Starting phenix.real_space_refine
on Wed Mar 12 08:44:53 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7zth_14960/03_2025/7zth_14960.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7zth_14960/03_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_14960/03_2025/7zth_14960.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7zth_14960/03_2025/7zth_14960.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7zth_14960/03_2025/7zth_14960.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7zth_14960/03_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-5624/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: 4.78, per 1000 atoms: 0.63
  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: 1.92
  Conformation dependent library (CDL) restraints added in 665.3 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: 2.20
  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: 2.18

  Time building geometry restraints manager: 2.27 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:             0.770
  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:         0.050
  Set scattering table:                    0.060
  Process input model:                     20.920
  Find NCS groups from input model:        0.210
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.710
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.050
-------------------------------------------------------------------------------
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  : 0.687 
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: 0.2451
  time to fit residues: 28.5344
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  : 0.689 
-------------------------------------------------------------------------------
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  : 0.700 
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: 0.1601
  time to fit residues: 20.5579
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  : 0.773 
-------------------------------------------------------------------------------
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:    7.9990
   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 = 0.4233 r_free = 0.4233 target = 0.161818 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.125592 restraints weight = 14827.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.127058 restraints weight = 13068.965|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.127598 restraints weight = 8975.862|
|-----------------------------------------------------------------------------|
r_work (final): 0.3753
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7619
moved from start:          0.1962

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= 0.421
  Angle     :  0.790   6.974  11152  Z= 0.427
  Chirality :  0.049   0.194   1221
  Planarity :  0.006   0.058   1133
  Dihedral  : 24.829 142.260   1748
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 11.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.36 %
    Favored  : 87.64 %
  Rotamer:
    Outliers :  5.90 %
    Allowed  : 19.57 %
    Favored  : 74.53 %
  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: -4.16 (0.28), residues: 712
  helix: -2.91 (0.29), residues: 229
  sheet: -2.18 (0.48), residues: 109
  loop : -2.86 (0.28), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A 124 
 HIS   0.013   0.002   HIS B 110 
 PHE   0.025   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
  101 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 63
  time to evaluate  : 0.691 
Fit side-chains
REVERT: A  122 GLU cc_start: 0.7746 (mp0) cc_final: 0.6726 (pm20)
REVERT: A  138 ARG cc_start: 0.7814 (mtt-85) cc_final: 0.7378 (mtp180)
  outliers start: 38
  outliers final: 27
  residues processed: 94
  average time/residue: 0.1552
  time to fit residues: 21.1964
Evaluate side-chains
  83 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 56
  time to evaluate  : 0.705 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 15 optimal weight:    3.9990
   chunk 31 optimal weight:    2.9990
   chunk 46 optimal weight:    0.1980
   chunk 18 optimal weight:    0.2980
   chunk 3 optimal weight:    4.9990
   chunk 8 optimal weight:    0.9990
   chunk 21 optimal weight:    6.9990
   chunk 74 optimal weight:   10.0000
   overall best weight:    1.0986

-------------------------------------------------------------------------------
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 145 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4312 r_free = 0.4312 target = 0.168223 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.132292 restraints weight = 14212.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.133595 restraints weight = 11730.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.135066 restraints weight = 8354.045|
|-----------------------------------------------------------------------------|
r_work (final): 0.3858
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7457
moved from start:          0.2406

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   7973  Z= 0.182
  Angle     :  0.611  10.189  11152  Z= 0.331
  Chirality :  0.042   0.166   1221
  Planarity :  0.005   0.055   1133
  Dihedral  : 24.462 144.900   1748
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.18 %
    Favored  : 93.82 %
  Rotamer:
    Outliers :  5.28 %
    Allowed  : 21.58 %
    Favored  : 73.14 %
  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: -3.60 (0.28), residues: 712
  helix: -2.39 (0.32), residues: 229
  sheet: -1.91 (0.48), residues: 106
  loop : -2.54 (0.29), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 124 
 HIS   0.004   0.001   HIS B 110 
 PHE   0.007   0.001   PHE B 128 
 TYR   0.015   0.001   TYR A 157 
 ARG   0.003   0.000   ARG B 343 

