Starting phenix.real_space_refine
on Fri Aug  2 23:58:05 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9enc_19831/08_2024/9enc_19831.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9enc_19831/08_2024/9enc_19831.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.36
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9enc_19831/08_2024/9enc_19831.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9enc_19831/08_2024/9enc_19831.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9enc_19831/08_2024/9enc_19831.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9enc_19831/08_2024/9enc_19831.cif"
  }
  resolution = 3.36
  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=   0.002 sd=   0.030
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      74      5.49       5
     S      30      5.16       5
     C    3699      2.51       5
     N    1089      2.21       5
     O    1357      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A TYR  195": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  262": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  297": "OE1" <-> "OE2"
    Residue "A PHE  320": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B ASP  326": "OD1" <-> "OD2"
  Time to flip residues: 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib"
  Total number of atoms: 6249
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 2304
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 281, 2304
          Classifications: {'peptide': 281}
          Link IDs: {'PTRANS': 10, 'TRANS': 270}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 2356
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 285, 2356
          Classifications: {'peptide': 285}
          Link IDs: {'PTRANS': 11, 'TRANS': 273}
          Chain breaks: 3
    Chain: "D"
      Number of atoms: 1589
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 1589
          Classifications: {'RNA': 75}
          Modifications used: {'5*END': 1, 'rna2p_pur': 9, 'rna2p_pyr': 7, 'rna3p_pur': 27, 'rna3p_pyr': 32}
          Link IDs: {'rna2p': 15, 'rna3p': 59}
  Time building chain proxies: 3.59, per 1000 atoms: 0.57
  Number of scatterers: 6249
  At special positions: 0
  Unit cell: (102.318, 127.686, 65.9568, 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      30     16.00
     P      74     15.00
     O    1357      8.00
     N    1089      7.00
     C    3699      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 114 " - pdb=" SG  CYS A 327 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 114 " - pdb=" SG  CYS B 327 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 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: 1.98
  Conformation dependent library (CDL) restraints added in 616.9 milliseconds
  

