Starting phenix.real_space_refine
on Tue Feb 11 20:17:03 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7xmr_33302/02_2025/7xmr_33302.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7xmr_33302/02_2025/7xmr_33302.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7xmr_33302/02_2025/7xmr_33302.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7xmr_33302/02_2025/7xmr_33302.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7xmr_33302/02_2025/7xmr_33302.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7xmr_33302/02_2025/7xmr_33302.cif"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
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      52      5.16       5
     C    4250      2.51       5
     N    1091      2.21       5
     O    1218      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 28 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 6611
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "R"
      Number of atoms: 2165
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 285, 2165
          Classifications: {'peptide': 285}
          Incomplete info: {'truncation_to_alanine': 23}
          Link IDs: {'PTRANS': 11, 'TRANS': 273}
          Unresolved non-hydrogen bonds: 90
          Unresolved non-hydrogen angles: 101
          Unresolved non-hydrogen dihedrals: 83
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'HIS:plan': 1, 'ARG:plan': 3, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 36
    Chain: "A"
      Number of atoms: 1728
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 224, 1728
          Classifications: {'peptide': 224}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 21}
          Link IDs: {'PTRANS': 2, 'TRANS': 221}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 79
          Unresolved non-hydrogen angles: 92
          Unresolved non-hydrogen dihedrals: 66
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 1, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 46
    Chain: "B"
      Number of atoms: 2351
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 314, 2351
          Classifications: {'peptide': 314}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 5, 'TRANS': 308}
          Unresolved non-hydrogen bonds: 54
          Unresolved non-hydrogen angles: 63
          Unresolved non-hydrogen dihedrals: 45
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 7}
          Unresolved non-hydrogen planarities: 43
    Chain: "C"
      Number of atoms: 253
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 34, 253
          Classifications: {'peptide': 34}
          Link IDs: {'PTRANS': 4, 'TRANS': 29}
    Chain: "L"
      Number of atoms: 114
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 14, 114
          Classifications: {'peptide': 14}
          Link IDs: {'TRANS': 13}
  Residues with excluded nonbonded symmetry interactions: 7
    residue:
      pdb=" N   LEU A 234 " occ=0.00
      ... (6 atoms not shown)
      pdb=" CD2 LEU A 234 " occ=0.00
    residue:
      pdb=" N   ALA A 235 " occ=0.00
      ... (3 atoms not shown)
      pdb=" CB  ALA A 235 " occ=0.00
    residue:
      pdb=" N   GLU A 236 " occ=0.00
      ... (3 atoms not shown)
      pdb=" CB  GLU A 236 " occ=0.00
    residue:
      pdb=" N   ASP A 237 " occ=0.00
      ... (3 atoms not shown)
      pdb=" CB  ASP A 237 " occ=0.00
    residue:
      pdb=" N   GLU A 238 " occ=0.00
      ... (3 atoms not shown)
      pdb=" CB  GLU A 238 " occ=0.00
    residue:
      pdb=" N   GLU A 239 " occ=0.00
      ... (3 atoms not shown)
      pdb=" CB  GLU A 239 " occ=0.00
    residue:
      pdb=" N   MET A 240 " occ=0.00
      ... (3 atoms not shown)
      pdb=" CB  MET A 240 " occ=0.00
  Time building chain proxies: 4.06, per 1000 atoms: 0.61
  Number of scatterers: 6611
  At special positions: 0
  Unit cell: (111.815, 114.95, 80.465, 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      52     16.00
     O    1218      8.00
     N    1091      7.00
     C    4250      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 115 " - pdb=" SG  CYS R 193 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L   3 " - pdb=" SG  CYS L  14 " 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: 1.53
  Conformation dependent library (CDL) restraints added in 981.1 milliseconds
  