*********************** 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
  101 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 67
  time to evaluate  : 0.701 
Fit side-chains
REVERT: A  122 GLU cc_start: 0.7627 (mp0) cc_final: 0.6651 (pm20)
REVERT: A  138 ARG cc_start: 0.7781 (mtt-85) cc_final: 0.7347 (mtp180)
REVERT: B  148 GLU cc_start: 0.7208 (mm-30) cc_final: 0.6635 (tp30)
REVERT: B  281 GLU cc_start: 0.7192 (pm20) cc_final: 0.6899 (pm20)
  outliers start: 34
  outliers final: 24
  residues processed: 92
  average time/residue: 0.1541
  time to fit residues: 20.7027
Evaluate side-chains
  81 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 57
  time to evaluate  : 0.679 
-------------------------------------------------------------------------------
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  202 TYR
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  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  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  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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 10 optimal weight:    1.9990
   chunk 27 optimal weight:    5.9990
   chunk 11 optimal weight:    0.7980
   chunk 78 optimal weight:    9.9990
   chunk 3 optimal weight:    7.9990
   chunk 59 optimal weight:    0.7980
   chunk 54 optimal weight:    7.9990
   chunk 66 optimal weight:    9.9990
   chunk 37 optimal weight:    0.4980
   chunk 24 optimal weight:    4.9990
   chunk 36 optimal weight:    0.9990
   overall best weight:    1.0184

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4324 r_free = 0.4324 target = 0.169439 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.132920 restraints weight = 14143.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.134346 restraints weight = 11650.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.135388 restraints weight = 8256.778|
|-----------------------------------------------------------------------------|
r_work (final): 0.3855
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7457
moved from start:          0.2680

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= 0.175
  Angle     :  0.597   9.193  11152  Z= 0.320
  Chirality :  0.042   0.218   1221
  Planarity :  0.005   0.054   1133
  Dihedral  : 24.302 145.814   1748
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 7.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.44 %
    Favored  : 92.56 %
  Rotamer:
    Outliers :  5.43 %
    Allowed  : 21.74 %
    Favored  : 72.83 %
  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: -3.29 (0.29), residues: 712
  helix: -2.27 (0.31), residues: 245
  sheet: -1.65 (0.47), residues: 108
  loop : -2.25 (0.30), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 264 
 HIS   0.003   0.001   HIS B 110 
 PHE   0.007   0.001   PHE B 307 
 TYR   0.019   0.001   TYR B 336 
 ARG   0.002   0.000   ARG B 393 

*********************** 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
  100 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 65
  time to evaluate  : 0.708 
Fit side-chains
REVERT: A  122 GLU cc_start: 0.7579 (mp0) cc_final: 0.6661 (pm20)
REVERT: A  138 ARG cc_start: 0.7772 (mtt-85) cc_final: 0.7304 (mtp180)
REVERT: A  307 PHE cc_start: 0.8536 (OUTLIER) cc_final: 0.7279 (t80)
REVERT: B  148 GLU cc_start: 0.7043 (mm-30) cc_final: 0.6514 (tp30)
REVERT: B  281 GLU cc_start: 0.6889 (pm20) cc_final: 0.6674 (pm20)
  outliers start: 35
  outliers final: 25
  residues processed: 90
  average time/residue: 0.1542
  time to fit residues: 20.6304
Evaluate side-chains
  83 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 57
  time to evaluate  : 0.751 
-------------------------------------------------------------------------------
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  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  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  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
Chi-restraints excluded: chain B residue  452 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 59 optimal weight:    6.9990
   chunk 71 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9990
   chunk 38 optimal weight:    3.9990
   chunk 77 optimal weight:   10.0000
   chunk 24 optimal weight:    4.9990
   chunk 48 optimal weight:    7.9990
   chunk 16 optimal weight:    8.9990
   chunk 31 optimal weight:    8.9990
   chunk 66 optimal weight:    8.9990
   chunk 12 optimal weight:    1.9990
   overall best weight:    2.7990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4280 r_free = 0.4280 target = 0.165390 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.129434 restraints weight = 14479.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.130021 restraints weight = 14680.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.130982 restraints weight = 10002.505|
|-----------------------------------------------------------------------------|
r_work (final): 0.3800
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7544
moved from start:          0.2645