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1080

  Finding SS restraints...
    Secondary structure from input PDB file:
      17 helices and 4 sheets defined
      35.3% alpha, 25.1% beta
      22 base pairs and 25 stacking pairs defined.
    Time for finding SS restraints: 1.41
  Creating SS restraints...
    Processing helix  chain 'A' and resid 88 through 100
    Processing helix  chain 'A' and resid 105 through 109
    Processing helix  chain 'A' and resid 159 through 168
      removed outlier: 3.924A  pdb=" N   VAL A 167 " --> pdb=" O   ILE A 163 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 205 through 214
      removed outlier: 3.766A  pdb=" N   TYR A 211 " --> pdb=" O   VAL A 207 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 259 through 262
    Processing helix  chain 'A' and resid 277 through 292
    Processing helix  chain 'A' and resid 297 through 304
      removed outlier: 3.746A  pdb=" N   GLU A 301 " --> pdb=" O   GLU A 297 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 337 through 369
    Processing helix  chain 'B' and resid 88 through 100
      removed outlier: 3.503A  pdb=" N   LYS B  92 " --> pdb=" O   THR B  88 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 105 through 109
    Processing helix  chain 'B' and resid 159 through 168
      removed outlier: 3.925A  pdb=" N   VAL B 167 " --> pdb=" O   ILE B 163 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 205 through 214
      removed outlier: 3.667A  pdb=" N   GLN B 214 " --> pdb=" O   ASP B 210 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 223 through 226
      removed outlier: 3.791A  pdb=" N   CYS B 226 " --> pdb=" O   ARG B 223 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 223 through 226'
    Processing helix  chain 'B' and resid 259 through 262
    Processing helix  chain 'B' and resid 277 through 291
      removed outlier: 3.659A  pdb=" N   LEU B 288 " --> pdb=" O   ALA B 284 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   ILE B 289 " --> pdb=" O   ILE B 285 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 297 through 303
      removed outlier: 3.518A  pdb=" N   GLU B 301 " --> pdb=" O   GLU B 297 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 337 through 369
    Processing sheet with id=AA1, first strand: chain 'A' and resid 112 through 113
      removed outlier: 5.122A  pdb=" N   PHE A 124 " --> pdb=" O   TYR A  71 " (cutoff:3.500A)
      removed outlier: 6.200A  pdb=" N   TYR A  71 " --> pdb=" O   PHE A 124 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   ARG A  63 " --> pdb=" O   LEU A 132 " (cutoff:3.500A)
      removed outlier: 7.908A  pdb=" N   HIS A  64 " --> pdb=" O   PRO A 179 " (cutoff:3.500A)
      removed outlier: 6.821A  pdb=" N   ALA A  66 " --> pdb=" O   TRP A 177 " (cutoff:3.500A)
      removed outlier: 4.738A  pdb=" N   TRP A 177 " --> pdb=" O   ALA A  66 " (cutoff:3.500A)
      removed outlier: 6.844A  pdb=" N   ARG A  68 " --> pdb=" O   LEU A 175 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 112 through 113
      removed outlier: 6.346A  pdb=" N   ASP A 326 " --> pdb=" O   PHE A 124 " (cutoff:3.500A)
      removed outlier: 7.039A  pdb=" N   GLN A 126 " --> pdb=" O   ASP A 326 " (cutoff:3.500A)
      removed outlier: 9.243A  pdb=" N   LYS A 328 " --> pdb=" O   GLN A 126 " (cutoff:3.500A)
      removed outlier: 11.007A  pdb=" N   ILE A 128 " --> pdb=" O   LYS A 328 " (cutoff:3.500A)
      removed outlier: 6.712A  pdb=" N   THR A 194 " --> pdb=" O   TYR A 325 " (cutoff:3.500A)
      removed outlier: 4.770A  pdb=" N   CYS A 327 " --> pdb=" O   GLU A 192 " (cutoff:3.500A)
      removed outlier: 6.851A  pdb=" N   GLU A 192 " --> pdb=" O   CYS A 327 " (cutoff:3.500A)
      removed outlier: 7.242A  pdb=" N   LEU A 264 " --> pdb=" O   LEU A 248 " (cutoff:3.500A)
      removed outlier: 5.173A  pdb=" N   LEU A 248 " --> pdb=" O   LEU A 264 " (cutoff:3.500A)
      removed outlier: 6.533A  pdb=" N   GLN A 266 " --> pdb=" O   VAL A 246 " (cutoff:3.500A)
      removed outlier: 4.500A  pdb=" N   VAL A 246 " --> pdb=" O   GLN A 266 " (cutoff:3.500A)
      removed outlier: 6.996A  pdb=" N   GLU A 268 " --> pdb=" O   ALA A 244 " (cutoff:3.500A)
      removed outlier: 4.321A  pdb=" N   ALA A 244 " --> pdb=" O   GLU A 268 " (cutoff:3.500A)
      removed outlier: 6.913A  pdb=" N   THR A 270 " --> pdb=" O   LEU A 242 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 112 through 113
      removed outlier: 5.056A  pdb=" N   PHE B 124 " --> pdb=" O   TYR B  71 " (cutoff:3.500A)
      removed outlier: 7.333A  pdb=" N   TYR B  71 " --> pdb=" O   PHE B 124 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   GLY B  61 " --> pdb=" O   SER B 134 " (cutoff:3.500A)
      removed outlier: 7.781A  pdb=" N   HIS B  64 " --> pdb=" O   PRO B 179 " (cutoff:3.500A)
      removed outlier: 6.724A  pdb=" N   ALA B  66 " --> pdb=" O   TRP B 177 " (cutoff:3.500A)
      removed outlier: 4.519A  pdb=" N   TRP B 177 " --> pdb=" O   ALA B  66 " (cutoff:3.500A)
      removed outlier: 6.770A  pdb=" N   ARG B  68 " --> pdb=" O   LEU B 175 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 112 through 113
      removed outlier: 7.226A  pdb=" N   SER B 122 " --> pdb=" O   LEU B 324 " (cutoff:3.500A)
      removed outlier: 8.631A  pdb=" N   ASP B 326 " --> pdb=" O   SER B 122 " (cutoff:3.500A)
      removed outlier: 8.588A  pdb=" N   PHE B 124 " --> pdb=" O   ASP B 326 " (cutoff:3.500A)
      removed outlier: 9.157A  pdb=" N   LYS B 328 " --> pdb=" O   PHE B 124 " (cutoff:3.500A)
      removed outlier: 10.704A  pdb=" N   GLN B 126 " --> pdb=" O   LYS B 328 " (cutoff:3.500A)
      removed outlier: 6.637A  pdb=" N   THR B 194 " --> pdb=" O   TYR B 325 " (cutoff:3.500A)
      removed outlier: 4.620A  pdb=" N   CYS B 327 " --> pdb=" O   GLU B 192 " (cutoff:3.500A)
      removed outlier: 6.804A  pdb=" N   GLU B 192 " --> pdb=" O   CYS B 327 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   PHE B 199 " --> pdb=" O   CYS B 265 " (cutoff:3.500A)
      removed outlier: 7.661A  pdb=" N   LEU B 264 " --> pdb=" O   LEU B 248 " (cutoff:3.500A)
      removed outlier: 5.190A  pdb=" N   LEU B 248 " --> pdb=" O   LEU B 264 " (cutoff:3.500A)
      removed outlier: 6.689A  pdb=" N   GLN B 266 " --> pdb=" O   VAL B 246 " (cutoff:3.500A)
      removed outlier: 4.535A  pdb=" N   VAL B 246 " --> pdb=" O   GLN B 266 " (cutoff:3.500A)
      removed outlier: 6.890A  pdb=" N   GLU B 268 " --> pdb=" O   ALA B 244 " (cutoff:3.500A)
      removed outlier: 4.159A  pdb=" N   ALA B 244 " --> pdb=" O   GLU B 268 " (cutoff:3.500A)
      removed outlier: 6.881A  pdb=" N   THR B 270 " --> pdb=" O   LEU B 242 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   ARG B 239 " --> pdb=" O   HIS B 220 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   HIS B 220 " --> pdb=" O   ARG B 239 " (cutoff:3.500A)

    185 hydrogen bonds defined for protein.
    516 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      58 hydrogen bonds
      102 hydrogen bond angles
      0 basepair planarities
      22 basepair parallelities
      25 stacking parallelities
  Total time for adding SS restraints: 1.25