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1640

  Finding SS restraints...
    Secondary structure from input PDB file:
      21 helices and 9 sheets defined
      43.2% alpha, 18.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.98
  Creating SS restraints...
    Processing helix  chain 'R' and resid 39 through 70
      removed outlier: 3.507A  pdb=" N   ASN R  43 " --> pdb=" O   ASP R  39 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 76 through 95
    Processing helix  chain 'R' and resid 95 through 105
      removed outlier: 3.539A  pdb=" N   LEU R 105 " --> pdb=" O   MET R 101 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 112 through 146
    Processing helix  chain 'R' and resid 149 through 154
    Processing helix  chain 'R' and resid 155 through 173
    Processing helix  chain 'R' and resid 174 through 180
    Processing helix  chain 'R' and resid 203 through 217
      removed outlier: 3.625A  pdb=" N   LEU R 215 " --> pdb=" O   TYR R 211 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 217 through 243
    Processing helix  chain 'R' and resid 246 through 282
      removed outlier: 3.796A  pdb=" N   SER R 250 " --> pdb=" O   LYS R 246 " (cutoff:3.500A)
      Proline residue:  R 271  - end of helix
      removed outlier: 3.560A  pdb=" N   MET R 282 " --> pdb=" O   SER R 278 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 287 through 315
      Proline residue:  R 309  - end of helix
      removed outlier: 3.590A  pdb=" N   LEU R 315 " --> pdb=" O   LEU R 311 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 316 through 323
      removed outlier: 3.531A  pdb=" N   LYS R 320 " --> pdb=" O   SER R 316 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 9 through 33
    Processing helix  chain 'A' and resid 47 through 53
      removed outlier: 3.856A  pdb=" N   LYS A  51 " --> pdb=" O   CYS A  47 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   GLN A  52 " --> pdb=" O   THR A  48 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 207 through 216
      removed outlier: 3.593A  pdb=" N   LYS A 210 " --> pdb=" O   GLU A 207 " (cutoff:3.500A)
      removed outlier: 4.727A  pdb=" N   ILE A 212 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
      removed outlier: 5.655A  pdb=" N   HIS A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   PHE A 215 " --> pdb=" O   ILE A 212 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   GLU A 216 " --> pdb=" O   HIS A 213 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 255
    Processing helix  chain 'A' and resid 270 through 279
    Processing helix  chain 'A' and resid 295 through 309
      removed outlier: 3.650A  pdb=" N   ALA A 299 " --> pdb=" O   THR A 295 " (cutoff:3.500A)
      removed outlier: 4.053A  pdb=" N   ALA A 301 " --> pdb=" O   GLU A 297 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 327 through 352
      removed outlier: 3.765A  pdb=" N   ASN A 331 " --> pdb=" O   THR A 327 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 29 through 44
    Processing helix  chain 'C' and resid 47 through 52
      removed outlier: 3.980A  pdb=" N   LEU C  51 " --> pdb=" O   GLU C  47 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'R' and resid 181 through 185
    Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 191
      removed outlier: 6.507A  pdb=" N   LYS A  35 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
      removed outlier: 7.864A  pdb=" N   ILE A 222 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.241A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 7.297A  pdb=" N   CYS A 224 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 6.220A  pdb=" N   LEU A  39 " --> pdb=" O   CYS A 224 " (cutoff:3.500A)
      removed outlier: 8.425A  pdb=" N   ALA A 226 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 6.154A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.350A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.343A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 7.074A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.640A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51
      removed outlier: 4.182A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  49 " (cutoff:3.500A)
      removed outlier: 6.856A  pdb=" N   ALA B 328 " --> pdb=" O   LEU B 318 " (cutoff:3.500A)
      removed outlier: 4.507A  pdb=" N   LEU B 318 " --> pdb=" O   ALA B 328 " (cutoff:3.500A)
      removed outlier: 6.871A  pdb=" N   GLY B 330 " --> pdb=" O   SER B 316 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63
      removed outlier: 7.306A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.480A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.825A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.364A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.801A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 4.253A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.401A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.574A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.178A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.118A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.339A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.891A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.473A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 190
    Processing sheet with id=AA8, first strand: chain 'B' and resid 231 through 234
      removed outlier: 3.723A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 277
      removed outlier: 3.934A  pdb=" N   TYR B 289 " --> pdb=" O   ASN B 293 " (cutoff:3.500A)
      removed outlier: 5.184A  pdb=" N   ASN B 293 " --> pdb=" O   TYR B 289 " (cutoff:3.500A)

    361 hydrogen bonds defined for protein.
    1044 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.11

  Time building geometry restraints manager: 1.81 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2095
        1.34 -     1.46: 1549
        1.46 -     1.58: 3039
        1.58 -     1.69: 0
        1.69 -     1.81: 71
  Bond restraints: 6754
  Sorted by residual:
  bond pdb=" C   ILE B 270 "
       pdb=" O   ILE B 270 "
    ideal  model  delta    sigma   weight residual
    1.236  1.245 -0.009 1.19e-02 7.06e+03 5.74e-01
  bond pdb=" C   LEU R 270 "
       pdb=" N   PRO R 271 "
    ideal  model  delta    sigma   weight residual
    1.335  1.342 -0.008 1.28e-02 6.10e+03 3.65e-01
  bond pdb=" C   GLY B 144 "
       pdb=" O   GLY B 144 "
    ideal  model  delta    sigma   weight residual
    1.230  1.237 -0.007 1.37e-02 5.33e+03 2.99e-01
  bond pdb=" C   ASP C  48 "
       pdb=" N   PRO C  49 "
    ideal  model  delta    sigma   weight residual
    1.335  1.341 -0.006 1.19e-02 7.06e+03 2.95e-01
  bond pdb=" C   LEU R  96 "
       pdb=" O   LEU R  96 "
    ideal  model  delta    sigma   weight residual
    1.238  1.244 -0.007 1.28e-02 6.10e+03 2.67e-01
  ... (remaining 6749 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.15: 9023
        1.15 -     2.29: 131
        2.29 -     3.44: 25
        3.44 -     4.58: 7
        4.58 -     5.73: 7
  Bond angle restraints: 9193
  Sorted by residual:
  angle pdb=" CA  LEU R  96 "
        pdb=" C   LEU R  96 "
        pdb=" N   PRO R  97 "
      ideal   model   delta    sigma   weight residual
     118.44  121.60   -3.16 1.59e+00 3.96e-01 3.95e+00
  angle pdb=" CA  ILE B 270 "
        pdb=" C   ILE B 270 "
        pdb=" N   CYS B 271 "
      ideal   model   delta    sigma   weight residual
     116.60  119.46   -2.86 1.45e+00 4.76e-01 3.90e+00
  angle pdb=" N   ILE R 210 "
        pdb=" CA  ILE R 210 "
        pdb=" C   ILE R 210 "
      ideal   model   delta    sigma   weight residual
     113.16  110.44    2.72 1.49e+00 4.50e-01 3.33e+00
  angle pdb=" N   ILE B 270 "
        pdb=" CA  ILE B 270 "
        pdb=" C   ILE B 270 "
      ideal   model   delta    sigma   weight residual
     109.34  113.08   -3.74 2.08e+00 2.31e-01 3.23e+00
  angle pdb=" N   LEU R  96 "
        pdb=" CA  LEU R  96 "
        pdb=" C   LEU R  96 "
      ideal   model   delta    sigma   weight residual
     109.81  113.55   -3.74 2.21e+00 2.05e-01 2.87e+00
  ... (remaining 9188 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.17: 3697
       17.17 -    34.35: 212
       34.35 -    51.52: 35
       51.52 -    68.69: 3
       68.69 -    85.87: 3
  Dihedral angle restraints: 3950
    sinusoidal: 1418
      harmonic: 2532
  Sorted by residual:
  dihedral pdb=" CB  CYS L   3 "
           pdb=" SG  CYS L   3 "
           pdb=" SG  CYS L  14 "
           pdb=" CB  CYS L  14 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -130.68   44.68     1      1.00e+01 1.00e-02 2.77e+01
  dihedral pdb=" CB  GLU B 215 "
           pdb=" CG  GLU B 215 "
           pdb=" CD  GLU B 215 "
           pdb=" OE1 GLU B 215 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   85.87  -85.87     1      3.00e+01 1.11e-03 9.90e+00
  dihedral pdb=" CB  GLU C  42 "
           pdb=" CG  GLU C  42 "
           pdb=" CD  GLU C  42 "
           pdb=" OE1 GLU C  42 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -85.81   85.81     1      3.00e+01 1.11e-03 9.89e+00
  ... (remaining 3947 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 685
       0.026 -    0.051: 257
       0.051 -    0.077: 81
       0.077 -    0.102: 38
       0.102 -    0.128: 24
  Chirality restraints: 1085
  Sorted by residual:
  chirality pdb=" CA  ILE B 232 "
            pdb=" N   ILE B 232 "
            pdb=" C   ILE B 232 "
            pdb=" CB  ILE B 232 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.08e-01
  chirality pdb=" CA  ILE B  93 "
            pdb=" N   ILE B  93 "
            pdb=" C   ILE B  93 "
            pdb=" CB  ILE B  93 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 3.91e-01
  chirality pdb=" CA  ILE A 265 "
            pdb=" N   ILE A 265 "
            pdb=" C   ILE A 265 "
            pdb=" CB  ILE A 265 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.83e-01
  ... (remaining 1082 not shown)