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= 0.279
  Angle     :  0.668   7.957  11152  Z= 0.358
  Chirality :  0.045   0.231   1221
  Planarity :  0.005   0.053   1133
  Dihedral  : 24.407 145.941   1748
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 8.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.39 %
    Favored  : 89.61 %
  Rotamer:
    Outliers :  5.43 %
    Allowed  : 21.43 %
    Favored  : 73.14 %
  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: -3.27 (0.29), residues: 712
  helix: -2.26 (0.31), residues: 241
  sheet: -1.61 (0.49), residues: 106
  loop : -2.25 (0.30), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 264 
 HIS   0.012   0.001   HIS B 110 
 PHE   0.017   0.002   PHE A 334 
 TYR   0.016   0.002   TYR B 336 
 ARG   0.002   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
  94 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 59
  time to evaluate  : 0.828 
Fit side-chains
REVERT: A  122 GLU cc_start: 0.7571 (mp0) cc_final: 0.6681 (pm20)
REVERT: A  138 ARG cc_start: 0.7827 (mtt-85) cc_final: 0.7366 (mtp180)
REVERT: B  148 GLU cc_start: 0.7323 (mm-30) cc_final: 0.6688 (tp30)
  outliers start: 35
  outliers final: 32
  residues processed: 85
  average time/residue: 0.1422
  time to fit residues: 18.3558
Evaluate side-chains
  92 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 60
  time to evaluate  : 0.675 
-------------------------------------------------------------------------------
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  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  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  412 VAL
Chi-restraints excluded: chain A residue  434 ILE
Chi-restraints excluded: chain A residue  441 LEU
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  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  310 SER
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 60 optimal weight:    0.6980
   chunk 66 optimal weight:    8.9990
   chunk 41 optimal weight:    1.9990
   chunk 67 optimal weight:    6.9990
   chunk 49 optimal weight:    3.9990
   chunk 11 optimal weight:    0.9980
   chunk 25 optimal weight:    7.9990
   chunk 68 optimal weight:    6.9990
   chunk 48 optimal weight:    7.9990
   chunk 18 optimal weight:    5.9990
   chunk 53 optimal weight:    4.9990
   overall best weight:    2.5386

-------------------------------------------------------------------------------
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 = 0.4281 r_free = 0.4281 target = 0.165506 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.129542 restraints weight = 14503.335|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.131014 restraints weight = 11166.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.131635 restraints weight = 8118.725|
|-----------------------------------------------------------------------------|
r_work (final): 0.3809
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7554
moved from start:          0.2741

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   7973  Z= 0.258
  Angle     :  0.668  10.670  11152  Z= 0.354
  Chirality :  0.045   0.219   1221
  Planarity :  0.005   0.053   1133
  Dihedral  : 24.416 146.338   1748
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 8.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.85 %
    Favored  : 91.15 %
  Rotamer:
    Outliers :  6.83 %
    Allowed  : 21.27 %
    Favored  : 71.89 %
  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: -3.13 (0.30), residues: 712
  helix: -2.16 (0.32), residues: 238
  sheet: -1.51 (0.49), residues: 106
  loop : -2.17 (0.31), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 264 
 HIS   0.012   0.001   HIS B 110 
 PHE   0.012   0.002   PHE A 307 
 TYR   0.014   0.002   TYR A 157 
 ARG   0.002   0.000   ARG B 283 

*********************** 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
  106 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 62
  time to evaluate  : 0.876 
Fit side-chains
REVERT: A  122 GLU cc_start: 0.7590 (mp0) cc_final: 0.6683 (pm20)
REVERT: A  138 ARG cc_start: 0.7813 (mtt-85) cc_final: 0.7381 (mtp180)
REVERT: A  307 PHE cc_start: 0.8622 (OUTLIER) cc_final: 0.7454 (t80)
REVERT: B  148 GLU cc_start: 0.7225 (mm-30) cc_final: 0.6663 (tp30)
  outliers start: 44
  outliers final: 35
  residues processed: 96
  average time/residue: 0.1564
  time to fit residues: 22.3526
Evaluate side-chains
  96 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 60
  time to evaluate  : 0.766 
-------------------------------------------------------------------------------
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  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  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  399 VAL
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  441 LEU
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  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
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 29 optimal weight:    0.7980
   chunk 11 optimal weight:    2.9990
   chunk 42 optimal weight:    0.0870
   chunk 7 optimal weight:    0.7980
   chunk 15 optimal weight:    0.0770
   chunk 10 optimal weight:    0.9990
   chunk 77 optimal weight:    9.9990
   chunk 34 optimal weight:    3.9990
   chunk 64 optimal weight:    8.9990
   chunk 78 optimal weight:    9.9990
   chunk 79 optimal weight:   10.0000
   overall best weight:    0.5518

-------------------------------------------------------------------------------
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 = 0.4347 r_free = 0.4347 target = 0.171253 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.135589 restraints weight = 14307.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.136674 restraints weight = 12868.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.137569 restraints weight = 8882.745|
|-----------------------------------------------------------------------------|
r_work (final): 0.3888
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7375
moved from start:          0.3193

