Starting phenix.real_space_refine
on Sun May  3 00:07:14 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9nzq_49956/05_2026/9nzq_49956.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9nzq_49956/05_2026/9nzq_49956.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.67
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9nzq_49956/05_2026/9nzq_49956.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9nzq_49956/05_2026/9nzq_49956.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9nzq_49956/05_2026/9nzq_49956.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9nzq_49956/05_2026/9nzq_49956.map"
  }
  resolution = 3.67
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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=   0.013
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: 6
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     P     152      5.49       5
     S      40      5.16       5
     C    5258      2.51       5
     N    1677      2.21       5
     O    2130      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9258
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 3386
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 423, 3386
          Classifications: {'peptide': 423}
          Link IDs: {'PTRANS': 11, 'TRANS': 411}
    Chain: "B"
      Number of atoms: 2629
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 327, 2629
          Classifications: {'peptide': 327}
          Link IDs: {'PTRANS': 9, 'TRANS': 317}
          Chain breaks: 5
    Chain: "C"
      Number of atoms: 331
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 16, 331
          Classifications: {'DNA': 16}
          Link IDs: {'rna3p': 15}
    Chain: "D"
      Number of atoms: 163
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 8, 163
          Classifications: {'DNA': 8}
          Link IDs: {'rna3p': 7}
    Chain: "E"
      Number of atoms: 2748
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 2748
          Classifications: {'RNA': 128}
          Modifications used: {'rna2p_pur': 14, 'rna2p_pyr': 10, 'rna3p_pur': 60, 'rna3p_pyr': 44}
          Link IDs: {'rna2p': 24, 'rna3p': 103}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   3013  SG  CYS A 377      18.032  83.772  72.324  1.00 55.33           S
  ATOM   3036  SG  CYS A 380      14.978  86.360  70.972  1.00 65.53           S
  ATOM   3157  SG  CYS A 396      18.685  87.212  70.940  1.00 62.24           S
  ATOM   3179  SG  CYS A 399      16.933  86.920  74.005  1.00 58.21           S

  Time building chain proxies: 2.35, per 1000 atoms: 0.25
  Number of scatterers: 9258
  At special positions: 0
  Unit cell: (94, 111.86, 121.26, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      1     29.99
     S      40     16.00
     P     152     15.00
     O    2130      8.00
     N    1677      7.00
     C    5258      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: 0.89
  Conformation dependent library (CDL) restraints added in 173.0 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 501 "
        pdb="ZN    ZN A 501 " - pdb=" SG  CYS A 399 "
        pdb="ZN    ZN A 501 " - pdb=" SG  CYS A 396 "
        pdb="ZN    ZN A 501 " - pdb=" SG  CYS A 380 "
        pdb="ZN    ZN A 501 " - pdb=" SG  CYS A 377 "
      Number of angles added : 6


  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1406

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 7 sheets defined
      50.9% alpha, 7.2% beta
      43 base pairs and 83 stacking pairs defined.
    Time for finding SS restraints: 1.03
  Creating SS restraints...
    Processing helix  chain 'A' and resid 25 through 62
    Processing helix  chain 'A' and resid 67 through 72
      removed outlier: 3.801A  pdb=" N   GLU A  71 " --> pdb=" O   ASP A  67 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 76 through 89
      removed outlier: 3.747A  pdb=" N   HIS A  80 " --> pdb=" O   ARG A  76 " (cutoff:3.500A)
      removed outlier: 4.244A  pdb=" N   GLY A  87 " --> pdb=" O   ASN A  83 " (cutoff:3.500A)
      removed outlier: 4.235A  pdb=" N   GLN A  88 " --> pdb=" O   CYS A  84 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 93 through 111
      removed outlier: 3.598A  pdb=" N   LYS A 107 " --> pdb=" O   LYS A 103 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 111 through 117
    Processing helix  chain 'A' and resid 134 through 136
      No H-bonds generated for 'chain 'A' and resid 134 through 136'
    Processing helix  chain 'A' and resid 156 through 162
    Processing helix  chain 'A' and resid 178 through 188
      removed outlier: 4.155A  pdb=" N   PHE A 182 " --> pdb=" O   GLN A 178 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 250 through 271
      removed outlier: 3.631A  pdb=" N   ALA A 257 " --> pdb=" O   ILE A 253 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   ALA A 271 " --> pdb=" O   MET A 267 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 287 through 319
    Processing helix  chain 'A' and resid 347 through 362
    Processing helix  chain 'A' and resid 384 through 388
      removed outlier: 3.596A  pdb=" N   ARG A 388 " --> pdb=" O   LYS A 385 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 404 through 415
    Processing helix  chain 'A' and resid 417 through 427
      removed outlier: 3.840A  pdb=" N   ILE A 421 " --> pdb=" O   ASN A 417 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 22 through 54
    Processing helix  chain 'B' and resid 77 through 89
    Processing helix  chain 'B' and resid 93 through 111
    Processing helix  chain 'B' and resid 111 through 117
    Processing helix  chain 'B' and resid 156 through 162
    Processing helix  chain 'B' and resid 178 through 188
      removed outlier: 3.883A  pdb=" N   PHE B 182 " --> pdb=" O   GLN B 178 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 250 through 274
    Processing helix  chain 'B' and resid 294 through 319
    Processing helix  chain 'B' and resid 346 through 361
      removed outlier: 3.822A  pdb=" N   LEU B 350 " --> pdb=" O   THR B 346 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 406 through 415
      removed outlier: 3.677A  pdb=" N   ILE B 415 " --> pdb=" O   GLN B 411 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 417 through 427
    Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 13
      removed outlier: 3.504A  pdb=" N   PHE A 205 " --> pdb=" O   TYR A 199 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   LEU A 197 " --> pdb=" O   PHE A 207 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   VAL A 198 " --> pdb=" O   LEU A 131 " (cutoff:3.500A)
      removed outlier: 3.970A  pdb=" N   LEU A 131 " --> pdb=" O   VAL A 198 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 138 through 141
      removed outlier: 3.691A  pdb=" N   ILE A 148 " --> pdb=" O   LEU A 173 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 235 through 237
      removed outlier: 3.598A  pdb=" N   LEU A 235 " --> pdb=" O   ILE A 248 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 133 through 134
    Processing sheet with id=AA5, first strand: chain 'B' and resid 138 through 140
    Processing sheet with id=AA6, first strand: chain 'B' and resid 226 through 230
      removed outlier: 5.115A  pdb=" N   GLY B 230 " --> pdb=" O   ALA B 234 " (cutoff:3.500A)
      removed outlier: 4.863A  pdb=" N   ALA B 234 " --> pdb=" O   GLY B 230 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 324 through 327
      removed outlier: 3.670A  pdb=" N   VAL B 366 " --> pdb=" O   ILE B 324 " (cutoff:3.500A)

    305 hydrogen bonds defined for protein.
    897 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      110 hydrogen bonds
      212 hydrogen bond angles
      0 basepair planarities
      43 basepair parallelities
      83 stacking parallelities
  Total time for adding SS restraints: 1.41