  Planarity restraints: 1148
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 193 "    0.019 5.00e-02 4.00e+02   2.82e-02 1.27e+00
        pdb=" N   PRO B 194 "   -0.049 5.00e-02 4.00e+02
        pdb=" CA  PRO B 194 "    0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO B 194 "    0.016 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU R  96 "    0.016 5.00e-02 4.00e+02   2.39e-02 9.15e-01
        pdb=" N   PRO R  97 "   -0.041 5.00e-02 4.00e+02
        pdb=" CA  PRO R  97 "    0.012 5.00e-02 4.00e+02
        pdb=" CD  PRO R  97 "    0.014 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG R 155 "    0.015 5.00e-02 4.00e+02   2.24e-02 8.00e-01
        pdb=" N   PRO R 156 "   -0.039 5.00e-02 4.00e+02
        pdb=" CA  PRO R 156 "    0.011 5.00e-02 4.00e+02
        pdb=" CD  PRO R 156 "    0.013 5.00e-02 4.00e+02
  ... (remaining 1145 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1492
        2.78 -     3.31: 6170
        3.31 -     3.84: 10874
        3.84 -     4.37: 12706
        4.37 -     4.90: 22023
  Nonbonded interactions: 53265
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 277 "
            pdb=" O   LEU B 318 "
     model   vdw
     2.250 3.040
  nonbonded pdb=" OG1 THR B  65 "
            pdb=" O   PRO B 107 "
     model   vdw
     2.287 3.040
  nonbonded pdb=" OG  SER B  74 "
            pdb=" OD1 ASP B  76 "
     model   vdw
     2.298 3.040
  nonbonded pdb=" OH  TYR R 205 "
            pdb=" O   ALA L   1 "
     model   vdw
     2.317 3.040
  nonbonded pdb=" O   ARG B  52 "
            pdb=" NZ  LYS B  89 "
     model   vdw
     2.318 3.120
  ... (remaining 53260 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=0.99
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:             1.850
  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:             0.010
  Extract box with map and model:          0.270
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     18.430
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.880
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.670
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6108
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      :  0.001   0.017   6754  Z= 0.084
  Angle     :  0.400   5.729   9193  Z= 0.231
  Chirality :  0.036   0.128   1085
  Planarity :  0.002   0.028   1148
  Dihedral  : 10.864  85.867   2304
  Min Nonbonded Distance : 2.250

Molprobity Statistics.
  All-atom Clashscore : 5.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.63 %
    Favored  : 98.37 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.39 (0.23), residues: 859
  helix: -2.56 (0.19), residues: 349
  sheet: -1.24 (0.38), residues: 155
  loop : -2.21 (0.29), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.000   TRP B  63 
 HIS   0.006   0.001   HIS A 188 
 PHE   0.006   0.000   PHE R  51 
 TYR   0.004   0.000   TYR B 289 
 ARG   0.001   0.000   ARG B 304 

