Starting phenix.real_space_refine
on Wed Feb 12 08:41:31 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7zth_14960/02_2025/7zth_14960.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7zth_14960/02_2025/7zth_14960.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7zth_14960/02_2025/7zth_14960.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7zth_14960/02_2025/7zth_14960.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7zth_14960/02_2025/7zth_14960.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7zth_14960/02_2025/7zth_14960.cif"
  }
  resolution = 4.0
  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=   1.000
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      84      5.49       5
     S      18      5.16       5
     C    4622      2.51       5
     N    1325      2.21       5
     O    1571      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 22 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: 7620
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 2962
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 360, 2962
          Classifications: {'peptide': 360}
          Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 343}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'LLP:plan-2': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "B"
      Number of atoms: 2977
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 362, 2977
          Classifications: {'peptide': 362}
          Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 345}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'LLP:plan-2': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "C"
      Number of atoms: 834
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 41, 834
          Classifications: {'DNA': 41}
          Link IDs: {'rna3p': 40}
    Chain: "D"
      Number of atoms: 847
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 41, 847
          Classifications: {'DNA': 41}
          Link IDs: {'rna3p': 40}
  Time building chain proxies: 5.02, per 1000 atoms: 0.66
  Number of scatterers: 7620
  At special positions: 0
  Unit cell: (82.677, 90.678, 132.461, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      18     16.00
     P      84     15.00
     O    1571      8.00
     N    1325      7.00
     C    4622      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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: 2.09
  Conformation dependent library (CDL) restraints added in 675.0 milliseconds
  

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1368

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 6 sheets defined
      37.4% alpha, 8.6% beta
      12 base pairs and 56 stacking pairs defined.
    Time for finding SS restraints: 2.39
  Creating SS restraints...
    Processing helix  chain 'A' and resid 120 through 125
    Processing helix  chain 'A' and resid 126 through 129
    Processing helix  chain 'A' and resid 148 through 159
      removed outlier: 3.545A  pdb=" N   ARG A 152 " --> pdb=" O   GLU A 148 " (cutoff:3.500A)
      removed outlier: 4.352A  pdb=" N   GLU A 154 " --> pdb=" O   SER A 150 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   ILE A 155 " --> pdb=" O   PHE A 151 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   TYR A 157 " --> pdb=" O   ARG A 153 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 178 through 190
      removed outlier: 4.151A  pdb=" N   GLN A 184 " --> pdb=" O   THR A 180 " (cutoff:3.500A)
      removed outlier: 4.470A  pdb=" N   LEU A 185 " --> pdb=" O   LEU A 181 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   LEU A 187 " --> pdb=" O   GLN A 183 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   LEU A 188 " --> pdb=" O   GLN A 184 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 204 through 209
      removed outlier: 3.695A  pdb=" N   LEU A 209 " --> pdb=" O   MET A 205 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 233
    Processing helix  chain 'A' and resid 255 through 267
      removed outlier: 3.554A  pdb=" N   LYS A 259 " --> pdb=" O   ILE A 255 " (cutoff:3.500A)
      removed outlier: 4.278A  pdb=" N   GLN A 260 " --> pdb=" O   ASN A 256 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   ALA A 265 " --> pdb=" O   LEU A 261 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   GLU A 266 " --> pdb=" O   LEU A 262 " (cutoff:3.500A)
      removed outlier: 4.030A  pdb=" N   ALA A 267 " --> pdb=" O   HIS A 263 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 312 through 316
      removed outlier: 4.130A  pdb=" N   VAL A 315 " --> pdb=" O   ILE A 312 " (cutoff:3.500A)
      removed outlier: 3.921A  pdb=" N   ARG A 316 " --> pdb=" O   PRO A 313 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 312 through 316'
    Processing helix  chain 'A' and resid 323 through 334
      removed outlier: 3.971A  pdb=" N   HIS A 328 " --> pdb=" O   ALA A 324 " (cutoff:3.500A)
      removed outlier: 4.651A  pdb=" N   LEU A 329 " --> pdb=" O   PRO A 325 " (cutoff:3.500A)
      removed outlier: 4.271A  pdb=" N   ASN A 332 " --> pdb=" O   HIS A 328 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 342 through 346
      removed outlier: 3.537A  pdb=" N   GLN A 346 " --> pdb=" O   ARG A 343 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 347 through 352
      removed outlier: 3.879A  pdb=" N   ALA A 351 " --> pdb=" O   GLN A 347 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 361 through 381
      removed outlier: 4.161A  pdb=" N   LYS A 367 " --> pdb=" O   ASN A 363 " (cutoff:3.500A)
      removed outlier: 3.879A  pdb=" N   ILE A 368 " --> pdb=" O   ARG A 364 " (cutoff:3.500A)
      removed outlier: 3.821A  pdb=" N   LYS A 372 " --> pdb=" O   ILE A 368 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   LYS A 375 " --> pdb=" O   ARG A 371 " (cutoff:3.500A)