  Time building geometry restraints manager: 1.16 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1366
        1.32 -     1.45: 3457
        1.45 -     1.57: 4577
        1.57 -     1.70: 301
        1.70 -     1.82: 61
  Bond restraints: 9762
  Sorted by residual:
  bond pdb=" SD  MET B  26 "
       pdb=" CE  MET B  26 "
    ideal  model  delta    sigma   weight residual
    1.791  1.722  0.069 2.50e-02 1.60e+03 7.62e+00
  bond pdb=" C   ARG B 201 "
       pdb=" N   PRO B 202 "
    ideal  model  delta    sigma   weight residual
    1.333  1.368 -0.035 1.44e-02 4.82e+03 6.01e+00
  bond pdb=" C   PRO B 213 "
       pdb=" N   PRO B 214 "
    ideal  model  delta    sigma   weight residual
    1.331  1.360 -0.029 1.27e-02 6.20e+03 5.16e+00
  bond pdb=" CB  LYS A 200 "
       pdb=" CG  LYS A 200 "
    ideal  model  delta    sigma   weight residual
    1.520  1.583 -0.063 3.00e-02 1.11e+03 4.37e+00
  bond pdb=" C   PRO A 213 "
       pdb=" N   PRO A 214 "
    ideal  model  delta    sigma   weight residual
    1.334  1.382 -0.048 2.34e-02 1.83e+03 4.26e+00
  ... (remaining 9757 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.56: 13248
        2.56 -     5.11: 496
        5.11 -     7.67: 105
        7.67 -    10.22: 24
       10.22 -    12.78: 12
  Bond angle restraints: 13885
  Sorted by residual:
  angle pdb=" N   MET B  26 "
        pdb=" CA  MET B  26 "
        pdb=" CB  MET B  26 "
      ideal   model   delta    sigma   weight residual
     110.01  120.25  -10.24 1.45e+00 4.76e-01 4.99e+01
  angle pdb=" CA  MET B 120 "
        pdb=" CB  MET B 120 "
        pdb=" CG  MET B 120 "
      ideal   model   delta    sigma   weight residual
     114.10  126.88  -12.78 2.00e+00 2.50e-01 4.08e+01
  angle pdb=" CA  LYS B 424 "
        pdb=" CB  LYS B 424 "
        pdb=" CG  LYS B 424 "
      ideal   model   delta    sigma   weight residual
     114.10  125.98  -11.88 2.00e+00 2.50e-01 3.53e+01
  angle pdb=" C3'   U E 140 "
        pdb=" O3'   U E 140 "
        pdb=" P     G E 141 "
      ideal   model   delta    sigma   weight residual
     120.20  127.87   -7.67 1.50e+00 4.44e-01 2.61e+01
  angle pdb=" CA  GLN B 162 "
        pdb=" CB  GLN B 162 "
        pdb=" CG  GLN B 162 "
      ideal   model   delta    sigma   weight residual
     114.10  124.18  -10.08 2.00e+00 2.50e-01 2.54e+01
  ... (remaining 13880 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    32.77: 5269
       32.77 -    65.54: 643
       65.54 -    98.32: 54
       98.32 -   131.09: 5
      131.09 -   163.86: 8
  Dihedral angle restraints: 5979
    sinusoidal: 3796
      harmonic: 2183
  Sorted by residual:
  dihedral pdb=" C5'   U E 140 "
           pdb=" C4'   U E 140 "
           pdb=" C3'   U E 140 "
           pdb=" O3'   U E 140 "
      ideal   model   delta sinusoidal    sigma   weight residual
     147.00   80.88   66.12     1      8.00e+00 1.56e-02 8.93e+01
  dihedral pdb=" C4'   U E 140 "
           pdb=" C3'   U E 140 "
           pdb=" C2'   U E 140 "
           pdb=" C1'   U E 140 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -35.00   28.90  -63.90     1      8.00e+00 1.56e-02 8.40e+01
  dihedral pdb=" O4'   C E  19 "
           pdb=" C1'   C E  19 "
           pdb=" N1    C E  19 "
           pdb=" C2    C E  19 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   45.28  154.72     1      1.50e+01 4.44e-03 8.12e+01
  ... (remaining 5976 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.073: 1359
       0.073 -    0.147: 219
       0.147 -    0.220: 30
       0.220 -    0.293: 8
       0.293 -    0.366: 3
  Chirality restraints: 1619
  Sorted by residual:
  chirality pdb=" CA  MET B  26 "
            pdb=" N   MET B  26 "
            pdb=" C   MET B  26 "
            pdb=" CB  MET B  26 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.14    0.37 2.00e-01 2.50e+01 3.35e+00
  chirality pdb=" CB  ILE B 324 "
            pdb=" CA  ILE B 324 "
            pdb=" CG1 ILE B 324 "
            pdb=" CG2 ILE B 324 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.30    0.35 2.00e-01 2.50e+01 2.99e+00
  chirality pdb=" C3'   U E 140 "
            pdb=" C4'   U E 140 "
            pdb=" O3'   U E 140 "
            pdb=" C2'   U E 140 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.74   -2.42   -0.32 2.00e-01 2.50e+01 2.62e+00
  ... (remaining 1616 not shown)

  Planarity restraints: 1207
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G E 127 "    0.031 2.00e-02 2.50e+03   2.76e-02 2.29e+01
        pdb=" N9    G E 127 "   -0.031 2.00e-02 2.50e+03
        pdb=" C8    G E 127 "   -0.000 2.00e-02 2.50e+03
        pdb=" N7    G E 127 "    0.004 2.00e-02 2.50e+03
        pdb=" C5    G E 127 "    0.001 2.00e-02 2.50e+03
        pdb=" C6    G E 127 "   -0.018 2.00e-02 2.50e+03
        pdb=" O6    G E 127 "    0.021 2.00e-02 2.50e+03
        pdb=" N1    G E 127 "    0.016 2.00e-02 2.50e+03
        pdb=" C2    G E 127 "   -0.069 2.00e-02 2.50e+03
        pdb=" N2    G E 127 "    0.037 2.00e-02 2.50e+03
        pdb=" N3    G E 127 "   -0.001 2.00e-02 2.50e+03
        pdb=" C4    G E 127 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 407 "    0.025 2.00e-02 2.50e+03   2.77e-02 1.34e+01
        pdb=" CG  PHE A 407 "   -0.064 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 407 "    0.012 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 407 "    0.019 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 407 "    0.008 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 407 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 407 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 240 "    0.018 2.00e-02 2.50e+03   2.66e-02 1.23e+01
        pdb=" CG  PHE B 240 "   -0.060 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 240 "    0.023 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 240 "    0.020 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 240 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 240 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 240 "   -0.000 2.00e-02 2.50e+03
  ... (remaining 1204 not shown)

  Histogram of nonbonded interaction distances:
        2.43 -     2.93: 3559
        2.93 -     3.42: 9246
        3.42 -     3.91: 17099
        3.91 -     4.41: 18315
        4.41 -     4.90: 26932
  Nonbonded interactions: 75151
  Sorted by model distance:
  nonbonded pdb=" N1    A E  34 "
            pdb=" O6    G E  64 "
     model   vdw
     2.434 2.496
  nonbonded pdb=" O4'   C E  70 "
            pdb=" C6    C E  70 "
     model   vdw
     2.481 2.672
  nonbonded pdb=" O5'   G E 116 "
            pdb=" O4'   G E 116 "
     model   vdw
     2.519 2.432
  nonbonded pdb=" O4'   C E  66 "
            pdb=" C6    C E  66 "
     model   vdw
     2.526 2.672
  nonbonded pdb=" N   ARG B 201 "
            pdb=" O   ARG B 201 "
     model   vdw
     2.527 2.496
  ... (remaining 75146 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=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:             2.060
  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:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     11.460
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  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:1.040
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.790
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6970
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   0.098   9766  Z= 0.291
  Angle     :  1.230  18.404  13891  Z= 0.641
  Chirality :  0.057   0.366   1619
  Planarity :  0.010   0.100   1207
  Dihedral  : 24.090 163.859   4573
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 5.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  : 28.68 %
    Favored  : 70.23 %
  Cbeta Deviations :  0.14 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.43 (0.30), residues: 736
  helix:  0.49 (0.27), residues: 347
  sheet: -2.25 (0.48), residues: 117
  loop : -2.20 (0.34), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.023   0.004   ARG B  76 
 TYR   0.034   0.003   TYR A 125 
 PHE   0.064   0.005   PHE A 407 
 TRP   0.033   0.003   TRP A  51 
 HIS   0.021   0.002   HIS B  80 

