Starting phenix.real_space_refine
on Thu Nov 14 10:35:07 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgg_41235/11_2024/8tgg_41235_trim.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgg_41235/11_2024/8tgg_41235.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgg_41235/11_2024/8tgg_41235.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgg_41235/11_2024/8tgg_41235.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgg_41235/11_2024/8tgg_41235_trim.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgg_41235/11_2024/8tgg_41235_trim.cif"
  }
  resolution = 3.6
  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=   0.001 sd=   0.019
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      57      5.16       5
     C    3802      2.51       5
     N     888      2.21       5
     O     970      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib"
  Total number of atoms: 5717
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 2856
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 383, 2856
          Classifications: {'peptide': 383}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 23, 'TRANS': 359}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "B"
      Number of atoms: 2804
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 375, 2804
          Classifications: {'peptide': 375}
          Link IDs: {'PTRANS': 21, 'TRANS': 353}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 13
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 13
          Unusual residues: {'WRF': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 44
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 44
          Unusual residues: {'YHR': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 4.56, per 1000 atoms: 0.80
  Number of scatterers: 5717
  At special positions: 0
  Unit cell: (76.1387, 64.6293, 115.093, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      57     16.00
     O     970      8.00
     N     888      7.00
     C    3802      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: 1.65
  Conformation dependent library (CDL) restraints added in 994.0 milliseconds
  

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1356

  Finding SS restraints...
    Secondary structure from input PDB file:
      39 helices and 0 sheets defined
      89.6% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.66
  Creating SS restraints...
    Processing helix  chain 'A' and resid 19 through 41
      removed outlier: 4.023A  pdb=" N   LEU A  24 " --> pdb=" O   ARG A  20 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   VAL A  25 " --> pdb=" O   GLN A  21 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   PHE A  38 " --> pdb=" O   ASP A  34 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   THR A  39 " --> pdb=" O   ASN A  35 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   VAL A  41 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 44 through 51
      removed outlier: 3.614A  pdb=" N   TYR A  50 " --> pdb=" O   PRO A  46 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   ASP A  51 " --> pdb=" O   THR A  47 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 135 through 144
    Processing helix  chain 'A' and resid 144 through 154
    Processing helix  chain 'A' and resid 160 through 165
    Processing helix  chain 'A' and resid 166 through 187
      removed outlier: 3.707A  pdb=" N   MET A 170 " --> pdb=" O   TYR A 166 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   PHE A 186 " --> pdb=" O   VAL A 182 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 191 through 219
      removed outlier: 3.906A  pdb=" N   VAL A 195 " --> pdb=" O   THR A 191 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   ALA A 196 " --> pdb=" O   LEU A 192 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   ARG A 197 " --> pdb=" O   LEU A 193 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 221 through 254
      removed outlier: 4.013A  pdb=" N   ARG A 227 " --> pdb=" O   HIS A 223 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   ALA A 228 " --> pdb=" O   GLU A 224 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   MET A 229 " --> pdb=" O   ARG A 225 " (cutoff:3.500A)
      removed outlier: 3.992A  pdb=" N   GLY A 230 " --> pdb=" O   GLY A 226 " (cutoff:3.500A)
      removed outlier: 4.435A  pdb=" N   ALA A 244 " --> pdb=" O   LEU A 240 " (cutoff:3.500A)
      Proline residue:  A 245  - end of helix
    Processing helix  chain 'A' and resid 256 through 278
      removed outlier: 4.550A  pdb=" N   PHE A 260 " --> pdb=" O   LYS A 256 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 292 through 297
      removed outlier: 3.634A  pdb=" N   LEU A 296 " --> pdb=" O   PRO A 292 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   LEU A 297 " --> pdb=" O   LEU A 293 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 292 through 297'
    Processing helix  chain 'A' and resid 299 through 320
      removed outlier: 3.681A  pdb=" N   GLY A 315 " --> pdb=" O   PHE A 311 " (cutoff:3.500A)
      removed outlier: 3.895A  pdb=" N   VAL A 316 " --> pdb=" O   ALA A 312 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   ALA A 317 " --> pdb=" O   ASN A 313 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 322 through 331
      removed outlier: 3.582A  pdb=" N   TRP A 326 " --> pdb=" O   THR A 322 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 337 through 342
      removed outlier: 4.158A  pdb=" N   PHE A 342 " --> pdb=" O   LEU A 338 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 342 through 364
      removed outlier: 5.050A  pdb=" N   ASN A 361 " --> pdb=" O   GLY A 357 " (cutoff:3.500A)
      removed outlier: 4.997A  pdb=" N   LYS A 362 " --> pdb=" O   VAL A 358 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 364 through 383
    Processing helix  chain 'A' and resid 384 through 386
      No H-bonds generated for 'chain 'A' and resid 384 through 386'
    Processing helix  chain 'A' and resid 388 through 391
    Processing helix  chain 'A' and resid 392 through 421
      Proline residue:  A 412  - end of helix
      removed outlier: 4.159A  pdb=" N   GLY A 415 " --> pdb=" O   MET A 411 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 426 through 455
      removed outlier: 3.517A  pdb=" N   TYR A 430 " --> pdb=" O   TYR A 426 " (cutoff:3.500A)
      removed outlier: 4.095A  pdb=" N   GLY A 440 " --> pdb=" O   ALA A 436 " (cutoff:3.500A)
      removed outlier: 4.094A  pdb=" N   PHE A 441 " --> pdb=" O   PHE A 437 " (cutoff:3.500A)
      Proline residue:  A 445  - end of helix
      removed outlier: 4.803A  pdb=" N   GLY A 449 " --> pdb=" O   PRO A 445 " (cutoff:3.500A)
      removed outlier: 5.375A  pdb=" N   ALA A 450 " --> pdb=" O   SER A 446 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 456 through 470
    Processing helix  chain 'A' and resid 471 through 480
      removed outlier: 3.828A  pdb=" N   TYR A 476 " --> pdb=" O   PRO A 473 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   ARG A 479 " --> pdb=" O   TYR A 476 " (cutoff:3.500A)
      removed outlier: 4.360A  pdb=" N   SER A 480 " --> pdb=" O   TYR A 477 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 20 through 42
      removed outlier: 3.602A  pdb=" N   PHE B  38 " --> pdb=" O   ASP B  34 " (cutoff:3.500A)
      removed outlier: 3.949A  pdb=" N   VAL B  42 " --> pdb=" O   PHE B  38 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 44 through 53
      removed outlier: 3.628A  pdb=" N   MET B  52 " --> pdb=" O   PHE B  48 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 131 through 154
      removed outlier: 4.289A  pdb=" N   GLU B 135 " --> pdb=" O   PHE B 131 " (cutoff:3.500A)
      removed outlier: 5.090A  pdb=" N   THR B 137 " --> pdb=" O   GLU B 133 " (cutoff:3.500A)
      removed outlier: 4.814A  pdb=" N   ARG B 138 " --> pdb=" O   GLU B 134 " (cutoff:3.500A)
      removed outlier: 4.543A  pdb=" N   LYS B 146 " --> pdb=" O   LEU B 142 " (cutoff:3.500A)
      removed outlier: 4.562A  pdb=" N   ALA B 147 " --> pdb=" O   PHE B 143 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 156 through 165
      removed outlier: 3.644A  pdb=" N   LEU B 160 " --> pdb=" O   PHE B 156 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 166 through 187
      removed outlier: 3.567A  pdb=" N   MET B 170 " --> pdb=" O   TYR B 166 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   ALA B 172 " --> pdb=" O   ILE B 168 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 189 through 219
      removed outlier: 3.840A  pdb=" N   LEU B 193 " --> pdb=" O   THR B 189 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   PHE B 194 " --> pdb=" O   TYR B 190 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   VAL B 195 " --> pdb=" O   THR B 191 " (cutoff:3.500A)
      removed outlier: 4.100A  pdb=" N   LEU B 212 " --> pdb=" O   SER B 208 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 223 through 250
      removed outlier: 4.006A  pdb=" N   ARG B 227 " --> pdb=" O   HIS B 223 " (cutoff:3.500A)
      removed outlier: 3.982A  pdb=" N   ALA B 244 " --> pdb=" O   LEU B 240 " (cutoff:3.500A)
      Proline residue:  B 245  - end of helix
      removed outlier: 4.197A  pdb=" N   SER B 248 " --> pdb=" O   ALA B 244 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 257 through 276
      removed outlier: 3.538A  pdb=" N   ALA B 272 " --> pdb=" O   LEU B 268 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 299 through 331
      removed outlier: 4.215A  pdb=" N   GLY B 315 " --> pdb=" O   PHE B 311 " (cutoff:3.500A)
      removed outlier: 4.581A  pdb=" N   VAL B 316 " --> pdb=" O   ALA B 312 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   GLU B 320 " --> pdb=" O   VAL B 316 " (cutoff:3.500A)
      Proline residue:  B 321  - end of helix
      Proline residue:  B 324  - end of helix
    Processing helix  chain 'B' and resid 339 through 341
      No H-bonds generated for 'chain 'B' and resid 339 through 341'
    Processing helix  chain 'B' and resid 342 through 360
      removed outlier: 3.698A  pdb=" N   TYR B 349 " --> pdb=" O   ALA B 345 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 364 through 383
    Processing helix  chain 'B' and resid 384 through 386
      No H-bonds generated for 'chain 'B' and resid 384 through 386'
    Processing helix  chain 'B' and resid 388 through 391
    Processing helix  chain 'B' and resid 392 through 422
      Proline residue:  B 412  - end of helix
      removed outlier: 3.568A  pdb=" N   ARG B 421 " --> pdb=" O   LEU B 417 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 427 through 455
      removed outlier: 3.648A  pdb=" N   ALA B 431 " --> pdb=" O   GLY B 427 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   ILE B 432 " --> pdb=" O   SER B 428 " (cutoff:3.500A)
      Proline residue:  B 445  - end of helix
      removed outlier: 3.745A  pdb=" N   ALA B 450 " --> pdb=" O   SER B 446 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 456 through 472
    Processing helix  chain 'B' and resid 473 through 479
      removed outlier: 3.844A  pdb=" N   TYR B 476 " --> pdb=" O   PRO B 473 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   TYR B 477 " --> pdb=" O   LEU B 474 " (cutoff:3.500A)