      removed outlier: 3.981A  pdb=" N   LEU A 379 " --> pdb=" O   LYS A 375 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 407 through 416
      removed outlier: 3.895A  pdb=" N   GLU A 413 " --> pdb=" O   GLN A 409 " (cutoff:3.500A)
      removed outlier: 4.097A  pdb=" N   ALA A 415 " --> pdb=" O   LEU A 411 " (cutoff:3.500A)
      removed outlier: 3.900A  pdb=" N   LEU A 416 " --> pdb=" O   VAL A 412 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 417 through 419
      No H-bonds generated for 'chain 'A' and resid 417 through 419'
    Processing helix  chain 'A' and resid 447 through 449
      No H-bonds generated for 'chain 'A' and resid 447 through 449'
    Processing helix  chain 'A' and resid 450 through 463
      removed outlier: 4.186A  pdb=" N   ALA A 456 " --> pdb=" O   GLU A 452 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 120 through 132
      removed outlier: 4.361A  pdb=" N   TYR B 127 " --> pdb=" O   GLN B 123 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   GLN B 130 " --> pdb=" O   LYS B 126 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   THR B 131 " --> pdb=" O   TYR B 127 " (cutoff:3.500A)
      removed outlier: 4.107A  pdb=" N   MET B 132 " --> pdb=" O   PHE B 128 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 150 through 156
      removed outlier: 3.715A  pdb=" N   ILE B 155 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   ALA B 156 " --> pdb=" O   ARG B 152 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 158 through 163
    Processing helix  chain 'B' and resid 178 through 183
    Processing helix  chain 'B' and resid 207 through 211
      removed outlier: 3.788A  pdb=" N   HIS B 211 " --> pdb=" O   LEU B 208 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 227 through 232
      removed outlier: 3.682A  pdb=" N   ILE B 231 " --> pdb=" O   ASP B 227 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   VAL B 232 " --> pdb=" O   VAL B 228 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 227 through 232'
    Processing helix  chain 'B' and resid 254 through 266
      removed outlier: 3.852A  pdb=" N   HIS B 263 " --> pdb=" O   LYS B 259 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   ALA B 265 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 291 through 296
      removed outlier: 3.588A  pdb=" N   MET B 295 " --> pdb=" O   SER B 291 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   ASP B 296 " --> pdb=" O   LEU B 292 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 291 through 296'
    Processing helix  chain 'B' and resid 323 through 334
      removed outlier: 3.843A  pdb=" N   HIS B 328 " --> pdb=" O   ALA B 324 " (cutoff:3.500A)
      removed outlier: 4.661A  pdb=" N   LEU B 329 " --> pdb=" O   PRO B 325 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   LYS B 333 " --> pdb=" O   LEU B 329 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 350 through 355
      removed outlier: 3.566A  pdb=" N   GLN B 355 " --> pdb=" O   ALA B 351 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 358 through 380
      removed outlier: 3.518A  pdb=" N   TYR B 369 " --> pdb=" O   MET B 365 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   ARG B 370 " --> pdb=" O   ARG B 366 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   LYS B 375 " --> pdb=" O   ARG B 371 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 381 through 383
      No H-bonds generated for 'chain 'B' and resid 381 through 383'
    Processing helix  chain 'B' and resid 407 through 415
      removed outlier: 3.951A  pdb=" N   LEU B 411 " --> pdb=" O   ASP B 407 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   VAL B 412 " --> pdb=" O   GLU B 408 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   GLU B 413 " --> pdb=" O   GLN B 409 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   ALA B 415 " --> pdb=" O   LEU B 411 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 447 through 449
      No H-bonds generated for 'chain 'B' and resid 447 through 449'
    Processing helix  chain 'B' and resid 450 through 462
      removed outlier: 3.663A  pdb=" N   ALA B 456 " --> pdb=" O   GLU B 452 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 172 through 175
    Processing sheet with id=AA2, first strand: chain 'A' and resid 215 through 219
      removed outlier: 3.532A  pdb=" N   ILE A 197 " --> pdb=" O   VAL A 217 " (cutoff:3.500A)
      removed outlier: 6.496A  pdb=" N   VAL A 194 " --> pdb=" O   VAL A 238 " (cutoff:3.500A)
      removed outlier: 8.687A  pdb=" N   TYR A 240 " --> pdb=" O   VAL A 194 " (cutoff:3.500A)
      removed outlier: 7.346A  pdb=" N   GLY A 196 " --> pdb=" O   TYR A 240 " (cutoff:3.500A)
      removed outlier: 6.663A  pdb=" N   VAL A 239 " --> pdb=" O   ILE A 274 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 387 through 390
      removed outlier: 3.544A  pdb=" N   ILE A 390 " --> pdb=" O   VAL A 399 " (cutoff:3.500A)
      removed outlier: 4.389A  pdb=" N   VAL A 399 " --> pdb=" O   ILE A 390 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 215 through 217
      removed outlier: 6.914A  pdb=" N   ILE B 273 " --> pdb=" O   ILE B 302 " (cutoff:3.500A)
      removed outlier: 8.261A  pdb=" N   LEU B 304 " --> pdb=" O   ILE B 273 " (cutoff:3.500A)
      removed outlier: 6.403A  pdb=" N   GLU B 275 " --> pdb=" O   LEU B 304 " (cutoff:3.500A)
      removed outlier: 8.725A  pdb=" N   ALA B 306 " --> pdb=" O   GLU B 275 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   GLY B 305 " --> pdb=" O   TYR B 319 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 221 through 222
    Processing sheet with id=AA6, first strand: chain 'B' and resid 389 through 390
      removed outlier: 3.971A  pdb=" N   VAL B 399 " --> pdb=" O   ILE B 390 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   ILE B 439 " --> pdb=" O   LEU B 400 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   TYR B 423 " --> pdb=" O   VAL B 440 " (cutoff:3.500A)