Details of bonding type rmsd
  covalent geometry    : bond        0.00617 ( 9762)
  covalent geometry    : angle       1.21631 (13885)
  hydrogen bonds       : bond        0.14312 (  415)
  hydrogen bonds       : angle       5.62870 ( 1109)
  metal coordination   : bond        0.01799 (    4)
  metal coordination   : angle       9.04006 (    6)

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

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

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 75
  time to evaluate  : 0.224 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  128 ASN cc_start: 0.7493 (t0) cc_final: 0.6939 (t0)
  outliers start: 7
  outliers final: 3
  residues processed: 81
  average time/residue: 0.1208
  time to fit residues: 12.7643
Evaluate side-chains
  59 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 56
  time to evaluate  : 0.208 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 ILE
Chi-restraints excluded: chain A residue  338 PHE
Chi-restraints excluded: chain A residue  372 HIS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    7.9990
   chunk 33 optimal weight:    6.9990
   chunk 65 optimal weight:   20.0000
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    5.9990
   chunk 61 optimal weight:    4.9990
   chunk 45 optimal weight:    1.9990
   chunk 74 optimal weight:    4.9990
   overall best weight:    3.3990

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

Flipped N/Q/H residues before XYZ refinement:
A  46 GLN
** A  59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 319 ASN
A 320 GLN
A 372 HIS
A 382 HIS
A 391 GLN
A 411 GLN
A 412 ASN
B  25 ASN
B  80 HIS
B 109 ASN
B 184 ASN
B 217 HIS
B 273 HIS
B 319 ASN
** B 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 15

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.070050 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.052296 restraints weight = 52239.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.053968 restraints weight = 25461.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.055007 restraints weight = 17036.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.055607 restraints weight = 13673.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 19)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.055845 restraints weight = 12163.329|
|-----------------------------------------------------------------------------|
r_work (final): 0.3235
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8153
moved from start:          0.2240

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.098   9766  Z= 0.293
  Angle     :  0.801  17.056  13891  Z= 0.409
  Chirality :  0.040   0.298   1619
  Planarity :  0.005   0.050   1207
  Dihedral  : 24.762 166.424   3083
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 17.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  5.43 %
    Allowed  : 24.34 %
    Favored  : 70.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.45 (0.31), residues: 736
  helix:  1.37 (0.26), residues: 355
  sheet: -1.66 (0.47), residues: 128
  loop : -1.95 (0.37), residues: 253

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 301 
 TYR   0.017   0.002   TYR A 125 
 PHE   0.017   0.003   PHE B 300 
 TRP   0.025   0.003   TRP A  51 
 HIS   0.008   0.001   HIS B  80 

Details of bonding type rmsd
  covalent geometry    : bond        0.00616 ( 9762)
  covalent geometry    : angle       0.77968 (13885)
  hydrogen bonds       : bond        0.06117 (  415)
  hydrogen bonds       : angle       4.44734 ( 1109)
  metal coordination   : bond        0.02249 (    4)
  metal coordination   : angle       8.87201 (    6)

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

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

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 57
  time to evaluate  : 0.293 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8599 (mp)
REVERT: A  267 MET cc_start: 0.9035 (tpp) cc_final: 0.8799 (mmm)
REVERT: A  302 ASP cc_start: 0.9011 (t0) cc_final: 0.8761 (t0)
REVERT: A  371 ARG cc_start: 0.8308 (tpt90) cc_final: 0.8071 (tpt90)
REVERT: A  389 THR cc_start: 0.8685 (OUTLIER) cc_final: 0.8427 (p)
REVERT: B   16 TYR cc_start: 0.7880 (OUTLIER) cc_final: 0.7083 (p90)
REVERT: B   26 MET cc_start: 0.8779 (mpp) cc_final: 0.8484 (mpp)
REVERT: B  245 TYR cc_start: 0.8699 (p90) cc_final: 0.8487 (p90)
REVERT: B  301 ARG cc_start: 0.9365 (OUTLIER) cc_final: 0.9068 (mtt180)
REVERT: B  306 HIS cc_start: 0.9567 (OUTLIER) cc_final: 0.9298 (t-90)
REVERT: B  372 HIS cc_start: 0.7230 (t70) cc_final: 0.6995 (t70)
  outliers start: 35
  outliers final: 13
  residues processed: 89
  average time/residue: 0.0901
  time to fit residues: 11.2262
Evaluate side-chains
  72 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 54
  time to evaluate  : 0.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 LEU
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue  124 SER
Chi-restraints excluded: chain A residue  174 HIS
Chi-restraints excluded: chain A residue  297 VAL
Chi-restraints excluded: chain A residue  323 THR
Chi-restraints excluded: chain A residue  330 THR
Chi-restraints excluded: chain A residue  338 PHE
Chi-restraints excluded: chain A residue  389 THR
Chi-restraints excluded: chain A residue  410 SER
Chi-restraints excluded: chain B residue   16 TYR
Chi-restraints excluded: chain B residue   40 ILE
Chi-restraints excluded: chain B residue  171 MET
Chi-restraints excluded: chain B residue  195 CYS
Chi-restraints excluded: chain B residue  198 VAL
Chi-restraints excluded: chain B residue  301 ARG
Chi-restraints excluded: chain B residue  306 HIS
Chi-restraints excluded: chain B residue  407 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 11 optimal weight:    4.9990
   chunk 12 optimal weight:    2.9990
   chunk 73 optimal weight:    9.9990
   chunk 24 optimal weight:    2.9990
   chunk 4 optimal weight:    0.6980
   chunk 38 optimal weight:    0.5980
   chunk 55 optimal weight:    9.9990
   chunk 32 optimal weight:    0.9990
   chunk 10 optimal weight:    3.9990
   chunk 65 optimal weight:    5.9990
   chunk 77 optimal weight:    6.9990
   overall best weight:    1.6586

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

Flipped N/Q/H residues before XYZ refinement:
** A  59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  80 HIS
B 372 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.070898 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.053562 restraints weight = 52193.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.055314 restraints weight = 24938.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.056394 restraints weight = 16517.798|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.056888 restraints weight = 13188.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.057316 restraints weight = 11845.087|
|-----------------------------------------------------------------------------|
r_work (final): 0.3277
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8107
moved from start:          0.2497