    440 hydrogen bonds defined for protein.
    1296 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.66

  Time building geometry restraints manager: 1.88 seconds

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

  Histogram of bond lengths:
        1.16 -     1.29: 855
        1.29 -     1.42: 1510
        1.42 -     1.55: 3393
        1.55 -     1.69: 2
        1.69 -     1.82: 100
  Bond restraints: 5860
  Sorted by residual:
  bond pdb=" C   VAL A 466 "
       pdb=" O   VAL A 466 "
    ideal  model  delta    sigma   weight residual
    1.237  1.161  0.076 1.17e-02 7.31e+03 4.25e+01
  bond pdb=" C   PRO A 473 "
       pdb=" O   PRO A 473 "
    ideal  model  delta    sigma   weight residual
    1.238  1.156  0.082 1.42e-02 4.96e+03 3.30e+01
  bond pdb=" C   ILE A 469 "
       pdb=" O   ILE A 469 "
    ideal  model  delta    sigma   weight residual
    1.237  1.166  0.071 1.29e-02 6.01e+03 3.03e+01
  bond pdb=" C   ALA A 472 "
       pdb=" O   ALA A 472 "
    ideal  model  delta    sigma   weight residual
    1.244  1.197  0.046 1.00e-02 1.00e+04 2.12e+01
  bond pdb=" C   TYR A 476 "
       pdb=" O   TYR A 476 "
    ideal  model  delta    sigma   weight residual
    1.235  1.180  0.055 1.26e-02 6.30e+03 1.90e+01
  ... (remaining 5855 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.60: 7882
        3.60 -     7.20: 94
        7.20 -    10.80: 5
       10.80 -    14.41: 0
       14.41 -    18.01: 1
  Bond angle restraints: 7982
  Sorted by residual:
  angle pdb=" C7  YHR B 601 "
        pdb=" N8  YHR B 601 "
        pdb=" C9  YHR B 601 "
      ideal   model   delta    sigma   weight residual
     111.89  129.90  -18.01 3.00e+00 1.11e-01 3.60e+01
  angle pdb=" CA  VAL A 466 "
        pdb=" C   VAL A 466 "
        pdb=" O   VAL A 466 "
      ideal   model   delta    sigma   weight residual
     120.95  115.35    5.60 1.04e+00 9.25e-01 2.90e+01
  angle pdb=" N   TYR A  50 "
        pdb=" CA  TYR A  50 "
        pdb=" C   TYR A  50 "
      ideal   model   delta    sigma   weight residual
     111.28  105.59    5.69 1.09e+00 8.42e-01 2.72e+01
  angle pdb=" N   LEU A  49 "
        pdb=" CA  LEU A  49 "
        pdb=" C   LEU A  49 "
      ideal   model   delta    sigma   weight residual
     111.28  105.61    5.67 1.09e+00 8.42e-01 2.71e+01
  angle pdb=" O   THR A 464 "
        pdb=" C   THR A 464 "
        pdb=" N   GLY A 465 "
      ideal   model   delta    sigma   weight residual
     122.07  126.97   -4.90 1.03e+00 9.43e-01 2.27e+01
  ... (remaining 7977 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.26: 3068
       24.26 -    48.51: 324
       48.51 -    72.76: 33
       72.76 -    97.02: 8
       97.02 -   121.27: 2
  Dihedral angle restraints: 3435
    sinusoidal: 1303
      harmonic: 2132
  Sorted by residual:
  dihedral pdb=" C13 YHR B 601 "
           pdb=" C7  YHR B 601 "
           pdb=" N8  YHR B 601 "
           pdb=" C6  YHR B 601 "
      ideal   model   delta sinusoidal    sigma   weight residual
      57.66  -63.61  121.27     1      3.00e+01 1.11e-03 1.62e+01
  dihedral pdb=" CA  PHE A 356 "
           pdb=" C   PHE A 356 "
           pdb=" N   GLY A 357 "
           pdb=" CA  GLY A 357 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.28   19.72     0      5.00e+00 4.00e-02 1.56e+01
  dihedral pdb=" C   TYR A 476 "
           pdb=" N   TYR A 476 "
           pdb=" CA  TYR A 476 "
           pdb=" CB  TYR A 476 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -113.42   -9.18     0      2.50e+00 1.60e-01 1.35e+01
  ... (remaining 3432 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.066: 830
       0.066 -    0.131: 113
       0.131 -    0.196: 8
       0.196 -    0.262: 3
       0.262 -    0.327: 3
  Chirality restraints: 957
  Sorted by residual:
  chirality pdb=" C13 YHR B 601 "
            pdb=" C12 YHR B 601 "
            pdb=" C14 YHR B 601 "
            pdb=" N8  YHR B 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.29   -2.62    0.33 2.00e-01 2.50e+01 2.68e+00
  chirality pdb=" CA  TYR A 476 "
            pdb=" N   TYR A 476 "
            pdb=" C   TYR A 476 "
            pdb=" CB  TYR A 476 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.82   -0.31 2.00e-01 2.50e+01 2.37e+00
  chirality pdb=" CB  VAL A 470 "
            pdb=" CA  VAL A 470 "
            pdb=" CG1 VAL A 470 "
            pdb=" CG2 VAL A 470 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.32   -0.31 2.00e-01 2.50e+01 2.34e+00
  ... (remaining 954 not shown)