    134 hydrogen bonds defined for protein.
    381 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      27 hydrogen bonds
      54 hydrogen bond angles
      0 basepair planarities
      12 basepair parallelities
      56 stacking parallelities
  Total time for adding SS restraints: 2.58

  Time building geometry restraints manager: 2.39 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: 1671
        1.33 -     1.45: 2151
        1.45 -     1.57: 3955
        1.57 -     1.69: 164
        1.69 -     1.81: 32
  Bond restraints: 7973
  Sorted by residual:
  bond pdb=" OP4 LLP B 309 "
       pdb=" P   LLP B 309 "
    ideal  model  delta    sigma   weight residual
    1.726  1.536  0.190 2.00e-02 2.50e+03 9.02e+01
  bond pdb=" OP4 LLP A 309 "
       pdb=" P   LLP A 309 "
    ideal  model  delta    sigma   weight residual
    1.726  1.540  0.186 2.00e-02 2.50e+03 8.67e+01
  bond pdb=" NZ  LLP A 309 "
       pdb=" C4' LLP A 309 "
    ideal  model  delta    sigma   weight residual
    1.273  1.437 -0.164 2.00e-02 2.50e+03 6.73e+01
  bond pdb=" NZ  LLP B 309 "
       pdb=" C4' LLP B 309 "
    ideal  model  delta    sigma   weight residual
    1.273  1.432 -0.159 2.00e-02 2.50e+03 6.32e+01
  bond pdb=" C4  LLP A 309 "
       pdb=" C4' LLP A 309 "
    ideal  model  delta    sigma   weight residual
    1.464  1.618 -0.154 2.00e-02 2.50e+03 5.89e+01
  ... (remaining 7968 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.16: 10570
        2.16 -     4.32: 499
        4.32 -     6.48: 59
        6.48 -     8.64: 14
        8.64 -    10.80: 10
  Bond angle restraints: 11152
  Sorted by residual:
  angle pdb=" N   ILE A 289 "
        pdb=" CA  ILE A 289 "
        pdb=" C   ILE A 289 "
      ideal   model   delta    sigma   weight residual
     109.01  100.06    8.95 1.13e+00 7.83e-01 6.28e+01
  angle pdb=" C   ASP A 277 "
        pdb=" N   TYR A 278 "
        pdb=" CA  TYR A 278 "
      ideal   model   delta    sigma   weight residual
     121.54  131.33   -9.79 1.91e+00 2.74e-01 2.62e+01
  angle pdb=" CA  ILE A 289 "
        pdb=" C   ILE A 289 "
        pdb=" N   PRO A 290 "
      ideal   model   delta    sigma   weight residual
     117.00  120.72   -3.72 9.50e-01 1.11e+00 1.54e+01
  angle pdb=" C   ILE A 105 "
        pdb=" N   ARG A 106 "
        pdb=" CA  ARG A 106 "
      ideal   model   delta    sigma   weight residual
     121.54  128.72   -7.18 1.91e+00 2.74e-01 1.42e+01
  angle pdb=" NZ  LLP B 309 "
        pdb=" C4' LLP B 309 "
        pdb=" C4  LLP B 309 "
      ideal   model   delta    sigma   weight residual
     120.09  109.29   10.80 3.00e+00 1.11e-01 1.30e+01
  ... (remaining 11147 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    29.96: 3953
       29.96 -    59.91: 576
       59.91 -    89.87: 27
       89.87 -   119.83: 0
      119.83 -   149.78: 3
  Dihedral angle restraints: 4559
    sinusoidal: 2427
      harmonic: 2132
  Sorted by residual:
  dihedral pdb=" CA  GLY B 286 "
           pdb=" C   GLY B 286 "
           pdb=" N   LYS B 287 "
           pdb=" CA  LYS B 287 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -136.34  -43.66     0      5.00e+00 4.00e-02 7.63e+01
  dihedral pdb=" CA  GLY B 177 "
           pdb=" C   GLY B 177 "
           pdb=" N   VAL B 178 "
           pdb=" CA  VAL B 178 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.51   28.49     0      5.00e+00 4.00e-02 3.25e+01
  dihedral pdb=" CA  ASN B 136 "
           pdb=" C   ASN B 136 "
           pdb=" N   HIS B 137 "
           pdb=" CA  HIS B 137 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.03   27.97     0      5.00e+00 4.00e-02 3.13e+01
  ... (remaining 4556 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.081: 1018
       0.081 -    0.161: 193
       0.161 -    0.241: 8
       0.241 -    0.322: 1
       0.322 -    0.402: 1
  Chirality restraints: 1221
  Sorted by residual:
  chirality pdb=" CB  ILE A 446 "
            pdb=" CA  ILE A 446 "
            pdb=" CG1 ILE A 446 "
            pdb=" CG2 ILE A 446 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.24    0.40 2.00e-01 2.50e+01 4.05e+00
  chirality pdb=" CA  ILE A 289 "
            pdb=" N   ILE A 289 "
            pdb=" C   ILE A 289 "
            pdb=" CB  ILE A 289 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.70   -0.26 2.00e-01 2.50e+01 1.72e+00
  chirality pdb=" CG  LEU B 187 "
            pdb=" CB  LEU B 187 "
            pdb=" CD1 LEU B 187 "
            pdb=" CD2 LEU B 187 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.40   -0.19 2.00e-01 2.50e+01 8.97e-01
  ... (remaining 1218 not shown)

  Planarity restraints: 1133
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CE  LLP A 309 "    0.157 2.00e-02 2.50e+03   2.82e-01 7.96e+02
        pdb=" NZ  LLP A 309 "   -0.384 2.00e-02 2.50e+03
        pdb=" C4  LLP A 309 "   -0.132 2.00e-02 2.50e+03
        pdb=" C4' LLP A 309 "    0.359 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CE  LLP B 309 "   -0.297 2.00e-02 2.50e+03   2.77e-01 7.65e+02
        pdb=" NZ  LLP B 309 "    0.311 2.00e-02 2.50e+03
        pdb=" C4  LLP B 309 "   -0.253 2.00e-02 2.50e+03
        pdb=" C4' LLP B 309 "    0.240 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 289 "    0.048 5.00e-02 4.00e+02   7.24e-02 8.40e+00
        pdb=" N   PRO A 290 "   -0.125 5.00e-02 4.00e+02
        pdb=" CA  PRO A 290 "    0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO A 290 "    0.040 5.00e-02 4.00e+02
  ... (remaining 1130 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.78: 1636
        2.78 -     3.31: 6210
        3.31 -     3.84: 12588
        3.84 -     4.37: 13923
        4.37 -     4.90: 22293
  Nonbonded interactions: 56650
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 240 "
            pdb=" OD2 ASP A 276 "
     model   vdw
     2.244 3.040
  nonbonded pdb=" O   SER A 314 "
            pdb=" OG  SER A 314 "
     model   vdw
     2.261 3.040
  nonbonded pdb=" OE1 GLN A 184 "
            pdb=" OH  TYR A 330 "
     model   vdw
     2.268 3.040
  nonbonded pdb=" O   GLU B 453 "
            pdb=" OG1 THR B 457 "
     model   vdw
     2.290 3.040
  nonbonded pdb=" O   GLY B 177 "
            pdb=" OG  SER B 318 "
     model   vdw
     2.294 3.040
  ... (remaining 56645 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
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'B' and resid 105 through 464)
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.800
  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:          0.290
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     22.320
  Find NCS groups from input model:        0.220
  Set up NCS constraints:                  0.030
  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:2.930
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.740
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7538
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      :  0.009   0.190   7973  Z= 0.574
  Angle     :  1.065  10.797  11152  Z= 0.585
  Chirality :  0.060   0.402   1221
  Planarity :  0.014   0.282   1133
  Dihedral  : 23.039 149.781   3191
  Min Nonbonded Distance : 2.244

Molprobity Statistics.
  All-atom Clashscore : 6.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.97 %
    Favored  : 90.03 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  : 15.06 %
    Favored  : 83.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.15 %

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: -5.31 (0.24), residues: 712
  helix: -4.33 (0.17), residues: 232
  sheet: -3.13 (0.41), residues: 112
  loop : -3.09 (0.28), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.003   TRP A 124 
 HIS   0.015   0.002   HIS B 113 
 PHE   0.025   0.004   PHE A 307 
 TYR   0.028   0.003   TYR B 202 
 ARG   0.010   0.001   ARG B 316 

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

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

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 85
  time to evaluate  : 0.721 
Fit side-chains
REVERT: A  122 GLU cc_start: 0.7871 (mp0) cc_final: 0.6732 (pm20)
REVERT: A  138 ARG cc_start: 0.7915 (mtt-85) cc_final: 0.7292 (mtp180)
REVERT: A  353 MET cc_start: 0.7643 (mtm) cc_final: 0.7435 (mtm)
  outliers start: 8
  outliers final: 4
  residues processed: 91
  average time/residue: 0.2636
  time to fit residues: 30.6408
Evaluate side-chains
  60 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 56
  time to evaluate  : 0.767 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  197 ILE
Chi-restraints excluded: chain A residue  434 ILE
Chi-restraints excluded: chain B residue  288 THR
Chi-restraints excluded: chain B residue  402 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 67 optimal weight:    4.9990
   chunk 60 optimal weight:    0.6980
   chunk 33 optimal weight:    3.9990
   chunk 20 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9980
   chunk 32 optimal weight:    0.0670
   chunk 62 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9990
   chunk 46 optimal weight:    0.8980
   chunk 72 optimal weight:   10.0000
   overall best weight:    0.7320