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   9766  Z= 0.171
  Angle     :  0.683  14.528  13891  Z= 0.344
  Chirality :  0.036   0.268   1619
  Planarity :  0.004   0.047   1207
  Dihedral  : 24.558 173.081   3079
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 13.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  4.96 %
    Allowed  : 26.36 %
    Favored  : 68.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.08 (0.31), residues: 736
  helix:  1.88 (0.26), residues: 355
  sheet: -1.58 (0.47), residues: 125
  loop : -1.72 (0.38), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  38 
 TYR   0.017   0.001   TYR B 199 
 PHE   0.024   0.002   PHE A 182 
 TRP   0.016   0.001   TRP A  51 
 HIS   0.005   0.001   HIS A 273 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 ( 9762)
  covalent geometry    : angle       0.66456 (13885)
  hydrogen bonds       : bond        0.05222 (  415)
  hydrogen bonds       : angle       3.91041 ( 1109)
  metal coordination   : bond        0.01235 (    4)
  metal coordination   : angle       7.56987 (    6)

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

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

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 56
  time to evaluate  : 0.256 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  267 MET cc_start: 0.8942 (tpp) cc_final: 0.8593 (mmm)
REVERT: A  314 ASP cc_start: 0.8350 (m-30) cc_final: 0.8138 (m-30)
REVERT: A  371 ARG cc_start: 0.8323 (tpt90) cc_final: 0.7885 (tpt90)
REVERT: B   16 TYR cc_start: 0.7840 (OUTLIER) cc_final: 0.6982 (p90)
REVERT: B   26 MET cc_start: 0.8776 (mpp) cc_final: 0.8122 (mpp)
REVERT: B  196 GLN cc_start: 0.8717 (mm-40) cc_final: 0.8404 (mp10)
REVERT: B  201 ARG cc_start: 0.7890 (OUTLIER) cc_final: 0.6930 (tpp-160)
REVERT: B  245 TYR cc_start: 0.8774 (p90) cc_final: 0.8449 (p90)
REVERT: B  306 HIS cc_start: 0.9555 (OUTLIER) cc_final: 0.9307 (t-90)
REVERT: B  372 HIS cc_start: 0.7158 (t-90) cc_final: 0.6906 (t70)
  outliers start: 32
  outliers final: 17
  residues processed: 83
  average time/residue: 0.0929
  time to fit residues: 10.7870
Evaluate side-chains
  75 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 55
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 MET
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue   62 THR
Chi-restraints excluded: chain A residue  124 SER
Chi-restraints excluded: chain A residue  135 LYS
Chi-restraints excluded: chain A residue  273 HIS
Chi-restraints excluded: chain A residue  313 ILE
Chi-restraints excluded: chain A residue  323 THR
Chi-restraints excluded: chain A residue  330 THR
Chi-restraints excluded: chain A residue  338 PHE
Chi-restraints excluded: chain A residue  372 HIS
Chi-restraints excluded: chain A residue  411 GLN
Chi-restraints excluded: chain B residue   16 TYR
Chi-restraints excluded: chain B residue   40 ILE
Chi-restraints excluded: chain B residue  171 MET
Chi-restraints excluded: chain B residue  195 CYS
Chi-restraints excluded: chain B residue  201 ARG
Chi-restraints excluded: chain B residue  206 LEU
Chi-restraints excluded: chain B residue  306 HIS
Chi-restraints excluded: chain B residue  407 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 24 optimal weight:    3.9990
   chunk 16 optimal weight:    1.9990
   chunk 59 optimal weight:    0.9990
   chunk 60 optimal weight:    3.9990
   chunk 68 optimal weight:    5.9990
   chunk 31 optimal weight:    5.9990
   chunk 82 optimal weight:    8.9990
   chunk 36 optimal weight:    0.8980
   chunk 8 optimal weight:    3.9990
   chunk 84 optimal weight:    8.9990
   chunk 7 optimal weight:    4.9990
   overall best weight:    2.3788

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

Flipped N/Q/H residues before XYZ refinement:
** A  59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 412 ASN
B  80 HIS
B 320 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.069062 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.052117 restraints weight = 52222.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.053573 restraints weight = 26322.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.054350 restraints weight = 16738.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.054329 restraints weight = 15585.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.054290 restraints weight = 13955.040|
|-----------------------------------------------------------------------------|
r_work (final): 0.3243
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8204
moved from start:          0.3169

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.068   9766  Z= 0.222
  Angle     :  0.707  15.528  13891  Z= 0.357
  Chirality :  0.037   0.248   1619
  Planarity :  0.005   0.049   1207
  Dihedral  : 24.485 167.962   3079
  Min Nonbonded Distance : 2.358

Molprobity Statistics.
  All-atom Clashscore : 16.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  6.20 %
    Allowed  : 24.96 %
    Favored  : 68.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.11 (0.31), residues: 736
  helix:  1.76 (0.26), residues: 360
  sheet: -1.38 (0.47), residues: 128
  loop : -1.64 (0.40), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 371 
 TYR   0.022   0.002   TYR B 199 
 PHE   0.014   0.002   PHE A  49 
 TRP   0.014   0.002   TRP A  51 
 HIS   0.006   0.001   HIS B  80 

Details of bonding type rmsd
  covalent geometry    : bond        0.00465 ( 9762)
  covalent geometry    : angle       0.68707 (13885)
  hydrogen bonds       : bond        0.05375 (  415)
  hydrogen bonds       : angle       3.90578 ( 1109)
  metal coordination   : bond        0.01318 (    4)
  metal coordination   : angle       8.03230 (    6)

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

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

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 55
  time to evaluate  : 0.297 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8578 (mp)
REVERT: A  371 ARG cc_start: 0.8495 (tpt90) cc_final: 0.8150 (tpm170)
REVERT: B   16 TYR cc_start: 0.7746 (OUTLIER) cc_final: 0.6921 (p90)
REVERT: B   26 MET cc_start: 0.8786 (mpp) cc_final: 0.8364 (mpp)
REVERT: B  201 ARG cc_start: 0.8007 (OUTLIER) cc_final: 0.7050 (tpp-160)
REVERT: B  206 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8044 (tp)
REVERT: B  245 TYR cc_start: 0.8895 (p90) cc_final: 0.8385 (p90)
REVERT: B  306 HIS cc_start: 0.9583 (OUTLIER) cc_final: 0.9317 (t-90)
  outliers start: 40
  outliers final: 18
  residues processed: 90
  average time/residue: 0.0909
  time to fit residues: 11.5923
Evaluate side-chains
  75 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 52
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 LEU
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue   81 ILE
Chi-restraints excluded: chain A residue  102 GLN
Chi-restraints excluded: chain A residue  124 SER
Chi-restraints excluded: chain A residue  135 LYS
Chi-restraints excluded: chain A residue  174 HIS
Chi-restraints excluded: chain A residue  210 TYR
Chi-restraints excluded: chain A residue  243 HIS
Chi-restraints excluded: chain A residue  273 HIS
Chi-restraints excluded: chain A residue  303 THR
Chi-restraints excluded: chain A residue  313 ILE
Chi-restraints excluded: chain A residue  323 THR
Chi-restraints excluded: chain A residue  330 THR
Chi-restraints excluded: chain A residue  338 PHE
Chi-restraints excluded: chain A residue  410 SER
Chi-restraints excluded: chain A residue  411 GLN
Chi-restraints excluded: chain B residue   16 TYR
Chi-restraints excluded: chain B residue  201 ARG
Chi-restraints excluded: chain B residue  206 LEU
Chi-restraints excluded: chain B residue  306 HIS
Chi-restraints excluded: chain B residue  328 ASP
Chi-restraints excluded: chain B residue  407 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 6 optimal weight:    7.9990
   chunk 0 optimal weight:    3.9990
   chunk 85 optimal weight:    9.9990
   chunk 71 optimal weight:    3.9990
   chunk 41 optimal weight:    3.9990
   chunk 7 optimal weight:    3.9990
   chunk 32 optimal weight:    6.9990
   chunk 13 optimal weight:    0.8980
   chunk 70 optimal weight:    5.9990
   chunk 16 optimal weight:    2.9990
   chunk 25 optimal weight:    3.9990
   overall best weight:    3.1788