  Planarity restraints: 973
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR A 471 "   -0.021 2.00e-02 2.50e+03   4.36e-02 1.90e+01
        pdb=" C   TYR A 471 "    0.075 2.00e-02 2.50e+03
        pdb=" O   TYR A 471 "   -0.028 2.00e-02 2.50e+03
        pdb=" N   ALA A 472 "   -0.026 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA A 472 "   -0.022 2.00e-02 2.50e+03   4.26e-02 1.82e+01
        pdb=" C   ALA A 472 "    0.074 2.00e-02 2.50e+03
        pdb=" O   ALA A 472 "   -0.026 2.00e-02 2.50e+03
        pdb=" N   PRO A 473 "   -0.026 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN A 468 "   -0.014 2.00e-02 2.50e+03   2.90e-02 8.39e+00
        pdb=" C   ASN A 468 "    0.050 2.00e-02 2.50e+03
        pdb=" O   ASN A 468 "   -0.018 2.00e-02 2.50e+03
        pdb=" N   ILE A 469 "   -0.017 2.00e-02 2.50e+03
  ... (remaining 970 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 733
        2.75 -     3.29: 5869
        3.29 -     3.82: 9636
        3.82 -     4.36: 10362
        4.36 -     4.90: 18960
  Nonbonded interactions: 45560
  Sorted by model distance:
  nonbonded pdb=" O   MET B 405 "
            pdb=" OG  SER B 409 "
     model   vdw
     2.212 3.040
  nonbonded pdb=" O   LEU A 142 "
            pdb=" OG  SER A 145 "
     model   vdw
     2.215 3.040
  nonbonded pdb=" O   GLY A 158 "
            pdb=" OG1 THR A 161 "
     model   vdw
     2.259 3.040
  nonbonded pdb=" O   GLN A 150 "
            pdb=" ND2 ASN A 154 "
     model   vdw
     2.304 3.120
  nonbonded pdb=" O   VAL A 375 "
            pdb=" OG  SER A 379 "
     model   vdw
     2.363 3.040
  ... (remaining 45555 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' and (resid 19 through 276 or resid 291 through 483))
  selection = (chain 'B' and (resid 19 through 51 or resid 134 through 483))
}

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:             1.350
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     18.180
  Find NCS groups from input model:        0.290
  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:             0.000
  Load rotamer database and sin/cos tables:2.840
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.030
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6958
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      :  0.006   0.082   5860  Z= 0.371
  Angle     :  0.858  18.007   7982  Z= 0.476
  Chirality :  0.048   0.327    957
  Planarity :  0.007   0.052    973
  Dihedral  : 18.104 121.271   2079
  Min Nonbonded Distance : 2.212

Molprobity Statistics.
  All-atom Clashscore : 22.24
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  2.01 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  0.49 %
    Allowed  : 33.88 %
    Favored  : 65.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.53 (0.29), residues: 746
  helix:  0.94 (0.21), residues: 586
  sheet:  None (None), residues: 0
  loop : -1.69 (0.44), residues: 160

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 336 
 HIS   0.004   0.001   HIS B 223 
 PHE   0.048   0.002   PHE B 178 
 TYR   0.035   0.002   TYR A 476 
 ARG   0.001   0.000   ARG B 421 

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

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

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 122
  time to evaluate  : 0.550 
Fit side-chains
REVERT: B  183 MET cc_start: 0.6919 (ptp) cc_final: 0.6620 (ptp)
  outliers start: 3
  outliers final: 1
  residues processed: 125
  average time/residue: 0.1352
  time to fit residues: 23.6421
Evaluate side-chains
  122 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 121
  time to evaluate  : 0.607 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  470 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 63 optimal weight:    0.9980
   chunk 56 optimal weight:    0.7980
   chunk 31 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9990
   chunk 38 optimal weight:    3.9990
   chunk 30 optimal weight:    0.2980
   chunk 58 optimal weight:    0.6980
   chunk 22 optimal weight:    2.9990
   chunk 35 optimal weight:    0.7980
   chunk 43 optimal weight:    0.8980
   chunk 68 optimal weight:    0.8980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 154 ASN
** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 396 ASN
B  35 ASN
B 274 GLN
B 468 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7037
moved from start:          0.1266