  Time building geometry restraints manager: 2.17 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1690
        1.34 -     1.45: 1630
        1.45 -     1.57: 3030
        1.57 -     1.69: 148
        1.69 -     1.81: 48
  Bond restraints: 6546
  Sorted by residual:
  bond pdb=" C   GLU B 260 "
       pdb=" N   PRO B 261 "
    ideal  model  delta    sigma   weight residual
    1.334  1.352 -0.018 8.40e-03 1.42e+04 4.65e+00
  bond pdb=" C   GLU A 260 "
       pdb=" N   PRO A 261 "
    ideal  model  delta    sigma   weight residual
    1.337  1.351 -0.014 1.11e-02 8.12e+03 1.69e+00
  bond pdb=" C3'   G D  36 "
       pdb=" O3'   G D  36 "
    ideal  model  delta    sigma   weight residual
    1.427  1.443 -0.016 1.50e-02 4.44e+03 1.14e+00
  bond pdb=" CA  ASN A 232 "
       pdb=" C   ASN A 232 "
    ideal  model  delta    sigma   weight residual
    1.523  1.535 -0.013 1.41e-02 5.03e+03 8.00e-01
  bond pdb=" O3'   G D  36 "
       pdb=" P     A D  37 "
    ideal  model  delta    sigma   weight residual
    1.607  1.620 -0.013 1.50e-02 4.44e+03 7.47e-01
  ... (remaining 6541 not shown)

  Histogram of bond angle deviations from ideal:
      100.37 -   107.09: 556
      107.09 -   113.81: 3675
      113.81 -   120.53: 2507
      120.53 -   127.25: 2285
      127.25 -   133.97: 190
  Bond angle restraints: 9213
  Sorted by residual:
  angle pdb=" C3'   G D  36 "
        pdb=" O3'   G D  36 "
        pdb=" P     A D  37 "
      ideal   model   delta    sigma   weight residual
     120.20  125.79   -5.59 1.50e+00 4.44e-01 1.39e+01
  angle pdb=" O3'   G D  36 "
        pdb=" P     A D  37 "
        pdb=" OP1   A D  37 "
      ideal   model   delta    sigma   weight residual
     108.00  118.34  -10.34 3.00e+00 1.11e-01 1.19e+01
  angle pdb=" C4'   G D  36 "
        pdb=" C3'   G D  36 "
        pdb=" O3'   G D  36 "
      ideal   model   delta    sigma   weight residual
     109.40  113.35   -3.95 1.50e+00 4.44e-01 6.93e+00
  angle pdb=" CA  PHE A 320 "
        pdb=" C   PHE A 320 "
        pdb=" N   PRO A 321 "
      ideal   model   delta    sigma   weight residual
     118.44  122.46   -4.02 1.59e+00 3.96e-01 6.39e+00
  angle pdb=" N   PHE A 320 "
        pdb=" CA  PHE A 320 "
        pdb=" C   PHE A 320 "
      ideal   model   delta    sigma   weight residual
     109.81  114.97   -5.16 2.21e+00 2.05e-01 5.44e+00
  ... (remaining 9208 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    31.20: 3647
       31.20 -    62.40: 282
       62.40 -    93.60: 79
       93.60 -   124.80: 2
      124.80 -   156.00: 4
  Dihedral angle restraints: 4014
    sinusoidal: 2349
      harmonic: 1665
  Sorted by residual:
  dihedral pdb=" O4'   U D  35 "
           pdb=" C1'   U D  35 "
           pdb=" N1    U D  35 "
           pdb=" C2    U D  35 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   44.00  156.00     1      1.50e+01 4.44e-03 8.16e+01
  dihedral pdb=" O4'   C D  48 "
           pdb=" C1'   C D  48 "
           pdb=" N1    C D  48 "
           pdb=" C2    C D  48 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -160.00  -25.27 -134.73     1      1.50e+01 4.44e-03 7.27e+01
  dihedral pdb=" O4'   A D  37 "
           pdb=" C1'   A D  37 "
           pdb=" N9    A D  37 "
           pdb=" C4    A D  37 "
      ideal   model   delta sinusoidal    sigma   weight residual
     254.00  175.33   78.67     1      1.70e+01 3.46e-03 2.67e+01
  ... (remaining 4011 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 870
       0.042 -    0.084: 148
       0.084 -    0.126: 40
       0.126 -    0.168: 3
       0.168 -    0.210: 2
  Chirality restraints: 1063
  Sorted by residual:
  chirality pdb=" P     A D  37 "
            pdb=" OP1   A D  37 "
            pdb=" OP2   A D  37 "
            pdb=" O5'   A D  37 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.62   -0.21 2.00e-01 2.50e+01 1.10e+00
  chirality pdb=" C1'   A D  58 "
            pdb=" O4'   A D  58 "
            pdb=" C2'   A D  58 "
            pdb=" N9    A D  58 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.46    2.28    0.18 2.00e-01 2.50e+01 7.95e-01
  chirality pdb=" CA  PHE A 320 "
            pdb=" N   PHE A 320 "
            pdb=" C   PHE A 320 "
            pdb=" CB  PHE A 320 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.80e-01
  ... (remaining 1060 not shown)