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

Flipped N/Q/H residues before XYZ refinement:
A  46 GLN
** A  98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 344 HIS
B  46 GLN
B 196 GLN
B 319 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.067675 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.050113 restraints weight = 52888.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.051746 restraints weight = 25915.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.052767 restraints weight = 17514.631|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.053324 restraints weight = 14130.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.053646 restraints weight = 12651.646|
|-----------------------------------------------------------------------------|
r_work (final): 0.3222
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8220
moved from start:          0.3826

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.084   9766  Z= 0.272
  Angle     :  0.749  17.847  13891  Z= 0.378
  Chirality :  0.039   0.246   1619
  Planarity :  0.005   0.048   1207
  Dihedral  : 24.579 173.700   3079
  Min Nonbonded Distance : 2.381

Molprobity Statistics.
  All-atom Clashscore : 17.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  6.98 %
    Allowed  : 24.50 %
    Favored  : 68.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.14 (0.31), residues: 736
  helix:  1.51 (0.25), residues: 360
  sheet: -1.40 (0.46), residues: 128
  loop : -1.75 (0.40), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  38 
 TYR   0.018   0.002   TYR A 348 
 PHE   0.013   0.002   PHE A 182 
 TRP   0.015   0.002   TRP A  51 
 HIS   0.006   0.002   HIS A 372 

Details of bonding type rmsd
  covalent geometry    : bond        0.00570 ( 9762)
  covalent geometry    : angle       0.72311 (13885)
  hydrogen bonds       : bond        0.05708 (  415)
  hydrogen bonds       : angle       4.10607 ( 1109)
  metal coordination   : bond        0.01532 (    4)
  metal coordination   : angle       9.39170 (    6)

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

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

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 56
  time to evaluate  : 0.289 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8571 (mp)
REVERT: A  267 MET cc_start: 0.8947 (tpp) cc_final: 0.8566 (mmm)
REVERT: A  302 ASP cc_start: 0.9126 (t0) cc_final: 0.8742 (t0)
REVERT: A  371 ARG cc_start: 0.8430 (tpt90) cc_final: 0.8203 (tpm170)
REVERT: B   26 MET cc_start: 0.8846 (OUTLIER) cc_final: 0.8135 (mpp)
REVERT: B  201 ARG cc_start: 0.7970 (OUTLIER) cc_final: 0.7132 (tpp-160)
REVERT: B  206 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8098 (tp)
REVERT: B  245 TYR cc_start: 0.8918 (p90) cc_final: 0.8519 (p90)
REVERT: B  306 HIS cc_start: 0.9581 (OUTLIER) cc_final: 0.9308 (t-90)
REVERT: B  312 LEU cc_start: 0.9658 (tp) cc_final: 0.9399 (pp)
  outliers start: 45
  outliers final: 30
  residues processed: 96
  average time/residue: 0.0858
  time to fit residues: 11.7769
Evaluate side-chains
  89 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 54
  time to evaluate  : 0.198 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 LEU
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue   37 THR
Chi-restraints excluded: chain A residue   81 ILE
Chi-restraints excluded: chain A residue  102 GLN
Chi-restraints excluded: chain A residue  124 SER
Chi-restraints excluded: chain A residue  154 PHE
Chi-restraints excluded: chain A residue  210 TYR
Chi-restraints excluded: chain A residue  243 HIS
Chi-restraints excluded: chain A residue  273 HIS
Chi-restraints excluded: chain A residue  296 LYS
Chi-restraints excluded: chain A residue  297 VAL
Chi-restraints excluded: chain A residue  303 THR
Chi-restraints excluded: chain A residue  313 ILE
Chi-restraints excluded: chain A residue  323 THR
Chi-restraints excluded: chain A residue  324 ILE
Chi-restraints excluded: chain A residue  330 THR
Chi-restraints excluded: chain A residue  338 PHE
Chi-restraints excluded: chain A residue  410 SER
Chi-restraints excluded: chain A residue  411 GLN
Chi-restraints excluded: chain B residue   16 TYR
Chi-restraints excluded: chain B residue   18 ASP
Chi-restraints excluded: chain B residue   26 MET
Chi-restraints excluded: chain B residue   80 HIS
Chi-restraints excluded: chain B residue  131 LEU
Chi-restraints excluded: chain B residue  171 MET
Chi-restraints excluded: chain B residue  174 HIS
Chi-restraints excluded: chain B residue  182 PHE
Chi-restraints excluded: chain B residue  195 CYS
Chi-restraints excluded: chain B residue  201 ARG
Chi-restraints excluded: chain B residue  206 LEU
Chi-restraints excluded: chain B residue  224 ILE
Chi-restraints excluded: chain B residue  306 HIS
Chi-restraints excluded: chain B residue  328 ASP
Chi-restraints excluded: chain B residue  407 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 46 optimal weight:    0.0970
   chunk 20 optimal weight:    0.9990
   chunk 3 optimal weight:    1.9990
   chunk 82 optimal weight:    8.9990
   chunk 54 optimal weight:   10.0000
   chunk 40 optimal weight:    0.7980
   chunk 63 optimal weight:    6.9990
   chunk 78 optimal weight:    9.9990
   chunk 85 optimal weight:    9.9990
   chunk 12 optimal weight:    7.9990
   chunk 86 optimal weight:    0.6980
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
A  46 GLN
** A  98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  80 HIS
B 273 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.070129 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.052641 restraints weight = 52327.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.054352 restraints weight = 25221.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.055433 restraints weight = 16856.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.056023 restraints weight = 13517.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.056288 restraints weight = 12041.550|
|-----------------------------------------------------------------------------|
r_work (final): 0.3299
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8135
moved from start:          0.3768

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9766  Z= 0.139
  Angle     :  0.659  13.469  13891  Z= 0.331
  Chirality :  0.036   0.232   1619
  Planarity :  0.004   0.041   1207
  Dihedral  : 24.435 172.966   3079
  Min Nonbonded Distance : 2.378

Molprobity Statistics.
  All-atom Clashscore : 13.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  5.89 %
    Allowed  : 25.74 %
    Favored  : 68.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.24 (0.32), residues: 736
  helix:  1.93 (0.26), residues: 354
  sheet: -1.21 (0.46), residues: 128
  loop : -1.68 (0.40), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 201 
 TYR   0.019   0.001   TYR B 199 
 PHE   0.016   0.001   PHE A 394 
 TRP   0.009   0.001   TRP A  51 
 HIS   0.011   0.001   HIS B 273 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 9762)
  covalent geometry    : angle       0.64298 (13885)
  hydrogen bonds       : bond        0.04901 (  415)
  hydrogen bonds       : angle       3.71763 ( 1109)
  metal coordination   : bond        0.01135 (    4)
  metal coordination   : angle       6.95698 (    6)

