
 PHE   0.027   0.001   PHE R 326 
 TRP   0.024   0.001   TRP R 134 
 HIS   0.001   0.000   HIS R 320 

Details of bonding type rmsd
  covalent geometry    : bond        0.00227 ( 6018)
  covalent geometry    : angle       0.49676 ( 8294)
  SS BOND              : bond        0.00384 (    1)
  SS BOND              : angle       2.12891 (    2)
  hydrogen bonds       : bond        0.03344 (  403)
  hydrogen bonds       : angle       3.85558 ( 1182)

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

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

  1774 Ramachandran restraints generated.
    887 Oldfield, 0 Emsley, 887 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1774 Ramachandran restraints generated.
    887 Oldfield, 0 Emsley, 887 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 78
  time to evaluate  : 0.181 
Fit side-chains
REVERT: B  283 ARG cc_start: 0.7829 (tpt-90) cc_final: 0.7560 (tpt170)
REVERT: R  100 THR cc_start: 0.7349 (m) cc_final: 0.6884 (t)
REVERT: R  171 CYS cc_start: 0.8224 (m) cc_final: 0.7979 (m)
REVERT: R  353 PHE cc_start: 0.8178 (t80) cc_final: 0.7821 (t80)
  outliers start: 7
  outliers final: 6
  residues processed: 82
  average time/residue: 0.2757
  time to fit residues: 24.5919
Evaluate side-chains
  83 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 77
  time to evaluate  : 0.201 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue   91 HIS
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  105 TYR
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  317 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 9 optimal weight:    0.0170
   chunk 32 optimal weight:    6.9990
   chunk 69 optimal weight:    0.0670
   chunk 50 optimal weight:    0.5980
   chunk 28 optimal weight:    2.9990
   chunk 82 optimal weight:    0.1980
   chunk 5 optimal weight:    0.7980
   chunk 27 optimal weight:    0.9980
   chunk 13 optimal weight:    4.9990
   chunk 81 optimal weight:    5.9990
   chunk 7 optimal weight:    0.9990
   overall best weight:    0.3356

-------------------------------------------------------------------------------
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 = 0.4553 r_free = 0.4553 target = 0.220376 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4144 r_free = 0.4144 target = 0.173257 restraints weight = 6724.960|
|-----------------------------------------------------------------------------|
r_work (start): 0.4065 rms_B_bonded: 2.28
r_work: 0.3892 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3766 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.3766
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7337
moved from start:          0.2139

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.051   6019  Z= 0.096
  Angle     :  0.497   9.059   8296  Z= 0.259
  Chirality :  0.042   0.206   1010
  Planarity :  0.003   0.039   1082
  Dihedral  :  3.301  18.856    948
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 4.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  : 29.22 %
    Favored  : 69.97 %
  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:  1.95 (0.30), residues: 887
  helix:  3.39 (0.25), residues: 410
  sheet: -0.11 (0.40), residues: 164
  loop : -0.87 (0.35), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 150 
 TYR   0.034   0.001   TYR R 153 
 PHE   0.027   0.001   PHE R 326 
 TRP   0.028   0.001   TRP R 134 
 HIS   0.002   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00198 ( 6018)
  covalent geometry    : angle       0.49604 ( 8294)
  SS BOND              : bond        0.00381 (    1)
  SS BOND              : angle       2.06044 (    2)
  hydrogen bonds       : bond        0.03148 (  403)
  hydrogen bonds       : angle       3.79739 ( 1182)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2394.46 seconds
wall clock time: 41 minutes 14.27 seconds (2474.27 seconds total)