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

Flipped N/Q/H residues before XYZ refinement:
A 142 ASN
A 146 GLN
A 211 HIS
B 211 HIS
B 328 HIS
B 332 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4323 r_free = 0.4323 target = 0.169352 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.133577 restraints weight = 14143.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.135278 restraints weight = 9776.512|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.135668 restraints weight = 6889.696|
|-----------------------------------------------------------------------------|
r_work (final): 0.3864
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7444
moved from start:          0.1667

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   7973  Z= 0.180
  Angle     :  0.637   7.957  11152  Z= 0.352
  Chirality :  0.043   0.237   1221
  Planarity :  0.006   0.059   1133
  Dihedral  : 24.654 145.674   1750
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 7.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.60 %
    Favored  : 93.40 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 18.63 %
    Favored  : 78.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.38 %
    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: -4.27 (0.27), residues: 712
  helix: -3.12 (0.27), residues: 240
  sheet: -2.09 (0.49), residues: 106
  loop : -2.86 (0.28), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 124 
 HIS   0.010   0.001   HIS B 110 
 PHE   0.011   0.001   PHE B 109 
 TYR   0.020   0.001   TYR A 157 
 ARG   0.003   0.000   ARG A 283 

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

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

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 79
  time to evaluate  : 0.719 
Fit side-chains
REVERT: A  122 GLU cc_start: 0.7676 (mp0) cc_final: 0.6651 (pm20)
REVERT: A  138 ARG cc_start: 0.7748 (mtt-85) cc_final: 0.7372 (mtp180)
REVERT: B  110 HIS cc_start: 0.7518 (t-90) cc_final: 0.7226 (t-90)
REVERT: B  370 ARG cc_start: 0.7632 (ttm-80) cc_final: 0.7343 (ttm110)
  outliers start: 16
  outliers final: 12
  residues processed: 89
  average time/residue: 0.1708
  time to fit residues: 21.7389
Evaluate side-chains
  77 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 65
  time to evaluate  : 0.863 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  197 ILE
Chi-restraints excluded: chain A residue  226 ILE
Chi-restraints excluded: chain A residue  278 TYR
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  178 VAL
Chi-restraints excluded: chain B residue  288 THR
Chi-restraints excluded: chain B residue  401 VAL
Chi-restraints excluded: chain B residue  402 VAL
Chi-restraints excluded: chain B residue  452 GLU
Chi-restraints excluded: chain B residue  458 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 24 optimal weight:    4.9990
   chunk 38 optimal weight:    4.9990
   chunk 70 optimal weight:    9.9990
   chunk 55 optimal weight:   10.0000
   chunk 68 optimal weight:    7.9990
   chunk 71 optimal weight:    2.9990
   chunk 79 optimal weight:   10.0000
   chunk 8 optimal weight:    3.9990
   chunk 35 optimal weight:    7.9990
   chunk 13 optimal weight:    6.9990
   chunk 48 optimal weight:    5.9990
   overall best weight:    4.5990

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

Flipped N/Q/H residues before XYZ refinement:
A 123 GLN
** B 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 123 GLN
** B 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 404 ASN
B 438 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4235 r_free = 0.4235 target = 0.161990 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.125766 restraints weight = 14822.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.127196 restraints weight = 13051.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.127587 restraints weight = 8986.264|
|-----------------------------------------------------------------------------|
r_work (final): 0.3753
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7619
moved from start:          0.1934

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.042   7973  Z= 0.415
  Angle     :  0.785   6.811  11152  Z= 0.424
  Chirality :  0.049   0.196   1221
  Planarity :  0.006   0.058   1133
  Dihedral  : 24.820 142.562   1748
  Min Nonbonded Distance : 2.374

Molprobity Statistics.
  All-atom Clashscore : 10.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.94 %
    Favored  : 88.06 %
  Rotamer:
    Outliers :  5.90 %
    Allowed  : 19.25 %
    Favored  : 74.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.15 %

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: -4.12 (0.28), residues: 712
  helix: -2.89 (0.30), residues: 228
  sheet: -2.18 (0.48), residues: 109
  loop : -2.83 (0.28), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 124 
 HIS   0.012   0.002   HIS B 110 
 PHE   0.023   0.003   PHE A 307 
 TYR   0.020   0.003   TYR B 212 
 ARG   0.004   0.001   ARG B 163 

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

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

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 61
  time to evaluate  : 0.708 
Fit side-chains
REVERT: A  122 GLU cc_start: 0.7735 (mp0) cc_final: 0.6726 (pm20)
REVERT: A  138 ARG cc_start: 0.7812 (mtt-85) cc_final: 0.7371 (mtp180)
  outliers start: 38
  outliers final: 27
  residues processed: 92
  average time/residue: 0.1621
  time to fit residues: 21.6235
Evaluate side-chains
  84 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 57
  time to evaluate  : 0.594 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  197 ILE
Chi-restraints excluded: chain A residue  226 ILE
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  244 SER
Chi-restraints excluded: chain A residue  278 TYR
Chi-restraints excluded: chain A residue  319 TYR
Chi-restraints excluded: chain A residue  320 MET
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  344 ILE
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  434 ILE
Chi-restraints excluded: chain A residue  458 VAL
Chi-restraints excluded: chain B residue  141 LEU
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  178 VAL
Chi-restraints excluded: chain B residue  202 TYR
Chi-restraints excluded: chain B residue  247 PHE
Chi-restraints excluded: chain B residue  288 THR
Chi-restraints excluded: chain B residue  301 VAL
Chi-restraints excluded: chain B residue  383 TYR
Chi-restraints excluded: chain B residue  401 VAL
Chi-restraints excluded: chain B residue  402 VAL
Chi-restraints excluded: chain B residue  439 ILE
Chi-restraints excluded: chain B residue  443 PHE
Chi-restraints excluded: chain B residue  452 GLU
Chi-restraints excluded: chain B residue  458 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 48 optimal weight:    5.9990
   chunk 77 optimal weight:   10.0000
   chunk 37 optimal weight:    1.9990
   chunk 15 optimal weight:    4.9990
   chunk 31 optimal weight:    3.9990
   chunk 46 optimal weight:    0.7980
   chunk 18 optimal weight:    4.9990
   chunk 3 optimal weight:    9.9990
   chunk 8 optimal weight:    0.0050
   chunk 21 optimal weight:    5.9990
   chunk 74 optimal weight:   10.0000
   overall best weight:    2.3600

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

Flipped N/Q/H residues before XYZ refinement:
** B 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 145 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4277 r_free = 0.4277 target = 0.165272 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.128924 restraints weight = 14420.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.130405 restraints weight = 11499.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.130833 restraints weight = 8272.380|
|-----------------------------------------------------------------------------|
r_work (final): 0.3799
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7557
moved from start:          0.2261