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   5860  Z= 0.326
  Angle     :  0.708   7.201   7982  Z= 0.346
  Chirality :  0.045   0.163    957
  Planarity :  0.006   0.041    973
  Dihedral  :  7.383  82.416    860
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 8.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  5.26 %
    Allowed  : 31.09 %
    Favored  : 63.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.14 (0.31), residues: 746
  helix:  1.29 (0.21), residues: 604
  sheet:  None (None), residues: 0
  loop : -1.41 (0.52), residues: 142

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 336 
 HIS   0.003   0.001   HIS A 422 
 PHE   0.015   0.002   PHE A 356 
 TYR   0.012   0.002   TYR A 349 
 ARG   0.002   0.000   ARG A 197 

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

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

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 133
  time to evaluate  : 0.630 
Fit side-chains
REVERT: A  154 ASN cc_start: 0.7826 (m110) cc_final: 0.7613 (m-40)
REVERT: A  177 MET cc_start: 0.6726 (tmm) cc_final: 0.5890 (tmm)
REVERT: A  434 ASP cc_start: 0.7227 (t0) cc_final: 0.6866 (t0)
REVERT: B  183 MET cc_start: 0.7126 (ptp) cc_final: 0.6776 (ptp)
REVERT: B  291 THR cc_start: 0.8251 (p) cc_final: 0.8030 (t)
  outliers start: 32
  outliers final: 20
  residues processed: 148
  average time/residue: 0.1206
  time to fit residues: 25.7682
Evaluate side-chains
  147 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 127
  time to evaluate  : 0.618 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 MET
Chi-restraints excluded: chain A residue   41 VAL
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  200 GLN
Chi-restraints excluded: chain A residue  231 THR
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  393 ILE
Chi-restraints excluded: chain A residue  420 LEU
Chi-restraints excluded: chain A residue  423 THR
Chi-restraints excluded: chain A residue  443 ILE
Chi-restraints excluded: chain A residue  447 THR
Chi-restraints excluded: chain A residue  455 ILE
Chi-restraints excluded: chain B residue  137 THR
Chi-restraints excluded: chain B residue  174 PHE
Chi-restraints excluded: chain B residue  316 VAL
Chi-restraints excluded: chain B residue  319 LEU
Chi-restraints excluded: chain B residue  330 THR
Chi-restraints excluded: chain B residue  413 ILE
Chi-restraints excluded: chain B residue  423 THR
Chi-restraints excluded: chain B residue  432 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 37 optimal weight:    0.4980
   chunk 21 optimal weight:    0.9980
   chunk 56 optimal weight:    0.5980
   chunk 46 optimal weight:    0.6980
   chunk 18 optimal weight:    0.8980
   chunk 68 optimal weight:    0.0050
   chunk 73 optimal weight:    0.5980
   chunk 60 optimal weight:    0.5980
   chunk 67 optimal weight:    0.5980
   chunk 23 optimal weight:    0.9980
   chunk 54 optimal weight:    4.9990
   overall best weight:    0.4594

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

Flipped N/Q/H residues before XYZ refinement:
A 162 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7023
moved from start:          0.1545

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   5860  Z= 0.242
  Angle     :  0.626   6.651   7982  Z= 0.307
  Chirality :  0.042   0.153    957
  Planarity :  0.005   0.039    973
  Dihedral  :  6.384  73.010    859
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 7.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  5.43 %
    Allowed  : 31.74 %
    Favored  : 62.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.39 (0.31), residues: 746
  helix:  1.50 (0.21), residues: 601
  sheet:  None (None), residues: 0
  loop : -1.48 (0.51), residues: 145

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 366 
 HIS   0.002   0.001   HIS A 422 
 PHE   0.013   0.001   PHE A 294 
 TYR   0.009   0.001   TYR A 476 
 ARG   0.002   0.000   ARG A 225 

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

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

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 132
  time to evaluate  : 0.524 
Fit side-chains
REVERT: A  177 MET cc_start: 0.6735 (tmm) cc_final: 0.5924 (tmm)
REVERT: A  434 ASP cc_start: 0.7190 (t0) cc_final: 0.6832 (t0)
REVERT: B  183 MET cc_start: 0.7087 (ptp) cc_final: 0.6587 (ptp)
  outliers start: 33
  outliers final: 24
  residues processed: 149
  average time/residue: 0.1265
  time to fit residues: 26.7658
Evaluate side-chains
  151 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 127
  time to evaluate  : 0.623 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 MET
Chi-restraints excluded: chain A residue   39 THR
Chi-restraints excluded: chain A residue   41 VAL
Chi-restraints excluded: chain A residue  152 LEU
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  200 GLN
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  314 MET
Chi-restraints excluded: chain A residue  333 SER
Chi-restraints excluded: chain A residue  392 LEU
Chi-restraints excluded: chain A residue  401 LEU
Chi-restraints excluded: chain A residue  443 ILE
Chi-restraints excluded: chain A residue  455 ILE
Chi-restraints excluded: chain B residue   35 ASN
Chi-restraints excluded: chain B residue   42 VAL
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  137 THR
Chi-restraints excluded: chain B residue  174 PHE
Chi-restraints excluded: chain B residue  316 VAL
Chi-restraints excluded: chain B residue  330 THR
Chi-restraints excluded: chain B residue  376 VAL
Chi-restraints excluded: chain B residue  413 ILE
Chi-restraints excluded: chain B residue  423 THR
Chi-restraints excluded: chain B residue  432 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 67 optimal weight:    0.8980
   chunk 51 optimal weight:    3.9990
   chunk 35 optimal weight:    0.9980
   chunk 7 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9980
   chunk 45 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9980
   chunk 72 optimal weight:    1.9990
   chunk 64 optimal weight:    0.5980
   chunk 19 optimal weight:    0.9980
   chunk 60 optimal weight:    0.7980
   overall best weight:    0.8580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7078
moved from start:          0.1966

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.049   5860  Z= 0.362
  Angle     :  0.684   7.066   7982  Z= 0.338
  Chirality :  0.045   0.158    957
  Planarity :  0.005   0.039    973
  Dihedral  :  6.634  76.893    859
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  7.57 %
    Allowed  : 31.25 %
    Favored  : 61.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.32 (0.31), residues: 746
  helix:  1.46 (0.21), residues: 599
  sheet:  None (None), residues: 0
  loop : -1.52 (0.50), residues: 147

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP B 366 
 HIS   0.004   0.001   HIS B 422 
 PHE   0.016   0.002   PHE A  28 
 TYR   0.016   0.002   TYR A 349 
 ARG   0.002   0.000   ARG A 197 