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

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

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 164
  time to evaluate  : 0.689 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  180 TYR cc_start: 0.7393 (m-80) cc_final: 0.6501 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 164
  average time/residue: 0.2280
  time to fit residues: 47.2421
Evaluate side-chains
  119 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 119
  time to evaluate  : 0.722 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 71 optimal weight:    0.9980
   chunk 64 optimal weight:    0.5980
   chunk 35 optimal weight:    4.9990
   chunk 22 optimal weight:    1.9990
   chunk 43 optimal weight:    9.9990
   chunk 34 optimal weight:    3.9990
   chunk 66 optimal weight:    0.9980
   chunk 25 optimal weight:    0.9980
   chunk 40 optimal weight:    0.6980
   chunk 49 optimal weight:    1.9990
   chunk 77 optimal weight:    2.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
R  43 ASN
R 146 HIS
R 186 ASN
** R 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 276 ASN
R 304 ASN
A  22 ASN
A 331 ASN
A 333 GLN
B  62 HIS
B  88 ASN
B 110 ASN
B 340 ASN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4700 r_free = 0.4700 target = 0.215418 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4382 r_free = 0.4382 target = 0.180879 restraints weight = 6850.685|
|-----------------------------------------------------------------------------|
r_work (start): 0.4380 rms_B_bonded: 2.27
r_work: 0.4249 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.4249
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6782
moved from start:          0.2564

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   6754  Z= 0.235
  Angle     :  0.584   7.459   9193  Z= 0.305
  Chirality :  0.042   0.142   1085
  Planarity :  0.004   0.046   1148
  Dihedral  :  3.459  24.340    921
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 8.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 11.48 %
    Favored  : 87.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.15 (0.27), residues: 859
  helix:  0.25 (0.26), residues: 348
  sheet: -1.04 (0.37), residues: 166
  loop : -1.59 (0.31), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  99 
 HIS   0.008   0.002   HIS B 311 
 PHE   0.011   0.001   PHE R 272 
 TYR   0.015   0.002   TYR R 228 
 ARG   0.009   0.001   ARG A 208 

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

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

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 128
  time to evaluate  : 0.726 
Fit side-chains
   revert: symmetry clash
REVERT: R  180 TYR cc_start: 0.8147 (m-80) cc_final: 0.7266 (m-10)
REVERT: R  241 ARG cc_start: 0.7320 (ttp-170) cc_final: 0.7099 (ttp-170)
REVERT: A  349 LYS cc_start: 0.7776 (mtpp) cc_final: 0.7531 (mttt)
  outliers start: 10
  outliers final: 8
  residues processed: 133
  average time/residue: 0.1987
  time to fit residues: 34.8577
Evaluate side-chains
  119 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 111
  time to evaluate  : 0.747 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  105 LEU
Chi-restraints excluded: chain R residue  153 TRP
Chi-restraints excluded: chain R residue  196 ASN
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  200 ASP
Chi-restraints excluded: chain A residue  331 ASN
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 24 optimal weight:    6.9990
   chunk 37 optimal weight:    2.9990
   chunk 55 optimal weight:    2.9990
   chunk 68 optimal weight:    3.9990
   chunk 54 optimal weight:    0.7980
   chunk 32 optimal weight:    1.9990
   chunk 9 optimal weight:    3.9990
   chunk 82 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9980
   chunk 64 optimal weight:    2.9990
   chunk 63 optimal weight:    0.9980
   overall best weight:    1.3584

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

Flipped N/Q/H residues before XYZ refinement:
A 213 HIS
** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 340 ASN
L   5 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4544 r_free = 0.4544 target = 0.199160 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4190 r_free = 0.4190 target = 0.163404 restraints weight = 7066.608|
|-----------------------------------------------------------------------------|
r_work (start): 0.4174 rms_B_bonded: 2.21
r_work: 0.4038 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work (final): 0.4038
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7084
moved from start:          0.3899

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   6754  Z= 0.325
  Angle     :  0.658   8.268   9193  Z= 0.346
  Chirality :  0.045   0.159   1085
  Planarity :  0.004   0.038   1148
  Dihedral  :  4.020  21.328    921
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 12.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 15.64 %
    Favored  : 82.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.54 (0.28), residues: 859
  helix:  0.90 (0.27), residues: 349
  sheet: -0.87 (0.37), residues: 169
  loop : -1.35 (0.32), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP B  82 
 HIS   0.006   0.002   HIS B  54 
 PHE   0.023   0.002   PHE R 272 
 TYR   0.014   0.002   TYR R 273 
 ARG   0.012   0.001   ARG A 208 

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

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

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 125
  time to evaluate  : 0.777 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  101 MET cc_start: 0.6162 (mmt) cc_final: 0.5828 (mmm)
REVERT: A  349 LYS cc_start: 0.7915 (mtpp) cc_final: 0.7635 (mttm)
REVERT: B  329 THR cc_start: 0.8775 (m) cc_final: 0.8371 (p)
  outliers start: 16
  outliers final: 12
  residues processed: 132
  average time/residue: 0.1831
  time to fit residues: 32.7640
Evaluate side-chains
  121 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 109
  time to evaluate  : 0.698 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  105 LEU
Chi-restraints excluded: chain R residue  153 TRP
Chi-restraints excluded: chain R residue  196 ASN
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue   55 THR
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain B residue   82 TRP
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  300 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 23 optimal weight:    0.9990
   chunk 41 optimal weight:    1.9990
   chunk 72 optimal weight:    0.7980
   chunk 37 optimal weight:    0.5980
   chunk 68 optimal weight:    0.9990
   chunk 48 optimal weight:    0.7980
   chunk 30 optimal weight:    0.9990
   chunk 13 optimal weight:    1.9990
   chunk 6 optimal weight:    4.9990
   chunk 43 optimal weight:    7.9990
   chunk 64 optimal weight:    0.0870
   overall best weight:    0.6560