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   7973  Z= 0.252
  Angle     :  0.660  10.005  11152  Z= 0.357
  Chirality :  0.044   0.171   1221
  Planarity :  0.005   0.057   1133
  Dihedral  : 24.593 143.924   1748
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 8.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.29 %
    Favored  : 91.71 %
  Rotamer:
    Outliers :  6.21 %
    Allowed  : 21.27 %
    Favored  : 72.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.38 %
    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: -3.74 (0.29), residues: 712
  helix: -2.44 (0.32), residues: 230
  sheet: -2.01 (0.49), residues: 106
  loop : -2.66 (0.29), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 124 
 HIS   0.004   0.001   HIS B 161 
 PHE   0.012   0.002   PHE A 307 
 TYR   0.016   0.002   TYR A 157 
 ARG   0.002   0.000   ARG A 245 

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

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

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 65
  time to evaluate  : 0.776 
Fit side-chains
REVERT: A  122 GLU cc_start: 0.7584 (mp0) cc_final: 0.6652 (pm20)
REVERT: A  138 ARG cc_start: 0.7835 (mtt-85) cc_final: 0.7347 (mtp180)
REVERT: B  148 GLU cc_start: 0.7280 (mm-30) cc_final: 0.6681 (tp30)
REVERT: B  281 GLU cc_start: 0.7233 (pm20) cc_final: 0.6953 (pm20)
  outliers start: 40
  outliers final: 30
  residues processed: 95
  average time/residue: 0.1564
  time to fit residues: 21.7409
Evaluate side-chains
  90 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 60
  time to evaluate  : 0.666 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  172 VAL
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  197 ILE
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  244 SER
Chi-restraints excluded: chain A residue  278 TYR
Chi-restraints excluded: chain A residue  289 ILE
Chi-restraints excluded: chain A residue  310 SER
Chi-restraints excluded: chain A residue  319 TYR
Chi-restraints excluded: chain A residue  320 MET
Chi-restraints excluded: chain A residue  329 LEU
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  344 ILE
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  412 VAL
Chi-restraints excluded: chain A residue  434 ILE
Chi-restraints excluded: chain B residue  141 LEU
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  178 VAL
Chi-restraints excluded: chain B residue  230 SER
Chi-restraints excluded: chain B residue  247 PHE
Chi-restraints excluded: chain B residue  288 THR
Chi-restraints excluded: chain B residue  312 ILE
Chi-restraints excluded: chain B residue  383 TYR
Chi-restraints excluded: chain B residue  401 VAL
Chi-restraints excluded: chain B residue  402 VAL
Chi-restraints excluded: chain B residue  439 ILE
Chi-restraints excluded: chain B residue  452 GLU
Chi-restraints excluded: chain B residue  458 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 10 optimal weight:    4.9990
   chunk 27 optimal weight:    5.9990
   chunk 11 optimal weight:    3.9990
   chunk 78 optimal weight:   10.0000
   chunk 3 optimal weight:    9.9990
   chunk 59 optimal weight:    4.9990
   chunk 54 optimal weight:    9.9990
   chunk 66 optimal weight:    3.9990
   chunk 37 optimal weight:    0.6980
   chunk 24 optimal weight:    5.9990
   chunk 36 optimal weight:    0.5980
   overall best weight:    2.8586

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

Flipped N/Q/H residues before XYZ refinement:
** B 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4263 r_free = 0.4263 target = 0.164111 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.127638 restraints weight = 14446.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.128406 restraints weight = 13205.660|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.129610 restraints weight = 9475.221|
|-----------------------------------------------------------------------------|
r_work (final): 0.3776
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7586
moved from start:          0.2371

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   7973  Z= 0.284
  Angle     :  0.693   9.508  11152  Z= 0.371
  Chirality :  0.046   0.195   1221
  Planarity :  0.005   0.055   1133
  Dihedral  : 24.595 144.161   1748
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 9.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.67 %
    Favored  : 89.33 %
  Rotamer:
    Outliers :  6.99 %
    Allowed  : 21.43 %
    Favored  : 71.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.38 %
    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: -3.59 (0.29), residues: 712
  helix: -2.35 (0.32), residues: 230
  sheet: -1.87 (0.49), residues: 106
  loop : -2.57 (0.30), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 124 
 HIS   0.005   0.001   HIS A 361 
 PHE   0.014   0.002   PHE A 334 
 TYR   0.017   0.002   TYR B 336 
 ARG   0.003   0.000   ARG A 245 

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

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

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 62
  time to evaluate  : 0.726 
Fit side-chains
REVERT: A  122 GLU cc_start: 0.7595 (mp0) cc_final: 0.6700 (pm20)
REVERT: A  138 ARG cc_start: 0.7818 (mtt-85) cc_final: 0.7360 (mtp180)
REVERT: B  148 GLU cc_start: 0.7324 (mm-30) cc_final: 0.6725 (tp30)
  outliers start: 45
  outliers final: 37
  residues processed: 97
  average time/residue: 0.1613
  time to fit residues: 22.6522
Evaluate side-chains
  93 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 56
  time to evaluate  : 0.748 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  172 VAL
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  197 ILE
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  244 SER
Chi-restraints excluded: chain A residue  278 TYR
Chi-restraints excluded: chain A residue  289 ILE
Chi-restraints excluded: chain A residue  310 SER
Chi-restraints excluded: chain A residue  311 LEU
Chi-restraints excluded: chain A residue  319 TYR
Chi-restraints excluded: chain A residue  320 MET
Chi-restraints excluded: chain A residue  329 LEU
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  344 ILE
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  412 VAL
Chi-restraints excluded: chain A residue  434 ILE
Chi-restraints excluded: chain B residue  141 LEU
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  172 VAL
Chi-restraints excluded: chain B residue  178 VAL
Chi-restraints excluded: chain B residue  202 TYR
Chi-restraints excluded: chain B residue  230 SER
Chi-restraints excluded: chain B residue  234 THR
Chi-restraints excluded: chain B residue  247 PHE
Chi-restraints excluded: chain B residue  251 SER
Chi-restraints excluded: chain B residue  254 SER
Chi-restraints excluded: chain B residue  288 THR
Chi-restraints excluded: chain B residue  310 SER
Chi-restraints excluded: chain B residue  312 ILE
Chi-restraints excluded: chain B residue  383 TYR
Chi-restraints excluded: chain B residue  401 VAL
Chi-restraints excluded: chain B residue  402 VAL
Chi-restraints excluded: chain B residue  439 ILE
Chi-restraints excluded: chain B residue  452 GLU
Chi-restraints excluded: chain B residue  458 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 59 optimal weight:    2.9990
   chunk 71 optimal weight:    5.9990
   chunk 23 optimal weight:    0.9980
   chunk 38 optimal weight:    4.9990
   chunk 77 optimal weight:   10.0000
   chunk 24 optimal weight:    1.9990
   chunk 48 optimal weight:    7.9990
   chunk 16 optimal weight:    3.9990
   chunk 31 optimal weight:    6.9990
   chunk 66 optimal weight:   10.0000
   chunk 12 optimal weight:    4.9990
   overall best weight:    2.9988