  Planarity restraints: 907
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   C D  32 "    0.026 2.00e-02 2.50e+03   1.32e-02 3.94e+00
        pdb=" N1    C D  32 "   -0.029 2.00e-02 2.50e+03
        pdb=" C2    C D  32 "   -0.003 2.00e-02 2.50e+03
        pdb=" O2    C D  32 "   -0.003 2.00e-02 2.50e+03
        pdb=" N3    C D  32 "    0.004 2.00e-02 2.50e+03
        pdb=" C4    C D  32 "    0.004 2.00e-02 2.50e+03
        pdb=" N4    C D  32 "    0.007 2.00e-02 2.50e+03
        pdb=" C5    C D  32 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6    C D  32 "   -0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A D  58 "   -0.017 2.00e-02 2.50e+03   8.90e-03 2.18e+00
        pdb=" N9    A D  58 "    0.023 2.00e-02 2.50e+03
        pdb=" C8    A D  58 "    0.000 2.00e-02 2.50e+03
        pdb=" N7    A D  58 "   -0.003 2.00e-02 2.50e+03
        pdb=" C5    A D  58 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6    A D  58 "   -0.004 2.00e-02 2.50e+03
        pdb=" N6    A D  58 "   -0.001 2.00e-02 2.50e+03
        pdb=" N1    A D  58 "   -0.002 2.00e-02 2.50e+03
        pdb=" C2    A D  58 "    0.001 2.00e-02 2.50e+03
        pdb=" N3    A D  58 "    0.003 2.00e-02 2.50e+03
        pdb=" C4    A D  58 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   C D  44 "   -0.018 2.00e-02 2.50e+03   9.34e-03 1.96e+00
        pdb=" N1    C D  44 "    0.020 2.00e-02 2.50e+03
        pdb=" C2    C D  44 "    0.002 2.00e-02 2.50e+03
        pdb=" O2    C D  44 "    0.002 2.00e-02 2.50e+03
        pdb=" N3    C D  44 "   -0.002 2.00e-02 2.50e+03
        pdb=" C4    C D  44 "   -0.001 2.00e-02 2.50e+03
        pdb=" N4    C D  44 "   -0.006 2.00e-02 2.50e+03
        pdb=" C5    C D  44 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6    C D  44 "    0.004 2.00e-02 2.50e+03
  ... (remaining 904 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.77: 1073
        2.77 -     3.30: 5518
        3.30 -     3.83: 10864
        3.83 -     4.37: 12384
        4.37 -     4.90: 20070
  Nonbonded interactions: 49909
  Sorted by model distance:
  nonbonded pdb=" OP2   G D  45 "
            pdb=" N2    G D  45 "
     model   vdw
     2.232 3.120
  nonbonded pdb=" O2'   U D  35 "
            pdb=" OP1   A D  37 "
     model   vdw
     2.234 3.040
  nonbonded pdb=" OG  SER B 105 "
            pdb=" OG1 THR B 108 "
     model   vdw
     2.235 3.040
  nonbonded pdb=" O2'   A D   7 "
            pdb=" O2    C D  48 "
     model   vdw
     2.280 3.040
  nonbonded pdb=" OH  TYR A 197 "
            pdb=" O   VAL A 318 "
     model   vdw
     2.305 3.040
  ... (remaining 49904 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 61 through 228 or resid 236 through 249 or resid 257 throu \ 
gh 369))
  selection = (chain 'B' and (resid 61 through 134 or resid 157 through 369))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.620
  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:          0.200
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     16.290
  Find NCS groups from input model:        0.120
  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:             0.000
  Load rotamer database and sin/cos tables:2.290
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.620
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8486
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      :  0.002   0.027   6546  Z= 0.153
  Angle     :  0.512  10.339   9213  Z= 0.292
  Chirality :  0.035   0.210   1063
  Planarity :  0.003   0.033    907
  Dihedral  : 21.396 156.003   2928
  Min Nonbonded Distance : 2.232

Molprobity Statistics.
  All-atom Clashscore : 3.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.25 %
    Favored  : 94.75 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  : 27.66 %
    Favored  : 72.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.18 (0.36), residues: 552
  helix:  1.24 (0.40), residues: 172
  sheet:  0.61 (0.57), residues: 87
  loop : -1.22 (0.37), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 352 
 HIS   0.003   0.001   HIS B 360 
 PHE   0.017   0.001   PHE B 320 
 TYR   0.006   0.001   TYR A 216 
 ARG   0.003   0.000   ARG A 187 

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

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

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  33 residues out of total 499 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 32
  time to evaluate  : 0.566 
Fit side-chains
REVERT: A  293 MET cc_start: 0.7799 (ttt) cc_final: 0.7592 (ttt)
REVERT: A  295 LYS cc_start: 0.8721 (OUTLIER) cc_final: 0.8216 (ttpp)
  outliers start: 1
  outliers final: 0
  residues processed: 33
  average time/residue: 0.2411
  time to fit residues: 10.2989
Evaluate side-chains
  22 residues out of total 499 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 21
  time to evaluate  : 0.454 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  295 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 53 optimal weight:    5.9990
   chunk 47 optimal weight:    1.9990
   chunk 26 optimal weight:    3.9990
   chunk 16 optimal weight:    0.8980
   chunk 32 optimal weight:    0.8980
   chunk 25 optimal weight:    2.9990
   chunk 49 optimal weight:    3.9990
   chunk 19 optimal weight:    1.9990
   chunk 30 optimal weight:    3.9990
   chunk 36 optimal weight:    0.5980
   chunk 57 optimal weight:    6.9990
   overall best weight:    1.2784