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

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

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 56
  time to evaluate  : 0.293 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8551 (mp)
REVERT: A  267 MET cc_start: 0.8950 (tpp) cc_final: 0.8644 (mmm)
REVERT: A  302 ASP cc_start: 0.9050 (OUTLIER) cc_final: 0.8625 (t0)
REVERT: A  371 ARG cc_start: 0.8428 (tpt90) cc_final: 0.8180 (tpm170)
REVERT: A  410 SER cc_start: 0.9414 (OUTLIER) cc_final: 0.9185 (t)
REVERT: B   16 TYR cc_start: 0.7702 (OUTLIER) cc_final: 0.6967 (p90)
REVERT: B   26 MET cc_start: 0.8822 (OUTLIER) cc_final: 0.8374 (mpp)
REVERT: B  201 ARG cc_start: 0.7915 (OUTLIER) cc_final: 0.7590 (tpp-160)
REVERT: B  245 TYR cc_start: 0.8896 (p90) cc_final: 0.8490 (p90)
REVERT: B  306 HIS cc_start: 0.9574 (OUTLIER) cc_final: 0.9303 (t-90)
REVERT: B  312 LEU cc_start: 0.9645 (tp) cc_final: 0.9378 (pp)
  outliers start: 38
  outliers final: 19
  residues processed: 88
  average time/residue: 0.0986
  time to fit residues: 12.0693
Evaluate side-chains
  78 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 52
  time to evaluate  : 0.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 LEU
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue   37 THR
Chi-restraints excluded: chain A residue  102 GLN
Chi-restraints excluded: chain A residue  124 SER
Chi-restraints excluded: chain A residue  210 TYR
Chi-restraints excluded: chain A residue  273 HIS
Chi-restraints excluded: chain A residue  302 ASP
Chi-restraints excluded: chain A residue  313 ILE
Chi-restraints excluded: chain A residue  317 LEU
Chi-restraints excluded: chain A residue  323 THR
Chi-restraints excluded: chain A residue  330 THR
Chi-restraints excluded: chain A residue  410 SER
Chi-restraints excluded: chain A residue  411 GLN
Chi-restraints excluded: chain B residue   16 TYR
Chi-restraints excluded: chain B residue   26 MET
Chi-restraints excluded: chain B residue  131 LEU
Chi-restraints excluded: chain B residue  171 MET
Chi-restraints excluded: chain B residue  195 CYS
Chi-restraints excluded: chain B residue  201 ARG
Chi-restraints excluded: chain B residue  206 LEU
Chi-restraints excluded: chain B residue  224 ILE
Chi-restraints excluded: chain B residue  235 LEU
Chi-restraints excluded: chain B residue  306 HIS
Chi-restraints excluded: chain B residue  328 ASP
Chi-restraints excluded: chain B residue  407 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 15 optimal weight:    4.9990
   chunk 37 optimal weight:    4.9990
   chunk 0 optimal weight:    5.9990
   chunk 70 optimal weight:    7.9990
   chunk 83 optimal weight:    7.9990
   chunk 13 optimal weight:    4.9990
   chunk 2 optimal weight:    2.9990
   chunk 48 optimal weight:    7.9990
   chunk 67 optimal weight:    2.9990
   chunk 7 optimal weight:    0.7980
   chunk 74 optimal weight:    4.9990
   overall best weight:    3.3588

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

Flipped N/Q/H residues before XYZ refinement:
A  46 GLN
** A  98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  80 HIS
B 273 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.067170 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.049489 restraints weight = 53075.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 63)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.051071 restraints weight = 26381.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.052040 restraints weight = 17964.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.052632 restraints weight = 14623.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.052862 restraints weight = 13036.133|
|-----------------------------------------------------------------------------|
r_work (final): 0.3204
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8244
moved from start:          0.4268

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.098   9766  Z= 0.287
  Angle     :  0.751  16.916  13891  Z= 0.380
  Chirality :  0.039   0.242   1619
  Planarity :  0.005   0.042   1207
  Dihedral  : 24.539 173.550   3077
  Min Nonbonded Distance : 2.357

Molprobity Statistics.
  All-atom Clashscore : 18.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  6.51 %
    Allowed  : 26.05 %
    Favored  : 67.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.04 (0.31), residues: 736
  helix:  1.71 (0.26), residues: 354
  sheet: -1.23 (0.46), residues: 128
  loop : -1.72 (0.40), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  38 
 TYR   0.025   0.002   TYR B 199 
 PHE   0.018   0.002   PHE A 212 
 TRP   0.013   0.002   TRP A  51 
 HIS   0.012   0.002   HIS B 273 

Details of bonding type rmsd
  covalent geometry    : bond        0.00607 ( 9762)
  covalent geometry    : angle       0.72835 (13885)
  hydrogen bonds       : bond        0.05671 (  415)
  hydrogen bonds       : angle       4.03289 ( 1109)
  metal coordination   : bond        0.01519 (    4)
  metal coordination   : angle       8.89379 (    6)

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

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

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 53
  time to evaluate  : 0.224 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8565 (mp)
REVERT: A  302 ASP cc_start: 0.9112 (OUTLIER) cc_final: 0.8737 (t0)
REVERT: A  371 ARG cc_start: 0.8519 (tpt90) cc_final: 0.8239 (tpm170)
REVERT: A  410 SER cc_start: 0.9480 (OUTLIER) cc_final: 0.8866 (t)
REVERT: B   26 MET cc_start: 0.8877 (OUTLIER) cc_final: 0.8181 (mpp)
REVERT: B  245 TYR cc_start: 0.8996 (p90) cc_final: 0.8571 (p90)
REVERT: B  306 HIS cc_start: 0.9571 (OUTLIER) cc_final: 0.9294 (t-90)
  outliers start: 42
  outliers final: 27
  residues processed: 91
  average time/residue: 0.0847
  time to fit residues: 11.0622
Evaluate side-chains
  85 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 53
  time to evaluate  : 0.213 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 LEU
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue   37 THR
Chi-restraints excluded: chain A residue  102 GLN
Chi-restraints excluded: chain A residue  124 SER
Chi-restraints excluded: chain A residue  154 PHE
Chi-restraints excluded: chain A residue  243 HIS
Chi-restraints excluded: chain A residue  273 HIS
Chi-restraints excluded: chain A residue  297 VAL
Chi-restraints excluded: chain A residue  302 ASP
Chi-restraints excluded: chain A residue  303 THR
Chi-restraints excluded: chain A residue  313 ILE
Chi-restraints excluded: chain A residue  317 LEU
Chi-restraints excluded: chain A residue  323 THR
Chi-restraints excluded: chain A residue  324 ILE
Chi-restraints excluded: chain A residue  389 THR
Chi-restraints excluded: chain A residue  410 SER
Chi-restraints excluded: chain A residue  411 GLN
Chi-restraints excluded: chain B residue   16 TYR
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain B residue   18 ASP
Chi-restraints excluded: chain B residue   26 MET
Chi-restraints excluded: chain B residue  131 LEU
Chi-restraints excluded: chain B residue  171 MET
Chi-restraints excluded: chain B residue  174 HIS
Chi-restraints excluded: chain B residue  195 CYS
Chi-restraints excluded: chain B residue  206 LEU
Chi-restraints excluded: chain B residue  224 ILE
Chi-restraints excluded: chain B residue  235 LEU
Chi-restraints excluded: chain B residue  306 HIS
Chi-restraints excluded: chain B residue  328 ASP
Chi-restraints excluded: chain B residue  407 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 45 optimal weight:    5.9990
   chunk 17 optimal weight:    0.8980
   chunk 7 optimal weight:    2.9990
   chunk 5 optimal weight:   20.0000
   chunk 8 optimal weight:    0.7980
   chunk 50 optimal weight:    3.9990
   chunk 26 optimal weight:    3.9990
   chunk 16 optimal weight:    3.9990
   chunk 27 optimal weight:    5.9990
   chunk 66 optimal weight:    0.7980
   chunk 81 optimal weight:    5.9990
   overall best weight:    1.8984