-------------------------------------------------------------------------------
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 = 0.4259 r_free = 0.4259 target = 0.163837 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.127397 restraints weight = 14533.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.128040 restraints weight = 13515.991|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.129281 restraints weight = 9650.971|
|-----------------------------------------------------------------------------|
r_work (final): 0.3771
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7595
moved from start:          0.2479

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   7973  Z= 0.293
  Angle     :  0.702   9.400  11152  Z= 0.375
  Chirality :  0.046   0.218   1221
  Planarity :  0.005   0.055   1133
  Dihedral  : 24.600 144.208   1748
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 9.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.11 %
    Favored  : 89.89 %
  Rotamer:
    Outliers :  7.30 %
    Allowed  : 22.05 %
    Favored  : 70.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.38 %
    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: -3.54 (0.29), residues: 712
  helix: -2.42 (0.31), residues: 236
  sheet: -1.77 (0.50), residues: 106
  loop : -2.48 (0.30), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 124 
 HIS   0.009   0.001   HIS B 110 
 PHE   0.016   0.002   PHE A 334 
 TYR   0.016   0.002   TYR B 336 
 ARG   0.003   0.000   ARG A 245 

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

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

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 60
  time to evaluate  : 0.723 
Fit side-chains
REVERT: A  122 GLU cc_start: 0.7602 (mp0) cc_final: 0.6700 (pm20)
REVERT: A  138 ARG cc_start: 0.7851 (mtt-85) cc_final: 0.7373 (mtp180)
REVERT: A  199 ASP cc_start: 0.8274 (OUTLIER) cc_final: 0.7944 (t0)
REVERT: A  446 ILE cc_start: 0.4982 (OUTLIER) cc_final: 0.4768 (tp)
REVERT: B  148 GLU cc_start: 0.7341 (mm-30) cc_final: 0.6714 (tp30)
REVERT: B  281 GLU cc_start: 0.7174 (pm20) cc_final: 0.6877 (pm20)
  outliers start: 47
  outliers final: 39
  residues processed: 96
  average time/residue: 0.1590
  time to fit residues: 22.0953
Evaluate side-chains
  98 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 57
  time to evaluate  : 0.733 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  172 VAL
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  197 ILE
Chi-restraints excluded: chain A residue  199 ASP
Chi-restraints excluded: chain A residue  202 TYR
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  244 SER
Chi-restraints excluded: chain A residue  278 TYR
Chi-restraints excluded: chain A residue  289 ILE
Chi-restraints excluded: chain A residue  310 SER
Chi-restraints excluded: chain A residue  311 LEU
Chi-restraints excluded: chain A residue  319 TYR
Chi-restraints excluded: chain A residue  320 MET
Chi-restraints excluded: chain A residue  329 LEU
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  344 ILE
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  412 VAL
Chi-restraints excluded: chain A residue  434 ILE
Chi-restraints excluded: chain A residue  446 ILE
Chi-restraints excluded: chain B residue  141 LEU
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  172 VAL
Chi-restraints excluded: chain B residue  178 VAL
Chi-restraints excluded: chain B residue  202 TYR
Chi-restraints excluded: chain B residue  230 SER
Chi-restraints excluded: chain B residue  234 THR
Chi-restraints excluded: chain B residue  247 PHE
Chi-restraints excluded: chain B residue  251 SER
Chi-restraints excluded: chain B residue  254 SER
Chi-restraints excluded: chain B residue  288 THR
Chi-restraints excluded: chain B residue  301 VAL
Chi-restraints excluded: chain B residue  310 SER
Chi-restraints excluded: chain B residue  312 ILE
Chi-restraints excluded: chain B residue  383 TYR
Chi-restraints excluded: chain B residue  401 VAL
Chi-restraints excluded: chain B residue  402 VAL
Chi-restraints excluded: chain B residue  439 ILE
Chi-restraints excluded: chain B residue  452 GLU
Chi-restraints excluded: chain B residue  458 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 60 optimal weight:    2.9990
   chunk 66 optimal weight:    0.0000
   chunk 41 optimal weight:    2.9990
   chunk 67 optimal weight:    8.9990
   chunk 49 optimal weight:    0.9980
   chunk 11 optimal weight:    5.9990
   chunk 25 optimal weight:    8.9990
   chunk 68 optimal weight:    0.5980
   chunk 48 optimal weight:    3.9990
   chunk 18 optimal weight:    4.9990
   chunk 53 optimal weight:    3.9990
   overall best weight:    1.5188

-------------------------------------------------------------------------------
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 = 0.4300 r_free = 0.4300 target = 0.167090 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.131710 restraints weight = 14403.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.132328 restraints weight = 12129.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.133086 restraints weight = 9266.725|
|-----------------------------------------------------------------------------|
r_work (final): 0.3829
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7495
moved from start:          0.2803

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   7973  Z= 0.194
  Angle     :  0.614   9.244  11152  Z= 0.330
  Chirality :  0.043   0.191   1221
  Planarity :  0.005   0.055   1133
  Dihedral  : 24.392 146.441   1748
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 7.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.43 %
    Favored  : 91.57 %
  Rotamer:
    Outliers :  5.75 %
    Allowed  : 23.91 %
    Favored  : 70.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.38 %
    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: -3.22 (0.30), residues: 712
  helix: -2.16 (0.32), residues: 239
  sheet: -1.63 (0.49), residues: 108
  loop : -2.24 (0.31), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 124 
 HIS   0.009   0.001   HIS B 110 
 PHE   0.011   0.001   PHE A 358 
 TYR   0.015   0.001   TYR B 336 
 ARG   0.002   0.000   ARG A 153 