-------------------------------------------------------------------------------
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: 0.8509
moved from start:          0.1151

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6546  Z= 0.217
  Angle     :  0.527  10.950   9213  Z= 0.275
  Chirality :  0.038   0.241   1063
  Planarity :  0.004   0.032    907
  Dihedral  : 20.786 154.016   1796
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 4.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.53 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 25.85 %
    Favored  : 72.55 %
  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:  0.20 (0.36), residues: 552
  helix:  2.07 (0.38), residues: 167
  sheet:  0.47 (0.58), residues: 84
  loop : -1.15 (0.35), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 258 
 HIS   0.005   0.001   HIS B 360 
 PHE   0.016   0.001   PHE B 320 
 TYR   0.009   0.001   TYR A 195 
 ARG   0.003   0.001   ARG A 257 

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

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

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  31 residues out of total 499 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 23
  time to evaluate  : 0.630 
Fit side-chains
   revert: symmetry clash
REVERT: A   72 MET cc_start: 0.8479 (mpp) cc_final: 0.8156 (mmm)
REVERT: A  258 TRP cc_start: 0.8516 (t60) cc_final: 0.7882 (t60)
REVERT: A  293 MET cc_start: 0.7759 (ttt) cc_final: 0.7553 (ttm)
  outliers start: 8
  outliers final: 2
  residues processed: 28
  average time/residue: 0.1499
  time to fit residues: 6.2400
Evaluate side-chains
  23 residues out of total 499 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 21
  time to evaluate  : 0.467 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  228 MET
Chi-restraints excluded: chain A residue  295 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 31 optimal weight:    4.9990
   chunk 17 optimal weight:    0.4980
   chunk 47 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 15 optimal weight:    7.9990
   chunk 57 optimal weight:    7.9990
   chunk 61 optimal weight:    4.9990
   chunk 51 optimal weight:    0.0670
   chunk 56 optimal weight:    7.9990
   chunk 19 optimal weight:    0.6980
   chunk 45 optimal weight:    2.9990
   overall best weight:    1.2522

-------------------------------------------------------------------------------
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: 0.8518
moved from start:          0.1529

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6546  Z= 0.208
  Angle     :  0.510   9.292   9213  Z= 0.265
  Chirality :  0.037   0.217   1063
  Planarity :  0.004   0.033    907
  Dihedral  : 20.770 155.186   1796
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 3.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.07 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 24.65 %
    Favored  : 73.35 %
  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:  0.27 (0.36), residues: 552
  helix:  2.32 (0.38), residues: 167
  sheet:  0.36 (0.58), residues: 84
  loop : -1.19 (0.35), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B  74 
 HIS   0.004   0.001   HIS B 360 
 PHE   0.016   0.001   PHE B 320 
 TYR   0.012   0.001   TYR B 216 
 ARG   0.003   0.000   ARG A 201 

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

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

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  32 residues out of total 499 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 22
  time to evaluate  : 0.622 
Fit side-chains
REVERT: A   72 MET cc_start: 0.8492 (mpp) cc_final: 0.8152 (mmm)
REVERT: A  258 TRP cc_start: 0.8530 (t60) cc_final: 0.7955 (t60)
REVERT: A  293 MET cc_start: 0.7740 (ttt) cc_final: 0.7307 (ttm)
REVERT: A  295 LYS cc_start: 0.8787 (OUTLIER) cc_final: 0.8295 (ttpp)
  outliers start: 10
  outliers final: 3
  residues processed: 29
  average time/residue: 0.1641
  time to fit residues: 7.1074
Evaluate side-chains
  25 residues out of total 499 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 21
  time to evaluate  : 0.623 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  122 SER
Chi-restraints excluded: chain A residue  228 MET
Chi-restraints excluded: chain A residue  295 LYS
Chi-restraints excluded: chain B residue  167 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 56 optimal weight:    8.9990
   chunk 43 optimal weight:    5.9990
   chunk 29 optimal weight:    4.9990
   chunk 6 optimal weight:    5.9990
   chunk 27 optimal weight:    4.9990
   chunk 38 optimal weight:    0.9980
   chunk 57 optimal weight:    6.9990
   chunk 60 optimal weight:    5.9990
   chunk 30 optimal weight:    0.9990
   chunk 54 optimal weight:    1.9990
   chunk 16 optimal weight:    0.5980
   overall best weight:    1.9186

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

Flipped N/Q/H residues before XYZ refinement:
B 110 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8560
moved from start:          0.1831

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   6546  Z= 0.298
  Angle     :  0.549   7.406   9213  Z= 0.284
  Chirality :  0.038   0.193   1063
  Planarity :  0.004   0.037    907
  Dihedral  : 20.924 157.682   1796
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 4.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.16 %
    Favored  : 93.84 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 23.45 %
    Favored  : 74.75 %
  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:  0.12 (0.36), residues: 552
  helix:  2.19 (0.38), residues: 167
  sheet:  0.17 (0.57), residues: 84
  loop : -1.24 (0.36), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  74 
 HIS   0.005   0.001   HIS A 360 
 PHE   0.017   0.002   PHE B  94 
 TYR   0.011   0.001   TYR A 195 
 ARG   0.003   0.000   ARG A 201 