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= 0.156
  Angle     :  0.591  10.240  11152  Z= 0.314
  Chirality :  0.041   0.166   1221
  Planarity :  0.005   0.054   1133
  Dihedral  : 24.165 149.037   1748
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 7.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.18 %
    Favored  : 93.82 %
  Rotamer:
    Outliers :  4.35 %
    Allowed  : 23.60 %
    Favored  : 72.05 %
  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: -2.76 (0.30), residues: 712
  helix: -1.91 (0.32), residues: 247
  sheet: -1.19 (0.48), residues: 108
  loop : -1.91 (0.32), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP A 124 
 HIS   0.007   0.001   HIS B 110 
 PHE   0.008   0.001   PHE B 352 
 TYR   0.018   0.001   TYR A 157 
 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
  106 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 78
  time to evaluate  : 0.763 
Fit side-chains
REVERT: A  122 GLU cc_start: 0.7486 (mp0) cc_final: 0.6747 (pm20)
REVERT: A  138 ARG cc_start: 0.7755 (mtt-85) cc_final: 0.7464 (mtp180)
REVERT: A  307 PHE cc_start: 0.8338 (OUTLIER) cc_final: 0.7077 (t80)
REVERT: A  343 ARG cc_start: 0.8162 (ttt180) cc_final: 0.7664 (ttt180)
REVERT: B  148 GLU cc_start: 0.7111 (mm-30) cc_final: 0.6444 (tp30)
  outliers start: 28
  outliers final: 22
  residues processed: 99
  average time/residue: 0.1659
  time to fit residues: 23.9840
Evaluate side-chains
  86 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 63
  time to evaluate  : 0.693 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 A residue  441 LEU
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  234 THR
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  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:    0.9990
   chunk 31 optimal weight:    8.9990
   chunk 61 optimal weight:    4.9990
   chunk 54 optimal weight:    6.9990
   chunk 35 optimal weight:    4.9990
   chunk 7 optimal weight:    1.9990
   chunk 16 optimal weight:    4.9990
   chunk 71 optimal weight:    4.9990
   chunk 37 optimal weight:    1.9990
   chunk 60 optimal weight:    0.2980
   chunk 66 optimal weight:   10.0000
   overall best weight:    2.0588

-------------------------------------------------------------------------------
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 = 0.4299 r_free = 0.4299 target = 0.167195 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.130973 restraints weight = 14567.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.131954 restraints weight = 13187.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.132848 restraints weight = 9492.272|
|-----------------------------------------------------------------------------|
r_work (final): 0.3821
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7484
moved from start:          0.3177

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= 0.225
  Angle     :  0.645   9.214  11152  Z= 0.342
  Chirality :  0.044   0.207   1221
  Planarity :  0.005   0.057   1133
  Dihedral  : 24.224 148.675   1746
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 8.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.85 %
    Favored  : 91.15 %
  Rotamer:
    Outliers :  4.66 %
    Allowed  : 23.45 %
    Favored  : 71.89 %
  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: -2.71 (0.30), residues: 712
  helix: -1.90 (0.31), residues: 247
  sheet: -1.04 (0.50), residues: 106
  loop : -1.91 (0.31), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A 124 
 HIS   0.008   0.001   HIS B 110 
 PHE   0.013   0.002   PHE B 219 
 TYR   0.016   0.002   TYR A 157 
 ARG   0.005   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: 30
    poor density    : 63
  time to evaluate  : 0.698 
Fit side-chains
   revert: symmetry clash
REVERT: A  122 GLU cc_start: 0.7573 (mp0) cc_final: 0.6743 (pm20)
REVERT: A  138 ARG cc_start: 0.7787 (mtt-85) cc_final: 0.7346 (mtp180)
REVERT: A  343 ARG cc_start: 0.8292 (ttt180) cc_final: 0.7709 (ttt180)
REVERT: B  148 GLU cc_start: 0.7222 (mm-30) cc_final: 0.6605 (tp30)
  outliers start: 30
  outliers final: 27
  residues processed: 85
  average time/residue: 0.1658
  time to fit residues: 20.0607
Evaluate side-chains
  89 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 62
  time to evaluate  : 0.686 
-------------------------------------------------------------------------------
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  202 TYR
Chi-restraints excluded: chain A residue  244 SER
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 A residue  441 LEU
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  234 THR
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  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  439 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 1 optimal weight:    0.0050
   chunk 23 optimal weight:    9.9990
   chunk 62 optimal weight:    7.9990
   chunk 6 optimal weight:    4.9990
   chunk 53 optimal weight:    9.9990
   chunk 10 optimal weight:    0.5980
   chunk 32 optimal weight:    3.9990
   chunk 15 optimal weight:    3.9990
   chunk 22 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 57 optimal weight:    3.9990
   overall best weight:    1.9200