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

Flipped N/Q/H residues before XYZ refinement:
A  46 GLN
** A  98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  80 HIS
B 273 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.068446 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.050798 restraints weight = 52035.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.052460 restraints weight = 25410.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.053495 restraints weight = 17090.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.053974 restraints weight = 13771.946|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.054347 restraints weight = 12436.633|
|-----------------------------------------------------------------------------|
r_work (final): 0.3243
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8192
moved from start:          0.4256

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061   9766  Z= 0.188
  Angle     :  0.691  14.575  13891  Z= 0.347
  Chirality :  0.038   0.341   1619
  Planarity :  0.004   0.040   1207
  Dihedral  : 24.435 171.934   3077
  Min Nonbonded Distance : 2.393

Molprobity Statistics.
  All-atom Clashscore : 14.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  4.65 %
    Allowed  : 27.91 %
    Favored  : 67.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.19 (0.32), residues: 736
  helix:  1.86 (0.26), residues: 354
  sheet: -1.15 (0.46), residues: 128
  loop : -1.69 (0.40), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 179 
 TYR   0.027   0.002   TYR B 199 
 PHE   0.023   0.001   PHE B 182 
 TRP   0.010   0.001   TRP A  51 
 HIS   0.009   0.001   HIS B 273 

Details of bonding type rmsd
  covalent geometry    : bond        0.00399 ( 9762)
  covalent geometry    : angle       0.67350 (13885)
  hydrogen bonds       : bond        0.05089 (  415)
  hydrogen bonds       : angle       3.80069 ( 1109)
  metal coordination   : bond        0.01168 (    4)
  metal coordination   : angle       7.52936 (    6)

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

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

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 51
  time to evaluate  : 0.290 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8555 (mp)
REVERT: A  267 MET cc_start: 0.8933 (tpp) cc_final: 0.8612 (mmm)
REVERT: A  302 ASP cc_start: 0.9106 (OUTLIER) cc_final: 0.8690 (t0)
REVERT: A  371 ARG cc_start: 0.8493 (tpt90) cc_final: 0.8245 (tpm170)
REVERT: A  410 SER cc_start: 0.9460 (OUTLIER) cc_final: 0.9257 (t)
REVERT: B   26 MET cc_start: 0.8835 (OUTLIER) cc_final: 0.8408 (mpp)
REVERT: B  245 TYR cc_start: 0.8934 (p90) cc_final: 0.8516 (p90)
REVERT: B  306 HIS cc_start: 0.9581 (OUTLIER) cc_final: 0.9281 (t-90)
REVERT: B  312 LEU cc_start: 0.9642 (tp) cc_final: 0.9368 (pp)
  outliers start: 30
  outliers final: 21
  residues processed: 78
  average time/residue: 0.0727
  time to fit residues: 8.6186
Evaluate side-chains
  76 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 50
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 LEU
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue   37 THR
Chi-restraints excluded: chain A residue  102 GLN
Chi-restraints excluded: chain A residue  124 SER
Chi-restraints excluded: chain A residue  243 HIS
Chi-restraints excluded: chain A residue  273 HIS
Chi-restraints excluded: chain A residue  302 ASP
Chi-restraints excluded: chain A residue  313 ILE
Chi-restraints excluded: chain A residue  317 LEU
Chi-restraints excluded: chain A residue  323 THR
Chi-restraints excluded: chain A residue  324 ILE
Chi-restraints excluded: chain A residue  389 THR
Chi-restraints excluded: chain A residue  410 SER
Chi-restraints excluded: chain A residue  411 GLN
Chi-restraints excluded: chain B residue   16 TYR
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain B residue   26 MET
Chi-restraints excluded: chain B residue  131 LEU
Chi-restraints excluded: chain B residue  171 MET
Chi-restraints excluded: chain B residue  206 LEU
Chi-restraints excluded: chain B residue  224 ILE
Chi-restraints excluded: chain B residue  235 LEU
Chi-restraints excluded: chain B residue  306 HIS
Chi-restraints excluded: chain B residue  328 ASP
Chi-restraints excluded: chain B residue  407 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 62 optimal weight:    7.9990
   chunk 0 optimal weight:    4.9990
   chunk 24 optimal weight:    0.9990
   chunk 8 optimal weight:    1.9990
   chunk 18 optimal weight:    0.4980
   chunk 17 optimal weight:    0.9980
   chunk 29 optimal weight:    0.6980
   chunk 85 optimal weight:   10.0000
   chunk 47 optimal weight:    0.8980
   chunk 22 optimal weight:    2.9990
   chunk 28 optimal weight:    3.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
** A  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  80 HIS
B 320 GLN
B 351 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.070765 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.053299 restraints weight = 52163.620|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.055023 restraints weight = 25240.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.056063 restraints weight = 16841.800|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.056704 restraints weight = 13531.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.056977 restraints weight = 11998.820|
|-----------------------------------------------------------------------------|
r_work (final): 0.3317
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8114
moved from start:          0.4249

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9766  Z= 0.131
  Angle     :  0.654  12.575  13891  Z= 0.328
  Chirality :  0.037   0.401   1619
  Planarity :  0.004   0.047   1207
  Dihedral  : 24.312 175.724   3077
  Min Nonbonded Distance : 2.376

Molprobity Statistics.
  All-atom Clashscore : 12.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.26 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 28.68 %
    Favored  : 67.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.44 (0.32), residues: 736
  helix:  2.12 (0.26), residues: 349
  sheet: -0.88 (0.45), residues: 131
  loop : -1.69 (0.40), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 179 
 TYR   0.024   0.001   TYR B 199 
 PHE   0.018   0.001   PHE B 182 
 TRP   0.008   0.001   TRP A 345 
 HIS   0.007   0.001   HIS B  80 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 9762)
  covalent geometry    : angle       0.64157 (13885)
  hydrogen bonds       : bond        0.04714 (  415)
  hydrogen bonds       : angle       3.52893 ( 1109)
  metal coordination   : bond        0.01528 (    4)
  metal coordination   : angle       6.24823 (    6)