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

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

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  30 residues out of total 499 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 21
  time to evaluate  : 0.582 
Fit side-chains
   revert: symmetry clash
REVERT: A   72 MET cc_start: 0.8534 (mpp) cc_final: 0.8176 (mmm)
REVERT: A  229 ASP cc_start: 0.8696 (OUTLIER) cc_final: 0.8260 (t70)
REVERT: A  258 TRP cc_start: 0.8624 (t60) cc_final: 0.8143 (t60)
REVERT: A  293 MET cc_start: 0.7752 (ttt) cc_final: 0.7548 (ttm)
  outliers start: 9
  outliers final: 4
  residues processed: 28
  average time/residue: 0.1790
  time to fit residues: 7.2196
Evaluate side-chains
  26 residues out of total 499 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 21
  time to evaluate  : 0.584 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  228 MET
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain B residue  133 ARG
Chi-restraints excluded: chain B residue  167 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 50 optimal weight:    6.9990
   chunk 34 optimal weight:    3.9990
   chunk 0 optimal weight:    6.9990
   chunk 45 optimal weight:    1.9990
   chunk 25 optimal weight:    6.9990
   chunk 51 optimal weight:    0.9980
   chunk 42 optimal weight:    4.9990
   chunk 31 optimal weight:    1.9990
   chunk 54 optimal weight:    0.9980
   chunk 15 optimal weight:    8.9990
   chunk 20 optimal weight:    0.0980
   overall best weight:    1.2184

-------------------------------------------------------------------------------
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: 0.8526
moved from start:          0.1964

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6546  Z= 0.201
  Angle     :  0.489   5.882   9213  Z= 0.253
  Chirality :  0.036   0.188   1063
  Planarity :  0.004   0.033    907
  Dihedral  : 20.925 159.945   1792
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 3.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.89 %
    Favored  : 95.11 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 23.85 %
    Favored  : 74.35 %
  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:  0.25 (0.36), residues: 552
  helix:  2.41 (0.38), residues: 167
  sheet:  0.10 (0.56), residues: 91
  loop : -1.21 (0.36), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 352 
 HIS   0.004   0.001   HIS A 360 
 PHE   0.018   0.001   PHE B 320 
 TYR   0.007   0.001   TYR A 195 
 ARG   0.002   0.000   ARG A 201 

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

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

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  30 residues out of total 499 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 21
  time to evaluate  : 0.630 
Fit side-chains
REVERT: A   72 MET cc_start: 0.8558 (mpp) cc_final: 0.8190 (mmm)
REVERT: A  229 ASP cc_start: 0.8714 (OUTLIER) cc_final: 0.8274 (t70)
REVERT: A  258 TRP cc_start: 0.8568 (t60) cc_final: 0.8080 (t60)
REVERT: A  293 MET cc_start: 0.7799 (ttt) cc_final: 0.7402 (ttm)
  outliers start: 9
  outliers final: 3
  residues processed: 29
  average time/residue: 0.1701
  time to fit residues: 7.3900
Evaluate side-chains
  25 residues out of total 499 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 21
  time to evaluate  : 0.665 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 THR
Chi-restraints excluded: chain A residue  228 MET
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain B residue  167 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 54 optimal weight:    1.9990
   chunk 12 optimal weight:    0.1980
   chunk 35 optimal weight:    3.9990
   chunk 15 optimal weight:    9.9990
   chunk 60 optimal weight:    7.9990
   chunk 50 optimal weight:    4.9990
   chunk 28 optimal weight:    0.0010
   chunk 5 optimal weight:    1.9990
   chunk 20 optimal weight:    0.1980
   chunk 32 optimal weight:    1.9990
   chunk 58 optimal weight:    4.9990
   overall best weight:    0.8790

-------------------------------------------------------------------------------
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: 0.8500
moved from start:          0.2108

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   6546  Z= 0.162
  Angle     :  0.461   5.920   9213  Z= 0.239
  Chirality :  0.035   0.177   1063
  Planarity :  0.004   0.035    907
  Dihedral  : 20.933 162.491   1792
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 3.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.89 %
    Favored  : 95.11 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 22.65 %
    Favored  : 75.55 %
  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:  0.36 (0.36), residues: 552
  helix:  2.52 (0.38), residues: 167
  sheet:  0.24 (0.57), residues: 89
  loop : -1.17 (0.36), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  74 
 HIS   0.004   0.001   HIS A 360 
 PHE   0.016   0.001   PHE B 320 
 TYR   0.006   0.001   TYR A 195 
 ARG   0.002   0.000   ARG A 201 

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

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

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  31 residues out of total 499 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 22
  time to evaluate  : 0.704 
Fit side-chains
REVERT: A   72 MET cc_start: 0.8596 (mpp) cc_final: 0.8208 (mmm)
REVERT: A  229 ASP cc_start: 0.8688 (OUTLIER) cc_final: 0.8070 (t0)
REVERT: A  258 TRP cc_start: 0.8579 (t60) cc_final: 0.8185 (t60)
REVERT: A  293 MET cc_start: 0.7748 (ttt) cc_final: 0.7400 (ttm)
  outliers start: 9
  outliers final: 5
  residues processed: 29
  average time/residue: 0.1296
  time to fit residues: 6.2140
Evaluate side-chains
  27 residues out of total 499 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 21
  time to evaluate  : 0.550 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 THR
Chi-restraints excluded: chain A residue  228 MET
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  287 PHE
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain B residue  167 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 6 optimal weight:    1.9990
   chunk 34 optimal weight:    3.9990
   chunk 44 optimal weight:    2.9990
   chunk 51 optimal weight:    0.5980
   chunk 60 optimal weight:    7.9990
   chunk 38 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 28 optimal weight:    6.9990
   chunk 24 optimal weight:    2.9990
   chunk 36 optimal weight:    1.9990
   chunk 18 optimal weight:    2.9990
   overall best weight:    1.7188