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

Flipped N/Q/H residues before XYZ refinement:
R  61 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4570 r_free = 0.4570 target = 0.202091 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4226 r_free = 0.4226 target = 0.166963 restraints weight = 7039.236|
|-----------------------------------------------------------------------------|
r_work (start): 0.4244 rms_B_bonded: 2.21
r_work: 0.4110 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work (final): 0.4110
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7023
moved from start:          0.4013

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6754  Z= 0.196
  Angle     :  0.560   8.105   9193  Z= 0.293
  Chirality :  0.042   0.175   1085
  Planarity :  0.003   0.042   1148
  Dihedral  :  3.856  22.014    921
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 9.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 18.36 %
    Favored  : 79.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.16 (0.29), residues: 859
  helix:  1.32 (0.28), residues: 355
  sheet: -0.74 (0.37), residues: 169
  loop : -1.29 (0.33), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP B  82 
 HIS   0.005   0.001   HIS A 188 
 PHE   0.012   0.001   PHE A 334 
 TYR   0.017   0.002   TYR B  59 
 ARG   0.011   0.001   ARG A 208 

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

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

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 121
  time to evaluate  : 0.738 
Fit side-chains
REVERT: A  182 THR cc_start: 0.6569 (m) cc_final: 0.6290 (t)
REVERT: A  349 LYS cc_start: 0.7888 (mtpp) cc_final: 0.7602 (mttm)
REVERT: B   95 LEU cc_start: 0.7824 (mt) cc_final: 0.7602 (mp)
REVERT: B  101 MET cc_start: 0.8326 (mtp) cc_final: 0.8113 (mtp)
REVERT: B  220 GLN cc_start: 0.7816 (mt0) cc_final: 0.7446 (mm-40)
REVERT: B  329 THR cc_start: 0.8820 (m) cc_final: 0.8333 (p)
  outliers start: 16
  outliers final: 13
  residues processed: 129
  average time/residue: 0.1991
  time to fit residues: 34.0825
Evaluate side-chains
  126 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 113
  time to evaluate  : 0.747 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  105 LEU
Chi-restraints excluded: chain R residue  153 TRP
Chi-restraints excluded: chain R residue  196 ASN
Chi-restraints excluded: chain A residue   55 THR
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  200 ASP
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain B residue   82 TRP
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain L residue    6 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 60 optimal weight:    0.8980
   chunk 5 optimal weight:    0.8980
   chunk 7 optimal weight:    0.9990
   chunk 48 optimal weight:    0.8980
   chunk 82 optimal weight:    0.6980
   chunk 59 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9980
   chunk 13 optimal weight:    1.9990
   chunk 4 optimal weight:    0.6980
   chunk 56 optimal weight:    0.3980
   chunk 10 optimal weight:    1.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
R 186 ASN
R 276 ASN
A 188 HIS
** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4539 r_free = 0.4539 target = 0.199369 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4200 r_free = 0.4200 target = 0.164964 restraints weight = 6952.140|
|-----------------------------------------------------------------------------|
r_work (start): 0.4207 rms_B_bonded: 2.11
r_work: 0.4079 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.3921 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.3921
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7150
moved from start:          0.4256

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6754  Z= 0.207
  Angle     :  0.557   6.924   9193  Z= 0.292
  Chirality :  0.042   0.155   1085
  Planarity :  0.004   0.042   1148
  Dihedral  :  3.847  21.843    921
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 8.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 18.51 %
    Favored  : 78.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.06 (0.29), residues: 859
  helix:  1.58 (0.28), residues: 349
  sheet: -0.77 (0.37), residues: 173
  loop : -1.11 (0.34), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP B  82 
 HIS   0.003   0.001   HIS B 311 
 PHE   0.028   0.001   PHE R 272 
 TYR   0.020   0.002   TYR B  59 
 ARG   0.010   0.001   ARG A 208 

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

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

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 119
  time to evaluate  : 0.713 
Fit side-chains
REVERT: R  101 MET cc_start: 0.6147 (mmt) cc_final: 0.5886 (mmm)
REVERT: A  182 THR cc_start: 0.6856 (m) cc_final: 0.6384 (t)
REVERT: A  349 LYS cc_start: 0.7949 (mtpp) cc_final: 0.7655 (mttt)
REVERT: B   95 LEU cc_start: 0.7892 (mt) cc_final: 0.7692 (mp)
REVERT: B  220 GLN cc_start: 0.7967 (mt0) cc_final: 0.7633 (mm-40)
REVERT: B  260 GLU cc_start: 0.7235 (tp30) cc_final: 0.6929 (tp30)
REVERT: B  329 THR cc_start: 0.8846 (m) cc_final: 0.8382 (p)
  outliers start: 18
  outliers final: 13
  residues processed: 129
  average time/residue: 0.1978
  time to fit residues: 34.0377
Evaluate side-chains
  121 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 108
  time to evaluate  : 0.684 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  105 LEU
Chi-restraints excluded: chain R residue  153 TRP
Chi-restraints excluded: chain R residue  196 ASN
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue   55 THR
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  200 ASP
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain B residue   82 TRP
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain L residue    6 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 34 optimal weight:    1.9990
   chunk 38 optimal weight:    8.9990
   chunk 66 optimal weight:    0.8980
   chunk 33 optimal weight:    0.7980
   chunk 15 optimal weight:    4.9990
   chunk 13 optimal weight:    0.8980
   chunk 36 optimal weight:    0.6980
   chunk 59 optimal weight:    0.0370
   chunk 26 optimal weight:    0.6980
   chunk 67 optimal weight:    0.6980
   chunk 43 optimal weight:    3.9990
   overall best weight:    0.5858