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

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

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 53
  time to evaluate  : 0.276 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8593 (mp)
REVERT: A  267 MET cc_start: 0.8906 (tpp) cc_final: 0.8575 (mmm)
REVERT: A  302 ASP cc_start: 0.8986 (OUTLIER) cc_final: 0.8579 (t0)
REVERT: A  371 ARG cc_start: 0.8468 (tpt90) cc_final: 0.8186 (tpm170)
REVERT: A  410 SER cc_start: 0.9446 (OUTLIER) cc_final: 0.9236 (t)
REVERT: B   16 TYR cc_start: 0.7751 (OUTLIER) cc_final: 0.6973 (p90)
REVERT: B   26 MET cc_start: 0.8853 (OUTLIER) cc_final: 0.8138 (mpp)
REVERT: B  184 ASN cc_start: 0.8909 (m110) cc_final: 0.8571 (p0)
REVERT: B  206 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8069 (tp)
REVERT: B  245 TYR cc_start: 0.8851 (p90) cc_final: 0.8508 (p90)
REVERT: B  306 HIS cc_start: 0.9570 (OUTLIER) cc_final: 0.9306 (t-90)
REVERT: B  312 LEU cc_start: 0.9629 (tp) cc_final: 0.9356 (pp)
REVERT: B  326 MET cc_start: 0.8533 (tmm) cc_final: 0.8236 (tmm)
  outliers start: 23
  outliers final: 12
  residues processed: 74
  average time/residue: 0.0864
  time to fit residues: 9.2005
Evaluate side-chains
  71 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 52
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 LEU
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue   37 THR
Chi-restraints excluded: chain A residue  102 GLN
Chi-restraints excluded: chain A residue  124 SER
Chi-restraints excluded: chain A residue  273 HIS
Chi-restraints excluded: chain A residue  302 ASP
Chi-restraints excluded: chain A residue  313 ILE
Chi-restraints excluded: chain A residue  317 LEU
Chi-restraints excluded: chain A residue  323 THR
Chi-restraints excluded: chain A residue  410 SER
Chi-restraints excluded: chain A residue  411 GLN
Chi-restraints excluded: chain B residue   16 TYR
Chi-restraints excluded: chain B residue   26 MET
Chi-restraints excluded: chain B residue  131 LEU
Chi-restraints excluded: chain B residue  206 LEU
Chi-restraints excluded: chain B residue  224 ILE
Chi-restraints excluded: chain B residue  306 HIS
Chi-restraints excluded: chain B residue  407 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 35 optimal weight:    7.9990
   chunk 30 optimal weight:    1.9990
   chunk 71 optimal weight:   10.0000
   chunk 56 optimal weight:    8.9990
   chunk 75 optimal weight:    5.9990
   chunk 7 optimal weight:    5.9990
   chunk 25 optimal weight:    4.9990
   chunk 19 optimal weight:    0.9980
   chunk 79 optimal weight:    9.9990
   chunk 72 optimal weight:   10.0000
   chunk 73 optimal weight:    2.9990
   overall best weight:    3.3988

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

Flipped N/Q/H residues before XYZ refinement:
A  46 GLN
** A  98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  80 HIS
B 320 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.067015 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.049326 restraints weight = 52657.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.050911 restraints weight = 26253.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.051898 restraints weight = 17904.263|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.052452 restraints weight = 14545.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.052558 restraints weight = 13026.916|
|-----------------------------------------------------------------------------|
r_work (final): 0.3197
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8251
moved from start:          0.4613

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.109   9766  Z= 0.290
  Angle     :  0.759  17.347  13891  Z= 0.383
  Chirality :  0.040   0.359   1619
  Planarity :  0.005   0.040   1207
  Dihedral  : 24.459 173.116   3077
  Min Nonbonded Distance : 2.367

Molprobity Statistics.
  All-atom Clashscore : 17.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 28.53 %
    Favored  : 67.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.25 (0.31), residues: 736
  helix:  1.89 (0.25), residues: 353
  sheet: -0.99 (0.46), residues: 128
  loop : -1.71 (0.40), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 278 
 TYR   0.029   0.002   TYR B 199 
 PHE   0.018   0.002   PHE B 182 
 TRP   0.012   0.002   TRP A  51 
 HIS   0.006   0.001   HIS B 306 

Details of bonding type rmsd
  covalent geometry    : bond        0.00611 ( 9762)
  covalent geometry    : angle       0.73787 (13885)
  hydrogen bonds       : bond        0.05666 (  415)
  hydrogen bonds       : angle       3.98822 ( 1109)
  metal coordination   : bond        0.01542 (    4)
  metal coordination   : angle       8.56664 (    6)

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

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

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 50
  time to evaluate  : 0.197 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8603 (mp)
REVERT: A  302 ASP cc_start: 0.9103 (OUTLIER) cc_final: 0.8739 (t0)
REVERT: A  371 ARG cc_start: 0.8542 (tpt90) cc_final: 0.8208 (tpm170)
REVERT: B   26 MET cc_start: 0.8879 (OUTLIER) cc_final: 0.8180 (mpp)
REVERT: B  126 LYS cc_start: 0.9227 (OUTLIER) cc_final: 0.8576 (mmmm)
REVERT: B  202 PRO cc_start: 0.8501 (Cg_endo) cc_final: 0.8280 (Cg_endo)
REVERT: B  206 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8132 (tp)
REVERT: B  306 HIS cc_start: 0.9577 (OUTLIER) cc_final: 0.9283 (t-90)
REVERT: B  326 MET cc_start: 0.8557 (tmm) cc_final: 0.8168 (tmm)
  outliers start: 24
  outliers final: 16
  residues processed: 72
  average time/residue: 0.0838
  time to fit residues: 8.7576
Evaluate side-chains
  72 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 50
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 LEU
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue   37 THR
Chi-restraints excluded: chain A residue  102 GLN
Chi-restraints excluded: chain A residue  124 SER
Chi-restraints excluded: chain A residue  273 HIS
Chi-restraints excluded: chain A residue  302 ASP
Chi-restraints excluded: chain A residue  313 ILE
Chi-restraints excluded: chain A residue  317 LEU
Chi-restraints excluded: chain A residue  323 THR
Chi-restraints excluded: chain A residue  411 GLN
Chi-restraints excluded: chain B residue   16 TYR
Chi-restraints excluded: chain B residue   18 ASP
Chi-restraints excluded: chain B residue   26 MET
Chi-restraints excluded: chain B residue  126 LYS
Chi-restraints excluded: chain B residue  131 LEU
Chi-restraints excluded: chain B residue  198 VAL
Chi-restraints excluded: chain B residue  206 LEU
Chi-restraints excluded: chain B residue  224 ILE
Chi-restraints excluded: chain B residue  235 LEU
Chi-restraints excluded: chain B residue  306 HIS
Chi-restraints excluded: chain B residue  407 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 61 optimal weight:   30.0000
   chunk 32 optimal weight:    3.9990
   chunk 41 optimal weight:    0.7980
   chunk 38 optimal weight:    0.9980
   chunk 82 optimal weight:    8.9990
   chunk 6 optimal weight:    7.9990
   chunk 12 optimal weight:    0.8980
   chunk 9 optimal weight:    0.7980
   chunk 58 optimal weight:    0.0980
   chunk 31 optimal weight:    1.9990
   chunk 83 optimal weight:    5.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  46 GLN
** A 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  80 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.070389 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.053034 restraints weight = 51252.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.054702 restraints weight = 24612.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.055754 restraints weight = 16431.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.056281 restraints weight = 13162.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.056604 restraints weight = 11792.779|
|-----------------------------------------------------------------------------|
r_work (final): 0.3312
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8122
moved from start:          0.4473

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9766  Z= 0.134
  Angle     :  0.660  12.905  13891  Z= 0.332
  Chirality :  0.037   0.380   1619
  Planarity :  0.004   0.046   1207
  Dihedral  : 24.307 174.857   3077
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 12.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.26 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 29.15 %
    Favored  : 67.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.52 (0.32), residues: 736
  helix:  2.09 (0.26), residues: 353
  sheet: -0.71 (0.46), residues: 131
  loop : -1.65 (0.41), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 179 
 TYR   0.024   0.001   TYR B 199 
 PHE   0.016   0.001   PHE B 182 
 TRP   0.009   0.001   TRP A  51 
 HIS   0.006   0.001   HIS B  80 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 9762)
  covalent geometry    : angle       0.64719 (13885)
  hydrogen bonds       : bond        0.04787 (  415)
  hydrogen bonds       : angle       3.58683 ( 1109)
  metal coordination   : bond        0.01184 (    4)
  metal coordination   : angle       6.33675 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1598.38 seconds
wall clock time: 28 minutes 27.17 seconds (1707.17 seconds total)