-------------------------------------------------------------------------------
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: 0.8547
moved from start:          0.2243

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   6546  Z= 0.269
  Angle     :  0.515   5.891   9213  Z= 0.265
  Chirality :  0.037   0.186   1063
  Planarity :  0.004   0.034    907
  Dihedral  : 21.042 165.923   1792
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 4.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.43 %
    Favored  : 94.57 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 23.85 %
    Favored  : 74.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.16 (0.36), residues: 552
  helix:  2.32 (0.38), residues: 167
  sheet:  0.02 (0.56), residues: 89
  loop : -1.23 (0.35), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 352 
 HIS   0.005   0.001   HIS B 360 
 PHE   0.017   0.002   PHE B 124 
 TYR   0.013   0.001   TYR A 216 
 ARG   0.002   0.000   ARG A 201 

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

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

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  29 residues out of total 499 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 22
  time to evaluate  : 0.641 
Fit side-chains
REVERT: A   72 MET cc_start: 0.8622 (mpp) cc_final: 0.8239 (mmm)
REVERT: A  229 ASP cc_start: 0.8680 (OUTLIER) cc_final: 0.8243 (t70)
REVERT: A  258 TRP cc_start: 0.8562 (t60) cc_final: 0.8102 (t60)
REVERT: A  282 MET cc_start: 0.7940 (mtm) cc_final: 0.7573 (mtt)
REVERT: A  293 MET cc_start: 0.7807 (ttt) cc_final: 0.7361 (ttm)
  outliers start: 7
  outliers final: 5
  residues processed: 28
  average time/residue: 0.1320
  time to fit residues: 6.1189
Evaluate side-chains
  28 residues out of total 499 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 22
  time to evaluate  : 0.561 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 THR
Chi-restraints excluded: chain A residue  221 ASP
Chi-restraints excluded: chain A residue  228 MET
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain B residue  167 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 11 optimal weight:    0.7980
   chunk 38 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9980
   chunk 5 optimal weight:    5.9990
   chunk 47 optimal weight:    0.5980
   chunk 55 optimal weight:    0.6980
   chunk 58 optimal weight:    7.9990
   chunk 53 optimal weight:    0.9980
   chunk 56 optimal weight:    8.9990
   chunk 34 optimal weight:    2.9990
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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: 0.8497
moved from start:          0.2305

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   6546  Z= 0.154
  Angle     :  0.453   5.876   9213  Z= 0.234
  Chirality :  0.035   0.173   1063
  Planarity :  0.003   0.034    907
  Dihedral  : 21.004 165.868   1792
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 3.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.53 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 23.85 %
    Favored  : 74.95 %
  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:  0.35 (0.36), residues: 552
  helix:  2.55 (0.38), residues: 167
  sheet:  0.20 (0.57), residues: 89
  loop : -1.19 (0.35), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 352 
 HIS   0.003   0.001   HIS A 360 
 PHE   0.022   0.001   PHE B 320 
 TYR   0.008   0.001   TYR A 216 
 ARG   0.001   0.000   ARG B 280 

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

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

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  28 residues out of total 499 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 22
  time to evaluate  : 0.623 
Fit side-chains
REVERT: A   72 MET cc_start: 0.8604 (mpp) cc_final: 0.8211 (mmm)
REVERT: A  229 ASP cc_start: 0.8677 (OUTLIER) cc_final: 0.8060 (t0)
REVERT: A  258 TRP cc_start: 0.8522 (t60) cc_final: 0.8126 (t60)
REVERT: A  293 MET cc_start: 0.7790 (ttt) cc_final: 0.7392 (ttm)
  outliers start: 6
  outliers final: 5
  residues processed: 27
  average time/residue: 0.1341
  time to fit residues: 5.9156
Evaluate side-chains
  28 residues out of total 499 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 22
  time to evaluate  : 0.617 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 THR
Chi-restraints excluded: chain A residue  221 ASP
Chi-restraints excluded: chain A residue  228 MET
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain B residue  167 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 44 optimal weight:    5.9990
   chunk 17 optimal weight:    0.9990
   chunk 51 optimal weight:    0.8980
   chunk 53 optimal weight:    5.9990
   chunk 56 optimal weight:    8.9990
   chunk 37 optimal weight:    1.9990
   chunk 59 optimal weight:   10.0000
   chunk 36 optimal weight:    0.9990
   chunk 28 optimal weight:    5.9990
   chunk 41 optimal weight:    1.9990
   overall best weight:    1.3788

-------------------------------------------------------------------------------
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: 0.8528
moved from start:          0.2357