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

Flipped N/Q/H residues before XYZ refinement:
A 269 ASN
A 331 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4542 r_free = 0.4542 target = 0.199949 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4211 r_free = 0.4211 target = 0.166091 restraints weight = 6872.600|
|-----------------------------------------------------------------------------|
r_work (start): 0.4218 rms_B_bonded: 2.08
r_work: 0.4091 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.3937 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.3937
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7132
moved from start:          0.4344

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6754  Z= 0.191
  Angle     :  0.551   6.958   9193  Z= 0.288
  Chirality :  0.042   0.158   1085
  Planarity :  0.004   0.045   1148
  Dihedral  :  3.844  19.951    921
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 8.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.26 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 18.65 %
    Favored  : 77.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.10 (0.29), residues: 859
  helix:  1.57 (0.28), residues: 354
  sheet: -0.78 (0.35), residues: 181
  loop : -1.05 (0.35), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP B  82 
 HIS   0.005   0.001   HIS B 183 
 PHE   0.026   0.001   PHE A 189 
 TYR   0.014   0.001   TYR B  59 
 ARG   0.011   0.001   ARG A 208 

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

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

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 117
  time to evaluate  : 0.797 
Fit side-chains
REVERT: R  101 MET cc_start: 0.6130 (mmt) cc_final: 0.5881 (mmm)
REVERT: A  349 LYS cc_start: 0.7971 (mtpp) cc_final: 0.7687 (mttt)
REVERT: B   95 LEU cc_start: 0.7879 (mt) cc_final: 0.7650 (mp)
REVERT: B  217 MET cc_start: 0.7631 (ppp) cc_final: 0.7426 (ppp)
REVERT: B  329 THR cc_start: 0.8864 (m) cc_final: 0.8428 (p)
  outliers start: 24
  outliers final: 21
  residues processed: 131
  average time/residue: 0.1898
  time to fit residues: 33.2110
Evaluate side-chains
  131 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 110
  time to evaluate  : 0.760 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  105 LEU
Chi-restraints excluded: chain R residue  121 VAL
Chi-restraints excluded: chain R residue  122 ASP
Chi-restraints excluded: chain R residue  153 TRP
Chi-restraints excluded: chain R residue  196 ASN
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue   55 THR
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  200 ASP
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  285 ILE
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain A residue  331 ASN
Chi-restraints excluded: chain B residue   82 TRP
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain L residue    6 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 42 optimal weight:    0.5980
   chunk 65 optimal weight:    5.9990
   chunk 57 optimal weight:    2.9990
   chunk 16 optimal weight:    0.2980
   chunk 72 optimal weight:    1.9990
   chunk 71 optimal weight:    0.4980
   chunk 35 optimal weight:    0.5980
   chunk 26 optimal weight:    0.7980
   chunk 7 optimal weight:    0.4980
   chunk 8 optimal weight:    0.8980
   chunk 83 optimal weight:    2.9990
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 331 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4561 r_free = 0.4561 target = 0.201787 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4228 r_free = 0.4228 target = 0.167335 restraints weight = 6861.234|
|-----------------------------------------------------------------------------|
r_work (start): 0.4245 rms_B_bonded: 2.16
r_work: 0.4114 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work (final): 0.4114
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7017
moved from start:          0.4381

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6754  Z= 0.178
  Angle     :  0.561   7.785   9193  Z= 0.291
  Chirality :  0.042   0.157   1085
  Planarity :  0.003   0.048   1148
  Dihedral  :  3.804  19.085    921
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 9.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  : 18.79 %
    Favored  : 77.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.16 (0.29), residues: 859
  helix:  1.61 (0.28), residues: 355
  sheet: -0.74 (0.35), residues: 181
  loop : -1.04 (0.35), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP B  82 
 HIS   0.007   0.001   HIS B 183 
 PHE   0.017   0.001   PHE A 189 
 TYR   0.014   0.001   TYR B  59 
 ARG   0.011   0.001   ARG A 208 