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

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

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 131
  time to evaluate  : 0.656 
Fit side-chains
   revert: symmetry clash
REVERT: A  154 ASN cc_start: 0.8176 (m-40) cc_final: 0.7839 (m-40)
REVERT: A  177 MET cc_start: 0.6765 (tmm) cc_final: 0.5840 (tmm)
REVERT: A  434 ASP cc_start: 0.7248 (t0) cc_final: 0.7025 (t0)
REVERT: B  183 MET cc_start: 0.7089 (ptp) cc_final: 0.6466 (ptp)
REVERT: B  199 LEU cc_start: 0.7731 (mt) cc_final: 0.7424 (mt)
  outliers start: 46
  outliers final: 34
  residues processed: 154
  average time/residue: 0.1295
  time to fit residues: 28.5215
Evaluate side-chains
  165 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 131
  time to evaluate  : 0.595 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 THR
Chi-restraints excluded: chain A residue   41 VAL
Chi-restraints excluded: chain A residue  151 LEU
Chi-restraints excluded: chain A residue  182 VAL
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  214 MET
Chi-restraints excluded: chain A residue  231 THR
Chi-restraints excluded: chain A residue  249 VAL
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  314 MET
Chi-restraints excluded: chain A residue  333 SER
Chi-restraints excluded: chain A residue  392 LEU
Chi-restraints excluded: chain A residue  401 LEU
Chi-restraints excluded: chain A residue  405 MET
Chi-restraints excluded: chain A residue  420 LEU
Chi-restraints excluded: chain A residue  423 THR
Chi-restraints excluded: chain A residue  425 VAL
Chi-restraints excluded: chain A residue  439 MET
Chi-restraints excluded: chain A residue  443 ILE
Chi-restraints excluded: chain A residue  447 THR
Chi-restraints excluded: chain A residue  455 ILE
Chi-restraints excluded: chain B residue   35 ASN
Chi-restraints excluded: chain B residue   42 VAL
Chi-restraints excluded: chain B residue  137 THR
Chi-restraints excluded: chain B residue  148 VAL
Chi-restraints excluded: chain B residue  174 PHE
Chi-restraints excluded: chain B residue  296 LEU
Chi-restraints excluded: chain B residue  316 VAL
Chi-restraints excluded: chain B residue  319 LEU
Chi-restraints excluded: chain B residue  330 THR
Chi-restraints excluded: chain B residue  376 VAL
Chi-restraints excluded: chain B residue  413 ILE
Chi-restraints excluded: chain B residue  423 THR
Chi-restraints excluded: chain B residue  432 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 41 optimal weight:    2.9990
   chunk 1 optimal weight:    0.5980
   chunk 53 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9980
   chunk 61 optimal weight:    2.9990
   chunk 50 optimal weight:    0.9980
   chunk 0 optimal weight:    0.9990
   chunk 37 optimal weight:    0.5980
   chunk 65 optimal weight:    0.9990
   chunk 18 optimal weight:    4.9990
   chunk 24 optimal weight:    0.9980
   overall best weight:    0.8380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7086
moved from start:          0.2176

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   5860  Z= 0.361
  Angle     :  0.682   6.808   7982  Z= 0.340
  Chirality :  0.045   0.158    957
  Planarity :  0.005   0.048    973
  Dihedral  :  6.693  78.364    859
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 7.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  7.24 %
    Allowed  : 31.41 %
    Favored  : 61.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.39 (0.31), residues: 746
  helix:  1.53 (0.21), residues: 585
  sheet:  None (None), residues: 0
  loop : -1.29 (0.49), residues: 161

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A 366 
 HIS   0.002   0.001   HIS B 422 
 PHE   0.016   0.001   PHE A  28 
 TYR   0.016   0.002   TYR A 349 
 ARG   0.003   0.000   ARG A 225 

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

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

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 134
  time to evaluate  : 0.606 
Fit side-chains
REVERT: A   38 PHE cc_start: 0.7498 (t80) cc_final: 0.7262 (t80)
REVERT: A  149 MET cc_start: 0.8001 (tpp) cc_final: 0.7390 (tpp)
REVERT: A  231 THR cc_start: 0.7317 (OUTLIER) cc_final: 0.6973 (p)
REVERT: A  434 ASP cc_start: 0.7269 (t0) cc_final: 0.6990 (t0)
REVERT: B   36 MET cc_start: 0.6698 (mmm) cc_final: 0.6493 (tpp)
REVERT: B  199 LEU cc_start: 0.7786 (mt) cc_final: 0.7421 (mt)
  outliers start: 44
  outliers final: 33
  residues processed: 154
  average time/residue: 0.1292
  time to fit residues: 27.9524
Evaluate side-chains
  166 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 132
  time to evaluate  : 0.594 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 THR
Chi-restraints excluded: chain A residue   41 VAL
Chi-restraints excluded: chain A residue  151 LEU
Chi-restraints excluded: chain A residue  152 LEU
Chi-restraints excluded: chain A residue  182 VAL
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  231 THR
Chi-restraints excluded: chain A residue  263 LEU
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  314 MET
Chi-restraints excluded: chain A residue  392 LEU
Chi-restraints excluded: chain A residue  401 LEU
Chi-restraints excluded: chain A residue  405 MET
Chi-restraints excluded: chain A residue  420 LEU
Chi-restraints excluded: chain A residue  423 THR
Chi-restraints excluded: chain A residue  425 VAL
Chi-restraints excluded: chain A residue  439 MET
Chi-restraints excluded: chain A residue  443 ILE
Chi-restraints excluded: chain A residue  447 THR
Chi-restraints excluded: chain A residue  455 ILE
Chi-restraints excluded: chain B residue   35 ASN
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  137 THR
Chi-restraints excluded: chain B residue  145 SER
Chi-restraints excluded: chain B residue  148 VAL
Chi-restraints excluded: chain B residue  174 PHE
Chi-restraints excluded: chain B residue  316 VAL
Chi-restraints excluded: chain B residue  319 LEU
Chi-restraints excluded: chain B residue  330 THR
Chi-restraints excluded: chain B residue  376 VAL
Chi-restraints excluded: chain B residue  383 VAL
Chi-restraints excluded: chain B residue  413 ILE
Chi-restraints excluded: chain B residue  423 THR
Chi-restraints excluded: chain B residue  432 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 65 optimal weight:    0.0270
   chunk 14 optimal weight:    0.9990
   chunk 42 optimal weight:    0.7980
   chunk 17 optimal weight:    0.9990
   chunk 72 optimal weight:    1.9990
   chunk 60 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9990
   chunk 6 optimal weight:    0.0870
   chunk 24 optimal weight:    0.9990
   chunk 38 optimal weight:    4.9990
   chunk 69 optimal weight:    0.7980
   overall best weight:    0.5418