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6546  Z= 0.220
  Angle     :  0.484   6.188   9213  Z= 0.248
  Chirality :  0.036   0.178   1063
  Planarity :  0.004   0.034    907
  Dihedral  : 21.057 167.197   1792
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 3.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.62 %
    Favored  : 94.38 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 23.65 %
    Favored  : 75.15 %
  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:  0.24 (0.36), residues: 552
  helix:  2.43 (0.38), residues: 167
  sheet:  0.09 (0.57), residues: 89
  loop : -1.22 (0.35), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 352 
 HIS   0.004   0.001   HIS B 360 
 PHE   0.023   0.001   PHE B 320 
 TYR   0.009   0.001   TYR A 216 
 ARG   0.001   0.000   ARG A 201 

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

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

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  29 residues out of total 499 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 23
  time to evaluate  : 0.609 
Fit side-chains
REVERT: A   72 MET cc_start: 0.8612 (mpp) cc_final: 0.8222 (mmm)
REVERT: A  229 ASP cc_start: 0.8659 (OUTLIER) cc_final: 0.8228 (t70)
REVERT: A  258 TRP cc_start: 0.8552 (t60) cc_final: 0.8116 (t60)
REVERT: A  293 MET cc_start: 0.7774 (ttt) cc_final: 0.7354 (ttm)
  outliers start: 6
  outliers final: 4
  residues processed: 28
  average time/residue: 0.1282
  time to fit residues: 5.8943
Evaluate side-chains
  27 residues out of total 499 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 22
  time to evaluate  : 0.581 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 THR
Chi-restraints excluded: chain A residue  228 MET
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain B residue  167 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 62 optimal weight:    8.9990
   chunk 57 optimal weight:    6.9990
   chunk 49 optimal weight:    0.8980
   chunk 5 optimal weight:    5.9990
   chunk 38 optimal weight:    0.9980
   chunk 30 optimal weight:    2.9990
   chunk 39 optimal weight:    5.9990
   chunk 53 optimal weight:    0.8980
   chunk 15 optimal weight:    9.9990
   chunk 46 optimal weight:    1.9990
   chunk 7 optimal weight:    4.9990
   overall best weight:    1.5584

-------------------------------------------------------------------------------
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: 0.8540
moved from start:          0.2436

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   6546  Z= 0.242
  Angle     :  0.497   5.978   9213  Z= 0.256
  Chirality :  0.036   0.183   1063
  Planarity :  0.004   0.033    907
  Dihedral  : 21.127 168.745   1792
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 3.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.07 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 23.45 %
    Favored  : 75.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.16 (0.36), residues: 552
  helix:  2.35 (0.38), residues: 167
  sheet: -0.06 (0.57), residues: 90
  loop : -1.24 (0.35), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 352 
 HIS   0.005   0.001   HIS B 360 
 PHE   0.022   0.001   PHE B 320 
 TYR   0.008   0.001   TYR A 195 
 ARG   0.002   0.000   ARG A 201 

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

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

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  27 residues out of total 499 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 22
  time to evaluate  : 0.614 
Fit side-chains
REVERT: A   72 MET cc_start: 0.8610 (mpp) cc_final: 0.8235 (mmm)
REVERT: A  229 ASP cc_start: 0.8655 (OUTLIER) cc_final: 0.8213 (t70)
REVERT: A  258 TRP cc_start: 0.8563 (t60) cc_final: 0.8124 (t60)
REVERT: A  293 MET cc_start: 0.7791 (ttt) cc_final: 0.7346 (ttm)
  outliers start: 5
  outliers final: 4
  residues processed: 26
  average time/residue: 0.1322
  time to fit residues: 5.6751
Evaluate side-chains
  27 residues out of total 499 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 22
  time to evaluate  : 0.588 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 THR
Chi-restraints excluded: chain A residue  228 MET
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain B residue  167 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 13 optimal weight:    3.9990
   chunk 50 optimal weight:    0.2980
   chunk 20 optimal weight:    0.8980
   chunk 51 optimal weight:    0.9990
   chunk 6 optimal weight:    0.7980
   chunk 9 optimal weight:    3.9990
   chunk 43 optimal weight:    2.9990
   chunk 2 optimal weight:    1.9990
   chunk 36 optimal weight:    0.9990
   chunk 57 optimal weight:    6.9990
   chunk 33 optimal weight:    0.8980
   overall best weight:    0.7782

-------------------------------------------------------------------------------
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 = 0.3494 r_free = 0.3494 target = 0.071001 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.050945 restraints weight = 20812.280|
|-----------------------------------------------------------------------------|
r_work (start): 0.3010 rms_B_bonded: 3.22
r_work: 0.2849 rms_B_bonded: 4.45 restraints_weight: 0.5000
r_work (final): 0.2849
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8387
moved from start:          0.2480

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   6546  Z= 0.151
  Angle     :  0.460   7.043   9213  Z= 0.235
  Chirality :  0.035   0.171   1063
  Planarity :  0.003   0.034    907
  Dihedral  : 21.058 168.139   1792
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 3.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 23.05 %
    Favored  : 75.55 %
  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:  0.28 (0.36), residues: 552
  helix:  2.49 (0.38), residues: 167
  sheet:  0.14 (0.57), residues: 89
  loop : -1.23 (0.35), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 352 
 HIS   0.003   0.001   HIS A 360 
 PHE   0.023   0.001   PHE B 320 
 TYR   0.005   0.001   TYR A 197 
 ARG   0.002   0.000   ARG B 280 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1388.54 seconds
wall clock time: 28 minutes 48.66 seconds (1728.66 seconds total)