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

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

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 117
  time to evaluate  : 0.670 
Fit side-chains
REVERT: R  101 MET cc_start: 0.6079 (mmt) cc_final: 0.5851 (mmm)
REVERT: A  349 LYS cc_start: 0.8044 (mtpp) cc_final: 0.7798 (mttt)
REVERT: B  329 THR cc_start: 0.8790 (m) cc_final: 0.8364 (p)
REVERT: C   46 LYS cc_start: 0.7085 (mmtt) cc_final: 0.6668 (mmtt)
  outliers start: 26
  outliers final: 23
  residues processed: 133
  average time/residue: 0.1896
  time to fit residues: 33.4802
Evaluate side-chains
  137 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 114
  time to evaluate  : 0.756 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   58 LEU
Chi-restraints excluded: chain R residue  105 LEU
Chi-restraints excluded: chain R residue  121 VAL
Chi-restraints excluded: chain R residue  122 ASP
Chi-restraints excluded: chain R residue  153 TRP
Chi-restraints excluded: chain R residue  196 ASN
Chi-restraints excluded: chain R residue  304 ASN
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue   55 THR
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  200 ASP
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  285 ILE
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain A residue  325 CYS
Chi-restraints excluded: chain A residue  331 ASN
Chi-restraints excluded: chain B residue   82 TRP
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain L residue    6 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 37 optimal weight:    0.8980
   chunk 33 optimal weight:    0.6980
   chunk 8 optimal weight:    0.7980
   chunk 22 optimal weight:    0.7980
   chunk 54 optimal weight:    0.7980
   chunk 36 optimal weight:    0.1980
   chunk 59 optimal weight:    2.9990
   chunk 18 optimal weight:    0.7980
   chunk 35 optimal weight:    2.9990
   chunk 46 optimal weight:    3.9990
   chunk 31 optimal weight:    0.9980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
R 276 ASN
** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 331 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4548 r_free = 0.4548 target = 0.200487 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4210 r_free = 0.4210 target = 0.165752 restraints weight = 6940.731|
|-----------------------------------------------------------------------------|
r_work (start): 0.4217 rms_B_bonded: 2.18
r_work: 0.4083 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work (final): 0.4083
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7042
moved from start:          0.4496

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6754  Z= 0.197
  Angle     :  0.568   7.440   9193  Z= 0.293
  Chirality :  0.042   0.162   1085
  Planarity :  0.004   0.056   1148
  Dihedral  :  3.845  17.992    921
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 9.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 18.94 %
    Favored  : 77.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.21 (0.29), residues: 859
  helix:  1.73 (0.28), residues: 349
  sheet: -0.76 (0.35), residues: 181
  loop : -1.02 (0.35), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP B  82 
 HIS   0.006   0.001   HIS B 183 
 PHE   0.017   0.001   PHE A 189 
 TYR   0.015   0.001   TYR B  59 
 ARG   0.011   0.001   ARG A 208 

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

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

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 114
  time to evaluate  : 0.750 
Fit side-chains
REVERT: R  101 MET cc_start: 0.6051 (mmt) cc_final: 0.5818 (mmm)
REVERT: A  349 LYS cc_start: 0.7889 (mtpp) cc_final: 0.7611 (mttt)
REVERT: B  329 THR cc_start: 0.8803 (m) cc_final: 0.8391 (p)
REVERT: C   46 LYS cc_start: 0.6956 (mmtt) cc_final: 0.6571 (mmtt)
  outliers start: 25
  outliers final: 23
  residues processed: 129
  average time/residue: 0.2073
  time to fit residues: 36.1464
Evaluate side-chains
  132 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 109
  time to evaluate  : 0.905 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   58 LEU
Chi-restraints excluded: chain R residue  105 LEU
Chi-restraints excluded: chain R residue  121 VAL
Chi-restraints excluded: chain R residue  122 ASP
Chi-restraints excluded: chain R residue  153 TRP
Chi-restraints excluded: chain R residue  196 ASN
Chi-restraints excluded: chain R residue  304 ASN
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue   55 THR
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  200 ASP
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  285 ILE
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain A residue  325 CYS
Chi-restraints excluded: chain A residue  331 ASN
Chi-restraints excluded: chain B residue   82 TRP
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain L residue    6 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 58 optimal weight:    0.6980
   chunk 41 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   chunk 3 optimal weight:   10.0000
   chunk 65 optimal weight:    5.9990
   chunk 64 optimal weight:    0.7980
   chunk 18 optimal weight:    0.5980
   chunk 31 optimal weight:    0.8980
   chunk 51 optimal weight:    4.9990
   chunk 49 optimal weight:    0.9980
   chunk 70 optimal weight:    1.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** R 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 331 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4530 r_free = 0.4530 target = 0.198509 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4189 r_free = 0.4189 target = 0.163609 restraints weight = 6988.030|
|-----------------------------------------------------------------------------|
r_work (start): 0.4186 rms_B_bonded: 2.18
r_work: 0.4050 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work (final): 0.4050
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7066
moved from start:          0.4591

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6754  Z= 0.223
  Angle     :  0.597   8.479   9193  Z= 0.306
  Chirality :  0.043   0.157   1085
  Planarity :  0.004   0.061   1148
  Dihedral  :  3.912  17.909    921
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 9.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 18.79 %
    Favored  : 77.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.19 (0.29), residues: 859
  helix:  1.70 (0.28), residues: 348
  sheet: -0.76 (0.35), residues: 179
  loop : -1.01 (0.35), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP B  82 
 HIS   0.006   0.001   HIS B 183 
 PHE   0.017   0.001   PHE A 189 
 TYR   0.016   0.001   TYR B  59 
 ARG   0.012   0.001   ARG A 208 