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

Flipped N/Q/H residues before XYZ refinement:
A 154 ASN
A 223 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7058
moved from start:          0.2262

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   5860  Z= 0.267
  Angle     :  0.638   6.634   7982  Z= 0.314
  Chirality :  0.043   0.159    957
  Planarity :  0.005   0.040    973
  Dihedral  :  6.500  77.106    859
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 7.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  6.09 %
    Allowed  : 33.55 %
    Favored  : 60.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.49 (0.31), residues: 746
  helix:  1.59 (0.21), residues: 595
  sheet:  None (None), residues: 0
  loop : -1.41 (0.50), residues: 151

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 336 
 HIS   0.002   0.001   HIS A 422 
 PHE   0.014   0.001   PHE B 178 
 TYR   0.010   0.001   TYR A 349 
 ARG   0.002   0.000   ARG A 197 

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

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

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 130
  time to evaluate  : 0.614 
Fit side-chains
REVERT: A  149 MET cc_start: 0.8001 (tpp) cc_final: 0.7366 (tpp)
REVERT: A  154 ASN cc_start: 0.8238 (OUTLIER) cc_final: 0.7831 (m-40)
REVERT: A  231 THR cc_start: 0.7223 (OUTLIER) cc_final: 0.6880 (p)
REVERT: A  434 ASP cc_start: 0.7198 (t0) cc_final: 0.6989 (t0)
REVERT: B  183 MET cc_start: 0.7020 (ptp) cc_final: 0.6562 (ptm)
REVERT: B  199 LEU cc_start: 0.7745 (mt) cc_final: 0.7386 (mt)
REVERT: B  439 MET cc_start: 0.6276 (mmt) cc_final: 0.6040 (mmt)
  outliers start: 37
  outliers final: 27
  residues processed: 146
  average time/residue: 0.1244
  time to fit residues: 25.9248
Evaluate side-chains
  158 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 129
  time to evaluate  : 0.560 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 MET
Chi-restraints excluded: chain A residue   39 THR
Chi-restraints excluded: chain A residue   41 VAL
Chi-restraints excluded: chain A residue  152 LEU
Chi-restraints excluded: chain A residue  154 ASN
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  231 THR
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  314 MET
Chi-restraints excluded: chain A residue  392 LEU
Chi-restraints excluded: chain A residue  401 LEU
Chi-restraints excluded: chain A residue  405 MET
Chi-restraints excluded: chain A residue  423 THR
Chi-restraints excluded: chain A residue  439 MET
Chi-restraints excluded: chain A residue  447 THR
Chi-restraints excluded: chain A residue  455 ILE
Chi-restraints excluded: chain B residue   35 ASN
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue  137 THR
Chi-restraints excluded: chain B residue  148 VAL
Chi-restraints excluded: chain B residue  174 PHE
Chi-restraints excluded: chain B residue  294 PHE
Chi-restraints excluded: chain B residue  316 VAL
Chi-restraints excluded: chain B residue  319 LEU
Chi-restraints excluded: chain B residue  330 THR
Chi-restraints excluded: chain B residue  413 ILE
Chi-restraints excluded: chain B residue  423 THR
Chi-restraints excluded: chain B residue  432 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 8 optimal weight:    0.8980
   chunk 41 optimal weight:    3.9990
   chunk 52 optimal weight:    2.9990
   chunk 61 optimal weight:    0.7980
   chunk 40 optimal weight:    0.5980
   chunk 72 optimal weight:    0.9980
   chunk 45 optimal weight:    0.4980
   chunk 44 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9990
   chunk 28 optimal weight:    0.7980
   chunk 43 optimal weight:    0.4980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 154 ASN
B 223 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7069
moved from start:          0.2336

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   5860  Z= 0.299
  Angle     :  0.653   7.630   7982  Z= 0.323
  Chirality :  0.043   0.159    957
  Planarity :  0.005   0.041    973
  Dihedral  :  6.556  78.037    859
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 7.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  7.73 %
    Allowed  : 31.41 %
    Favored  : 60.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.44 (0.31), residues: 746
  helix:  1.55 (0.21), residues: 595
  sheet:  None (None), residues: 0
  loop : -1.44 (0.50), residues: 151

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 336 
 HIS   0.010   0.001   HIS B 223 
 PHE   0.014   0.001   PHE A  28 
 TYR   0.012   0.002   TYR A 349 
 ARG   0.002   0.000   ARG A 197 

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

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

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 130
  time to evaluate  : 0.649 
Fit side-chains
   revert: symmetry clash
REVERT: A  149 MET cc_start: 0.8035 (tpp) cc_final: 0.7506 (tpp)
REVERT: A  231 THR cc_start: 0.7318 (OUTLIER) cc_final: 0.6963 (p)
REVERT: A  434 ASP cc_start: 0.7142 (t0) cc_final: 0.6892 (t0)
REVERT: B  183 MET cc_start: 0.7064 (ptp) cc_final: 0.6627 (ptm)
REVERT: B  199 LEU cc_start: 0.7760 (mt) cc_final: 0.7403 (mt)
REVERT: B  439 MET cc_start: 0.6316 (mmt) cc_final: 0.6085 (mmt)
  outliers start: 47
  outliers final: 38
  residues processed: 155
  average time/residue: 0.1239
  time to fit residues: 27.3927
Evaluate side-chains
  168 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 129
  time to evaluate  : 0.596 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 MET
Chi-restraints excluded: chain A residue   39 THR
Chi-restraints excluded: chain A residue   41 VAL
Chi-restraints excluded: chain A residue   45 VAL
Chi-restraints excluded: chain A residue  152 LEU
Chi-restraints excluded: chain A residue  154 ASN
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  231 THR
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  314 MET
Chi-restraints excluded: chain A residue  392 LEU
Chi-restraints excluded: chain A residue  401 LEU
Chi-restraints excluded: chain A residue  405 MET
Chi-restraints excluded: chain A residue  420 LEU
Chi-restraints excluded: chain A residue  423 THR
Chi-restraints excluded: chain A residue  425 VAL
Chi-restraints excluded: chain A residue  439 MET
Chi-restraints excluded: chain A residue  447 THR
Chi-restraints excluded: chain A residue  455 ILE
Chi-restraints excluded: chain B residue   35 ASN
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue  137 THR
Chi-restraints excluded: chain B residue  145 SER
Chi-restraints excluded: chain B residue  148 VAL
Chi-restraints excluded: chain B residue  174 PHE
Chi-restraints excluded: chain B residue  223 HIS
Chi-restraints excluded: chain B residue  246 PHE
Chi-restraints excluded: chain B residue  291 THR
Chi-restraints excluded: chain B residue  316 VAL
Chi-restraints excluded: chain B residue  319 LEU
Chi-restraints excluded: chain B residue  330 THR
Chi-restraints excluded: chain B residue  376 VAL
Chi-restraints excluded: chain B residue  380 LEU
Chi-restraints excluded: chain B residue  383 VAL
Chi-restraints excluded: chain B residue  413 ILE
Chi-restraints excluded: chain B residue  423 THR
Chi-restraints excluded: chain B residue  432 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 21 optimal weight:    0.1980
   chunk 14 optimal weight:    0.9980
   chunk 45 optimal weight:    0.3980
   chunk 49 optimal weight:    0.7980
   chunk 35 optimal weight:    0.7980
   chunk 6 optimal weight:    0.5980
   chunk 56 optimal weight:    4.9990
   chunk 65 optimal weight:    0.0670
   chunk 69 optimal weight:    0.2980
   chunk 63 optimal weight:    0.9990
   chunk 67 optimal weight:    0.6980
   overall best weight:    0.3118