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

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

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 66
  time to evaluate  : 0.730 
Fit side-chains
REVERT: A  114 ILE cc_start: 0.6409 (tt) cc_final: 0.6034 (tt)
REVERT: A  122 GLU cc_start: 0.7592 (mp0) cc_final: 0.6679 (pm20)
REVERT: A  138 ARG cc_start: 0.7752 (mtt-85) cc_final: 0.7338 (mtp180)
REVERT: A  307 PHE cc_start: 0.8496 (OUTLIER) cc_final: 0.7367 (t80)
REVERT: B  148 GLU cc_start: 0.7143 (mm-30) cc_final: 0.6579 (tp30)
REVERT: B  281 GLU cc_start: 0.6976 (pm20) cc_final: 0.6751 (pm20)
  outliers start: 37
  outliers final: 30
  residues processed: 94
  average time/residue: 0.1589
  time to fit residues: 21.7153
Evaluate side-chains
  92 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 61
  time to evaluate  : 0.809 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  197 ILE
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  244 SER
Chi-restraints excluded: chain A residue  273 ILE
Chi-restraints excluded: chain A residue  278 TYR
Chi-restraints excluded: chain A residue  289 ILE
Chi-restraints excluded: chain A residue  307 PHE
Chi-restraints excluded: chain A residue  310 SER
Chi-restraints excluded: chain A residue  319 TYR
Chi-restraints excluded: chain A residue  320 MET
Chi-restraints excluded: chain A residue  329 LEU
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  412 VAL
Chi-restraints excluded: chain A residue  434 ILE
Chi-restraints excluded: chain B residue  141 LEU
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  172 VAL
Chi-restraints excluded: chain B residue  202 TYR
Chi-restraints excluded: chain B residue  230 SER
Chi-restraints excluded: chain B residue  247 PHE
Chi-restraints excluded: chain B residue  251 SER
Chi-restraints excluded: chain B residue  254 SER
Chi-restraints excluded: chain B residue  288 THR
Chi-restraints excluded: chain B residue  312 ILE
Chi-restraints excluded: chain B residue  401 VAL
Chi-restraints excluded: chain B residue  402 VAL
Chi-restraints excluded: chain B residue  439 ILE
Chi-restraints excluded: chain B residue  452 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 29 optimal weight:    0.5980
   chunk 11 optimal weight:    1.9990
   chunk 42 optimal weight:    0.0030
   chunk 7 optimal weight:    0.2980
   chunk 15 optimal weight:    7.9990
   chunk 10 optimal weight:    0.9990
   chunk 77 optimal weight:   10.0000
   chunk 34 optimal weight:    7.9990
   chunk 64 optimal weight:    0.9990
   chunk 78 optimal weight:   10.0000
   chunk 79 optimal weight:   10.0000
   overall best weight:    0.5794

-------------------------------------------------------------------------------
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 = 0.4339 r_free = 0.4339 target = 0.170734 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.134899 restraints weight = 14318.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.136205 restraints weight = 11689.965|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.137187 restraints weight = 8344.544|
|-----------------------------------------------------------------------------|
r_work (final): 0.3877
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7403
moved from start:          0.3163

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   7973  Z= 0.155
  Angle     :  0.594  13.685  11152  Z= 0.315
  Chirality :  0.041   0.163   1221
  Planarity :  0.005   0.054   1133
  Dihedral  : 24.182 148.309   1748
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 7.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.62 %
    Favored  : 94.38 %
  Rotamer:
    Outliers :  4.66 %
    Allowed  : 25.00 %
    Favored  : 70.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.38 %
    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: -2.87 (0.30), residues: 712
  helix: -1.98 (0.32), residues: 247
  sheet: -1.27 (0.48), residues: 108
  loop : -2.00 (0.31), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 264 
 HIS   0.006   0.001   HIS B 110 
 PHE   0.008   0.001   PHE B 352 
 TYR   0.016   0.001   TYR B 336 
 ARG   0.003   0.000   ARG B 370 

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

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

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 74
  time to evaluate  : 0.735 
Fit side-chains
REVERT: A  114 ILE cc_start: 0.6141 (tt) cc_final: 0.5807 (tt)
REVERT: A  122 GLU cc_start: 0.7548 (mp0) cc_final: 0.6712 (pm20)
REVERT: A  138 ARG cc_start: 0.7714 (mtt-85) cc_final: 0.7496 (mtp180)
REVERT: A  307 PHE cc_start: 0.8372 (OUTLIER) cc_final: 0.7053 (t80)
REVERT: B  148 GLU cc_start: 0.7003 (mm-30) cc_final: 0.6439 (tp30)
  outliers start: 30
  outliers final: 22
  residues processed: 96
  average time/residue: 0.1729
  time to fit residues: 23.5451
Evaluate side-chains
  85 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 62
  time to evaluate  : 0.763 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  202 TYR
Chi-restraints excluded: chain A residue  273 ILE
Chi-restraints excluded: chain A residue  278 TYR
Chi-restraints excluded: chain A residue  307 PHE
Chi-restraints excluded: chain A residue  310 SER
Chi-restraints excluded: chain A residue  320 MET
Chi-restraints excluded: chain A residue  329 LEU
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  399 VAL
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  434 ILE
Chi-restraints excluded: chain B residue  141 LEU
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  247 PHE
Chi-restraints excluded: chain B residue  251 SER
Chi-restraints excluded: chain B residue  254 SER
Chi-restraints excluded: chain B residue  288 THR
Chi-restraints excluded: chain B residue  312 ILE
Chi-restraints excluded: chain B residue  401 VAL
Chi-restraints excluded: chain B residue  402 VAL
Chi-restraints excluded: chain B residue  439 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 63 optimal weight:    1.9990
   chunk 31 optimal weight:    8.9990
   chunk 61 optimal weight:    4.9990
   chunk 54 optimal weight:    0.4980
   chunk 35 optimal weight:    5.9990
   chunk 7 optimal weight:    0.0040
   chunk 16 optimal weight:    2.9990
   chunk 71 optimal weight:    0.7980
   chunk 37 optimal weight:    0.7980
   chunk 60 optimal weight:    0.4980
   chunk 66 optimal weight:    8.9990
   overall best weight:    0.5192

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

Flipped N/Q/H residues before XYZ refinement:
A 361 HIS
** B 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4354 r_free = 0.4354 target = 0.172020 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.136374 restraints weight = 14475.226|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.137094 restraints weight = 13133.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.138155 restraints weight = 9471.127|
|-----------------------------------------------------------------------------|
r_work (final): 0.3892
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7370
moved from start:          0.3435

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   7973  Z= 0.160
  Angle     :  0.601  13.054  11152  Z= 0.317
  Chirality :  0.041   0.173   1221
  Planarity :  0.005   0.058   1133
  Dihedral  : 24.104 149.628   1746
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.04 %
    Favored  : 93.96 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 26.24 %
    Favored  : 70.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.38 %
    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: -2.61 (0.30), residues: 712
  helix: -1.86 (0.31), residues: 247
  sheet: -0.96 (0.49), residues: 108
  loop : -1.83 (0.32), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 264 
 HIS   0.003   0.001   HIS B 113 
 PHE   0.006   0.001   PHE B 307 
 TYR   0.014   0.001   TYR B 303 
 ARG   0.006   0.000   ARG B 152 