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

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

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 116
  time to evaluate  : 0.716 
Fit side-chains
REVERT: A  182 THR cc_start: 0.6840 (OUTLIER) cc_final: 0.6480 (t)
REVERT: A  349 LYS cc_start: 0.7875 (mtpp) cc_final: 0.7607 (mttt)
REVERT: B  329 THR cc_start: 0.8841 (m) cc_final: 0.8427 (p)
REVERT: L    4 LYS cc_start: 0.8158 (mmtt) cc_final: 0.7896 (mmtt)
  outliers start: 25
  outliers final: 22
  residues processed: 132
  average time/residue: 0.1973
  time to fit residues: 34.5712
Evaluate side-chains
  136 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 113
  time to evaluate  : 0.753 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  105 LEU
Chi-restraints excluded: chain R residue  121 VAL
Chi-restraints excluded: chain R residue  122 ASP
Chi-restraints excluded: chain R residue  153 TRP
Chi-restraints excluded: chain R residue  196 ASN
Chi-restraints excluded: chain R residue  304 ASN
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue   55 THR
Chi-restraints excluded: chain A residue  182 THR
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  285 ILE
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain A residue  325 CYS
Chi-restraints excluded: chain A residue  331 ASN
Chi-restraints excluded: chain B residue   82 TRP
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain L residue    6 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 67 optimal weight:    0.4980
   chunk 48 optimal weight:    0.7980
   chunk 84 optimal weight:    0.3980
   chunk 46 optimal weight:    3.9990
   chunk 36 optimal weight:    0.7980
   chunk 0 optimal weight:   10.0000
   chunk 65 optimal weight:    4.9990
   chunk 11 optimal weight:    0.7980
   chunk 74 optimal weight:    0.0060
   chunk 51 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9980
   overall best weight:    0.4996

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

Flipped N/Q/H residues before XYZ refinement:
** R 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 269 ASN
A 331 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4535 r_free = 0.4535 target = 0.199398 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4200 r_free = 0.4200 target = 0.165070 restraints weight = 7087.829|
|-----------------------------------------------------------------------------|
r_work (start): 0.4228 rms_B_bonded: 2.15
r_work: 0.4103 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.3944 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.3944
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7131
moved from start:          0.4614

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6754  Z= 0.184
  Angle     :  0.590   9.175   9193  Z= 0.300
  Chirality :  0.042   0.162   1085
  Planarity :  0.004   0.056   1148
  Dihedral  :  3.884  18.115    921
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 9.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 19.51 %
    Favored  : 77.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.25 (0.29), residues: 859
  helix:  1.74 (0.28), residues: 348
  sheet: -0.76 (0.35), residues: 179
  loop : -0.96 (0.36), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP B  82 
 HIS   0.005   0.001   HIS B 183 
 PHE   0.016   0.001   PHE A 189 
 TYR   0.013   0.001   TYR B  59 
 ARG   0.012   0.001   ARG A 208 

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

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

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 117
  time to evaluate  : 0.823 
Fit side-chains
REVERT: R  101 MET cc_start: 0.6107 (mmt) cc_final: 0.5862 (mmm)
REVERT: A  182 THR cc_start: 0.6930 (OUTLIER) cc_final: 0.6447 (t)
REVERT: A  308 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7585 (mt-10)
REVERT: A  349 LYS cc_start: 0.8125 (mtpp) cc_final: 0.7850 (mttt)
REVERT: B  329 THR cc_start: 0.8823 (m) cc_final: 0.8432 (p)
REVERT: L    4 LYS cc_start: 0.8225 (mmtt) cc_final: 0.7963 (mmtt)
  outliers start: 23
  outliers final: 21
  residues processed: 130
  average time/residue: 0.2059
  time to fit residues: 35.5881
Evaluate side-chains
  135 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 113
  time to evaluate  : 0.769 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  105 LEU
Chi-restraints excluded: chain R residue  121 VAL
Chi-restraints excluded: chain R residue  122 ASP
Chi-restraints excluded: chain R residue  153 TRP
Chi-restraints excluded: chain R residue  196 ASN
Chi-restraints excluded: chain R residue  304 ASN
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue   55 THR
Chi-restraints excluded: chain A residue  182 THR
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  285 ILE
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain A residue  325 CYS
Chi-restraints excluded: chain A residue  331 ASN
Chi-restraints excluded: chain B residue   82 TRP
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain L residue    6 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 40 optimal weight:    1.9990
   chunk 32 optimal weight:    8.9990
   chunk 22 optimal weight:    0.5980
   chunk 26 optimal weight:    1.9990
   chunk 3 optimal weight:    8.9990
   chunk 35 optimal weight:    5.9990
   chunk 6 optimal weight:    0.9990
   chunk 5 optimal weight:    0.8980
   chunk 24 optimal weight:    3.9990
   chunk 11 optimal weight:    0.4980
   chunk 50 optimal weight:    0.0870
   overall best weight:    0.6160

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

Flipped N/Q/H residues before XYZ refinement:
** R 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 269 ASN
A 331 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4548 r_free = 0.4548 target = 0.200897 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4207 r_free = 0.4207 target = 0.165863 restraints weight = 7118.433|
|-----------------------------------------------------------------------------|
r_work (start): 0.4214 rms_B_bonded: 2.25
r_work: 0.4083 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work (final): 0.4083
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7041
moved from start:          0.4666

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6754  Z= 0.200
  Angle     :  0.596  10.099   9193  Z= 0.303
  Chirality :  0.042   0.160   1085
  Planarity :  0.004   0.055   1148
  Dihedral  :  3.903  18.229    921
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 9.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 20.37 %
    Favored  : 76.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.22 (0.29), residues: 859
  helix:  1.72 (0.28), residues: 349
  sheet: -0.78 (0.35), residues: 179
  loop : -0.98 (0.36), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP B  82 
 HIS   0.005   0.001   HIS B 183 
 PHE   0.018   0.001   PHE A 189 
 TYR   0.013   0.001   TYR B  59 
 ARG   0.011   0.001   ARG A 208 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4869.26 seconds
wall clock time: 87 minutes 5.55 seconds (5225.55 seconds total)