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

Flipped N/Q/H residues before XYZ refinement:
A 154 ASN
B 223 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7036
moved from start:          0.2360

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5860  Z= 0.208
  Angle     :  0.623   8.409   7982  Z= 0.305
  Chirality :  0.041   0.158    957
  Planarity :  0.005   0.041    973
  Dihedral  :  6.378  75.506    859
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 7.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  7.40 %
    Allowed  : 31.41 %
    Favored  : 61.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.62 (0.31), residues: 746
  helix:  1.69 (0.21), residues: 595
  sheet:  None (None), residues: 0
  loop : -1.40 (0.50), residues: 151

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 336 
 HIS   0.013   0.001   HIS B 223 
 PHE   0.018   0.001   PHE B 178 
 TYR   0.009   0.001   TYR A 430 
 ARG   0.001   0.000   ARG B 225 

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

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

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 125
  time to evaluate  : 0.524 
Fit side-chains
   revert: symmetry clash
REVERT: A  149 MET cc_start: 0.8003 (tpp) cc_final: 0.7604 (tpp)
REVERT: A  231 THR cc_start: 0.7180 (OUTLIER) cc_final: 0.6825 (p)
REVERT: B  183 MET cc_start: 0.7050 (ptp) cc_final: 0.6659 (ptm)
REVERT: B  439 MET cc_start: 0.6257 (mmt) cc_final: 0.6016 (mmt)
  outliers start: 45
  outliers final: 38
  residues processed: 148
  average time/residue: 0.1262
  time to fit residues: 26.6314
Evaluate side-chains
  164 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 125
  time to evaluate  : 0.702 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 MET
Chi-restraints excluded: chain A residue   39 THR
Chi-restraints excluded: chain A residue   41 VAL
Chi-restraints excluded: chain A residue   45 VAL
Chi-restraints excluded: chain A residue  152 LEU
Chi-restraints excluded: chain A residue  154 ASN
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  231 THR
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  263 LEU
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  314 MET
Chi-restraints excluded: chain A residue  392 LEU
Chi-restraints excluded: chain A residue  401 LEU
Chi-restraints excluded: chain A residue  405 MET
Chi-restraints excluded: chain A residue  423 THR
Chi-restraints excluded: chain A residue  425 VAL
Chi-restraints excluded: chain A residue  439 MET
Chi-restraints excluded: chain A residue  443 ILE
Chi-restraints excluded: chain A residue  455 ILE
Chi-restraints excluded: chain B residue   35 ASN
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue  137 THR
Chi-restraints excluded: chain B residue  145 SER
Chi-restraints excluded: chain B residue  148 VAL
Chi-restraints excluded: chain B residue  174 PHE
Chi-restraints excluded: chain B residue  223 HIS
Chi-restraints excluded: chain B residue  246 PHE
Chi-restraints excluded: chain B residue  291 THR
Chi-restraints excluded: chain B residue  297 LEU
Chi-restraints excluded: chain B residue  316 VAL
Chi-restraints excluded: chain B residue  319 LEU
Chi-restraints excluded: chain B residue  380 LEU
Chi-restraints excluded: chain B residue  383 VAL
Chi-restraints excluded: chain B residue  413 ILE
Chi-restraints excluded: chain B residue  423 THR
Chi-restraints excluded: chain B residue  432 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 69 optimal weight:    0.4980
   chunk 40 optimal weight:    0.6980
   chunk 29 optimal weight:    0.5980
   chunk 52 optimal weight:    1.9990
   chunk 20 optimal weight:    0.5980
   chunk 60 optimal weight:    0.8980
   chunk 63 optimal weight:    0.7980
   chunk 67 optimal weight:    0.9990
   chunk 44 optimal weight:    0.0570
   chunk 71 optimal weight:    0.9990
   chunk 43 optimal weight:    1.9990
   overall best weight:    0.4898

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

Flipped N/Q/H residues before XYZ refinement:
A 154 ASN
B 223 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7048
moved from start:          0.2388

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   5860  Z= 0.252
  Angle     :  0.634   8.813   7982  Z= 0.311
  Chirality :  0.042   0.161    957
  Planarity :  0.005   0.041    973
  Dihedral  :  6.388  75.617    859
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 7.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  7.07 %
    Allowed  : 31.74 %
    Favored  : 61.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.61 (0.31), residues: 746
  helix:  1.68 (0.21), residues: 595
  sheet:  None (None), residues: 0
  loop : -1.38 (0.50), residues: 151

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 366 
 HIS   0.015   0.001   HIS B 223 
 PHE   0.013   0.001   PHE A  28 
 TYR   0.010   0.001   TYR A 430 
 ARG   0.001   0.000   ARG A 197 