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

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

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 71
  time to evaluate  : 0.787 
Fit side-chains
REVERT: A  114 ILE cc_start: 0.6165 (tt) cc_final: 0.5764 (tt)
REVERT: A  122 GLU cc_start: 0.7515 (mp0) cc_final: 0.6743 (pm20)
REVERT: A  138 ARG cc_start: 0.7712 (mtt-85) cc_final: 0.7425 (mtp180)
REVERT: A  307 PHE cc_start: 0.8297 (OUTLIER) cc_final: 0.6992 (t80)
REVERT: B  148 GLU cc_start: 0.7021 (mm-30) cc_final: 0.6392 (tp30)
  outliers start: 22
  outliers final: 20
  residues processed: 87
  average time/residue: 0.1711
  time to fit residues: 21.1987
Evaluate side-chains
  85 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 64
  time to evaluate  : 0.685 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  172 VAL
Chi-restraints excluded: chain A residue  202 TYR
Chi-restraints excluded: chain A residue  273 ILE
Chi-restraints excluded: chain A residue  278 TYR
Chi-restraints excluded: chain A residue  307 PHE
Chi-restraints excluded: chain A residue  310 SER
Chi-restraints excluded: chain A residue  320 MET
Chi-restraints excluded: chain A residue  329 LEU
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  399 VAL
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  434 ILE
Chi-restraints excluded: chain B residue  141 LEU
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  247 PHE
Chi-restraints excluded: chain B residue  254 SER
Chi-restraints excluded: chain B residue  288 THR
Chi-restraints excluded: chain B residue  312 ILE
Chi-restraints excluded: chain B residue  401 VAL
Chi-restraints excluded: chain B residue  402 VAL
Chi-restraints excluded: chain B residue  439 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 1 optimal weight:    0.7980
   chunk 23 optimal weight:    9.9990
   chunk 62 optimal weight:    7.9990
   chunk 6 optimal weight:    4.9990
   chunk 53 optimal weight:   10.0000
   chunk 10 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9990
   chunk 15 optimal weight:    4.9990
   chunk 22 optimal weight:    2.9990
   chunk 29 optimal weight:    2.9990
   chunk 57 optimal weight:    4.9990
   overall best weight:    2.1588

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

Flipped N/Q/H residues before XYZ refinement:
A 214 ASN
** B 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4302 r_free = 0.4302 target = 0.167250 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.132018 restraints weight = 14567.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.133338 restraints weight = 12319.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.134132 restraints weight = 8708.191|
|-----------------------------------------------------------------------------|
r_work (final): 0.3838
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7476
moved from start:          0.3318

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   7973  Z= 0.241
  Angle     :  0.663  12.405  11152  Z= 0.350
  Chirality :  0.044   0.209   1221
  Planarity :  0.005   0.062   1133
  Dihedral  : 24.168 149.400   1746
  Min Nonbonded Distance : 2.358

Molprobity Statistics.
  All-atom Clashscore : 8.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.27 %
    Favored  : 90.73 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 25.78 %
    Favored  : 70.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.38 %
    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: -2.72 (0.30), residues: 712
  helix: -1.96 (0.31), residues: 249
  sheet: -0.95 (0.50), residues: 102
  loop : -1.90 (0.32), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 264 
 HIS   0.004   0.001   HIS B 113 
 PHE   0.010   0.002   PHE A 307 
 TYR   0.015   0.002   TYR A 157 
 ARG   0.005   0.000   ARG A 343 

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

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

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 61
  time to evaluate  : 0.789 
Fit side-chains
REVERT: A  122 GLU cc_start: 0.7551 (mp0) cc_final: 0.6714 (pm20)
REVERT: A  138 ARG cc_start: 0.7779 (mtt-85) cc_final: 0.7420 (mtp180)
REVERT: B  148 GLU cc_start: 0.7145 (mm-30) cc_final: 0.6554 (tp30)
  outliers start: 26
  outliers final: 25
  residues processed: 82
  average time/residue: 0.1501
  time to fit residues: 18.4182
Evaluate side-chains
  86 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 61
  time to evaluate  : 0.765 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  172 VAL
Chi-restraints excluded: chain A residue  197 ILE
Chi-restraints excluded: chain A residue  202 TYR
Chi-restraints excluded: chain A residue  278 TYR
Chi-restraints excluded: chain A residue  310 SER
Chi-restraints excluded: chain A residue  320 MET
Chi-restraints excluded: chain A residue  329 LEU
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  399 VAL
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  434 ILE
Chi-restraints excluded: chain B residue  141 LEU
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  234 THR
Chi-restraints excluded: chain B residue  247 PHE
Chi-restraints excluded: chain B residue  251 SER
Chi-restraints excluded: chain B residue  254 SER
Chi-restraints excluded: chain B residue  288 THR
Chi-restraints excluded: chain B residue  312 ILE
Chi-restraints excluded: chain B residue  328 HIS
Chi-restraints excluded: chain B residue  396 LEU
Chi-restraints excluded: chain B residue  401 VAL
Chi-restraints excluded: chain B residue  402 VAL
Chi-restraints excluded: chain B residue  416 LEU
Chi-restraints excluded: chain B residue  439 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 10 optimal weight:    0.5980
   chunk 37 optimal weight:    0.7980
   chunk 64 optimal weight:    9.9990
   chunk 56 optimal weight:    5.9990
   chunk 13 optimal weight:    6.9990
   chunk 62 optimal weight:    6.9990
   chunk 39 optimal weight:    7.9990
   chunk 60 optimal weight:    0.8980
   chunk 71 optimal weight:    4.9990
   chunk 74 optimal weight:   10.0000
   chunk 1 optimal weight:    0.0000
   overall best weight:    1.4586

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

Flipped N/Q/H residues before XYZ refinement:
** B 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4322 r_free = 0.4322 target = 0.168968 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.133163 restraints weight = 14541.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.134750 restraints weight = 12113.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.135723 restraints weight = 8209.188|
|-----------------------------------------------------------------------------|
r_work (final): 0.3864
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7434
moved from start:          0.3478

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7973  Z= 0.191
  Angle     :  0.625  12.013  11152  Z= 0.331
  Chirality :  0.042   0.179   1221
  Planarity :  0.005   0.062   1133
  Dihedral  : 24.111 150.690   1746
  Min Nonbonded Distance : 2.340

Molprobity Statistics.
  All-atom Clashscore : 8.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.02 %
    Favored  : 92.98 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 26.09 %
    Favored  : 70.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.38 %
    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: -2.54 (0.30), residues: 712
  helix: -1.81 (0.32), residues: 247
  sheet: -0.85 (0.50), residues: 105
  loop : -1.80 (0.32), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 264 
 HIS   0.004   0.001   HIS B 113 
 PHE   0.008   0.001   PHE A 307 
 TYR   0.017   0.001   TYR A 157 
 ARG   0.004   0.000   ARG A 343 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2017.71 seconds
wall clock time: 37 minutes 1.57 seconds (2221.57 seconds total)