-------------------------------------------------------------------------------
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 = 0.4302 r_free = 0.4302 target = 0.167401 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.130885 restraints weight = 14415.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.131768 restraints weight = 12429.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.133007 restraints weight = 9047.049|
|-----------------------------------------------------------------------------|
r_work (final): 0.3820
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7482
moved from start:          0.3256

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   7973  Z= 0.217
  Angle     :  0.633   8.762  11152  Z= 0.337
  Chirality :  0.043   0.200   1221
  Planarity :  0.005   0.058   1133
  Dihedral  : 24.196 149.445   1746
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 8.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.15 %
    Favored  : 91.85 %
  Rotamer:
    Outliers :  4.35 %
    Allowed  : 24.07 %
    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: -2.69 (0.30), residues: 712
  helix: -1.87 (0.32), residues: 247
  sheet: -1.06 (0.49), residues: 103
  loop : -1.89 (0.31), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A 124 
 HIS   0.008   0.001   HIS B 110 
 PHE   0.013   0.002   PHE B 219 
 TYR   0.017   0.002   TYR A 157 
 ARG   0.002   0.000   ARG B 370 

********************** 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
  89 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 61
  time to evaluate  : 0.772 
Fit side-chains
   revert: symmetry clash
REVERT: A  122 GLU cc_start: 0.7592 (mp0) cc_final: 0.6726 (pm20)
REVERT: A  138 ARG cc_start: 0.7806 (mtt-85) cc_final: 0.7366 (mtp180)
REVERT: A  320 MET cc_start: 0.8077 (OUTLIER) cc_final: 0.7851 (ttp)
REVERT: B  148 GLU cc_start: 0.7213 (mm-30) cc_final: 0.6615 (tp30)
  outliers start: 28
  outliers final: 27
  residues processed: 83
  average time/residue: 0.1656
  time to fit residues: 20.3462
Evaluate side-chains
  87 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 59
  time to evaluate  : 0.819 
-------------------------------------------------------------------------------
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  202 TYR
Chi-restraints excluded: chain A residue  244 SER
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 A residue  441 LEU
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  234 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  310 SER
Chi-restraints excluded: chain B residue  312 ILE
Chi-restraints excluded: chain B residue  328 HIS
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 10 optimal weight:    0.9980
   chunk 37 optimal weight:    7.9990
   chunk 64 optimal weight:    9.9990
   chunk 56 optimal weight:    6.9990
   chunk 13 optimal weight:    1.9990
   chunk 62 optimal weight:    0.7980
   chunk 39 optimal weight:    4.9990
   chunk 60 optimal weight:    0.8980
   chunk 71 optimal weight:    4.9990
   chunk 74 optimal weight:   10.0000
   chunk 1 optimal weight:    0.9990
   overall best weight:    1.1384

-------------------------------------------------------------------------------
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 = 0.4327 r_free = 0.4327 target = 0.169804 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.133954 restraints weight = 14330.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.134779 restraints weight = 13420.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.135705 restraints weight = 9449.475|
|-----------------------------------------------------------------------------|
r_work (final): 0.3877
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7417
moved from start:          0.3505

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= 0.175
  Angle     :  0.606   8.914  11152  Z= 0.323
  Chirality :  0.042   0.186   1221
  Planarity :  0.005   0.058   1133
  Dihedral  : 24.129 150.335   1746
  Min Nonbonded Distance : 2.360

Molprobity Statistics.
  All-atom Clashscore : 7.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.88 %
    Favored  : 93.12 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 24.84 %
    Favored  : 71.27 %
  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: -2.42 (0.30), residues: 712
  helix: -1.65 (0.32), residues: 247
  sheet: -0.86 (0.50), residues: 106
  loop : -1.76 (0.32), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 124 
 HIS   0.007   0.001   HIS B 110 
 PHE   0.007   0.001   PHE B 219 
 TYR   0.017   0.001   TYR A 157 
 ARG   0.002   0.000   ARG B 370 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2057.37 seconds
wall clock time: 36 minutes 40.62 seconds (2200.62 seconds total)