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

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

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 125
  time to evaluate  : 0.667 
Fit side-chains
   revert: symmetry clash
REVERT: A  149 MET cc_start: 0.8033 (tpp) cc_final: 0.7610 (tpp)
REVERT: A  231 THR cc_start: 0.7191 (OUTLIER) cc_final: 0.6841 (p)
REVERT: B  183 MET cc_start: 0.7016 (ptp) cc_final: 0.6613 (ptm)
REVERT: B  439 MET cc_start: 0.6298 (mmt) cc_final: 0.6052 (mmt)
  outliers start: 43
  outliers final: 37
  residues processed: 146
  average time/residue: 0.1264
  time to fit residues: 26.3869
Evaluate side-chains
  163 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 125
  time to evaluate  : 0.627 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 MET
Chi-restraints excluded: chain A residue   39 THR
Chi-restraints excluded: chain A residue   41 VAL
Chi-restraints excluded: chain A residue   45 VAL
Chi-restraints excluded: chain A residue  152 LEU
Chi-restraints excluded: chain A residue  154 ASN
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  214 MET
Chi-restraints excluded: chain A residue  231 THR
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  263 LEU
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  314 MET
Chi-restraints excluded: chain A residue  392 LEU
Chi-restraints excluded: chain A residue  401 LEU
Chi-restraints excluded: chain A residue  405 MET
Chi-restraints excluded: chain A residue  423 THR
Chi-restraints excluded: chain A residue  425 VAL
Chi-restraints excluded: chain A residue  439 MET
Chi-restraints excluded: chain A residue  455 ILE
Chi-restraints excluded: chain B residue   35 ASN
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue  137 THR
Chi-restraints excluded: chain B residue  145 SER
Chi-restraints excluded: chain B residue  148 VAL
Chi-restraints excluded: chain B residue  174 PHE
Chi-restraints excluded: chain B residue  223 HIS
Chi-restraints excluded: chain B residue  246 PHE
Chi-restraints excluded: chain B residue  291 THR
Chi-restraints excluded: chain B residue  297 LEU
Chi-restraints excluded: chain B residue  316 VAL
Chi-restraints excluded: chain B residue  319 LEU
Chi-restraints excluded: chain B residue  380 LEU
Chi-restraints excluded: chain B residue  383 VAL
Chi-restraints excluded: chain B residue  413 ILE
Chi-restraints excluded: chain B residue  423 THR
Chi-restraints excluded: chain B residue  432 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 33 optimal weight:    0.9990
   chunk 49 optimal weight:    4.9990
   chunk 74 optimal weight:    0.0170
   chunk 68 optimal weight:    0.5980
   chunk 59 optimal weight:    0.6980
   chunk 6 optimal weight:    0.0270
   chunk 45 optimal weight:    0.8980
   chunk 36 optimal weight:    0.6980
   chunk 47 optimal weight:    0.8980
   chunk 63 optimal weight:    0.9990
   chunk 18 optimal weight:    3.9990
   overall best weight:    0.4076

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

Flipped N/Q/H residues before XYZ refinement:
A 154 ASN
B 223 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7038
moved from start:          0.2426

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   5860  Z= 0.230
  Angle     :  0.630   8.561   7982  Z= 0.309
  Chirality :  0.042   0.159    957
  Planarity :  0.005   0.041    973
  Dihedral  :  6.345  74.754    859
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 7.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  6.25 %
    Allowed  : 32.73 %
    Favored  : 61.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.64 (0.31), residues: 746
  helix:  1.70 (0.21), residues: 595
  sheet:  None (None), residues: 0
  loop : -1.34 (0.50), residues: 151

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 366 
 HIS   0.016   0.001   HIS B 223 
 PHE   0.013   0.001   PHE A 356 
 TYR   0.010   0.001   TYR A 430 
 ARG   0.010   0.000   ARG A 479 

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

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

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 123
  time to evaluate  : 0.636 
Fit side-chains
   revert: symmetry clash
REVERT: A  149 MET cc_start: 0.8031 (tpp) cc_final: 0.7606 (tpp)
REVERT: A  231 THR cc_start: 0.7176 (OUTLIER) cc_final: 0.6823 (p)
REVERT: B  183 MET cc_start: 0.7050 (ptp) cc_final: 0.6648 (ptm)
REVERT: B  439 MET cc_start: 0.6293 (mmt) cc_final: 0.6048 (mmt)
  outliers start: 38
  outliers final: 35
  residues processed: 143
  average time/residue: 0.1267
  time to fit residues: 25.6481
Evaluate side-chains
  159 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 123
  time to evaluate  : 0.609 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 MET
Chi-restraints excluded: chain A residue   39 THR
Chi-restraints excluded: chain A residue   41 VAL
Chi-restraints excluded: chain A residue   45 VAL
Chi-restraints excluded: chain A residue  154 ASN
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  214 MET
Chi-restraints excluded: chain A residue  231 THR
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  263 LEU
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  314 MET
Chi-restraints excluded: chain A residue  392 LEU
Chi-restraints excluded: chain A residue  401 LEU
Chi-restraints excluded: chain A residue  405 MET
Chi-restraints excluded: chain A residue  423 THR
Chi-restraints excluded: chain A residue  425 VAL
Chi-restraints excluded: chain A residue  439 MET
Chi-restraints excluded: chain A residue  455 ILE
Chi-restraints excluded: chain B residue   35 ASN
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue  137 THR
Chi-restraints excluded: chain B residue  145 SER
Chi-restraints excluded: chain B residue  148 VAL
Chi-restraints excluded: chain B residue  174 PHE
Chi-restraints excluded: chain B residue  223 HIS
Chi-restraints excluded: chain B residue  246 PHE
Chi-restraints excluded: chain B residue  291 THR
Chi-restraints excluded: chain B residue  316 VAL
Chi-restraints excluded: chain B residue  319 LEU
Chi-restraints excluded: chain B residue  380 LEU
Chi-restraints excluded: chain B residue  383 VAL
Chi-restraints excluded: chain B residue  413 ILE
Chi-restraints excluded: chain B residue  423 THR
Chi-restraints excluded: chain B residue  432 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 54 optimal weight:    0.8980
   chunk 8 optimal weight:    0.5980
   chunk 16 optimal weight:    0.5980
   chunk 59 optimal weight:    0.8980
   chunk 24 optimal weight:    0.4980
   chunk 61 optimal weight:    0.8980
   chunk 7 optimal weight:    0.5980
   chunk 10 optimal weight:    0.9990
   chunk 52 optimal weight:    0.7980
   chunk 3 optimal weight:    3.9990
   chunk 43 optimal weight:    0.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 154 ASN
B 223 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.144041 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.122386 restraints weight = 8206.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.124964 restraints weight = 4446.777|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.128265 restraints weight = 2832.933|
|-----------------------------------------------------------------------------|
r_work (final): 0.3621
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7061
moved from start:          0.2481

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   5860  Z= 0.289
  Angle     :  0.646   7.753   7982  Z= 0.317
  Chirality :  0.043   0.161    957
  Planarity :  0.005   0.041    973
  Dihedral  :  6.445  76.575    859
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 8.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  6.25 %
    Allowed  : 33.06 %
    Favored  : 60.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.55 (0.31), residues: 746
  helix:  1.63 (0.21), residues: 595
  sheet:  None (None), residues: 0
  loop : -1.37 (0.50), residues: 151

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 366 
 HIS   0.017   0.002   HIS B 223 
 PHE   0.014   0.001   PHE A  28 
 TYR   0.011   0.001   TYR A 349 
 ARG   0.009   0.001   ARG A 479 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1498.45 seconds
wall clock time: 27 minutes 46.18 seconds (1666.18 seconds total)