Starting phenix.real_space_refine
on Wed Aug  5 00:31:57 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8gkh_40184/08_2026/8gkh_40184_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8gkh_40184/08_2026/8gkh_40184.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8gkh_40184/08_2026/8gkh_40184_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8gkh_40184/08_2026/8gkh_40184_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8gkh_40184/08_2026/8gkh_40184.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8gkh_40184/08_2026/8gkh_40184.map"
  }
  resolution = 2.7
  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=   0.026
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: 7
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     P     125      5.49       5
     Mg      2      5.21       5
     S      32      5.16       5
     C    4337      2.51       5
     N    1358      2.21       5
     O    1715      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 7570
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "N"
      Number of atoms: 308
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 15, 308
          Classifications: {'DNA': 15}
          Link IDs: {'rna3p': 14}
    Chain: "P"
      Number of atoms: 4946
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 600, 4946
          Classifications: {'peptide': 600}
          Link IDs: {'PTRANS': 25, 'TRANS': 574}
          Chain breaks: 1
    Chain: "T"
      Number of atoms: 695
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 34, 695
          Classifications: {'DNA': 34}
          Link IDs: {'rna3p': 33}
          Chain breaks: 1
    Chain: "W"
      Number of atoms: 1615
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 1615
          Classifications: {'RNA': 76}
          Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 30, 'rna3p_pyr': 35}
          Link IDs: {'rna2p': 11, 'rna3p': 64}
          Chain breaks: 1
    Chain: "P"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 4
          Unusual residues: {' MG': 2, ' ZN': 1}
          Classifications: {'undetermined': 3, 'water': 1}
          Link IDs: {None: 3}
    Chain: "T"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
    Chain: "W"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   4558  SG  CYS P 548      32.953  45.640  21.668  1.00 51.02           S
  ATOM   4582  SG  CYS P 551      30.062  44.068  19.775  1.00 57.06           S
  ATOM   4875  SG  CYS P 586      33.492  42.516  19.547  1.00 52.44           S
  ATOM   4911  SG  CYS P 591      32.800  45.814  17.814  1.00 44.29           S

  Time building chain proxies: 1.47, per 1000 atoms: 0.19
  Number of scatterers: 7570
  At special positions: 0
  Unit cell: (75.9, 107.25, 139.425, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Zn      1     29.99
     S      32     16.00
     P     125     15.00
     Mg      2     11.99
     O    1715      8.00
     N    1358      7.00
     C    4337      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: 0.53
  Conformation dependent library (CDL) restraints added in 231.8 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN P 703 "
        pdb="ZN    ZN P 703 " - pdb=" SG  CYS P 551 "
        pdb="ZN    ZN P 703 " - pdb=" SG  CYS P 586 "
        pdb="ZN    ZN P 703 " - pdb=" SG  CYS P 591 "
        pdb="ZN    ZN P 703 " - pdb=" SG  CYS P 548 "
      Number of angles added : 6


  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1156

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 4 sheets defined
      61.0% alpha, 7.7% beta
      52 base pairs and 76 stacking pairs defined.
    Time for finding SS restraints: 0.82
  Creating SS restraints...
    Processing helix  chain 'P' and resid 28 through 32
    Processing helix  chain 'P' and resid 35 through 68
    Processing helix  chain 'P' and resid 76 through 90
    Processing helix  chain 'P' and resid 91 through 93
      No H-bonds generated for 'chain 'P' and resid 91 through 93'
    Processing helix  chain 'P' and resid 97 through 119
      Proline residue:  P 109  - end of helix
      removed outlier: 4.072A  pdb=" N   GLN P 112 " --> pdb=" O   LEU P 108 " (cutoff:3.500A)
      removed outlier: 4.205A  pdb=" N   ARG P 113 " --> pdb=" O   PRO P 109 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 128 through 151
    Processing helix  chain 'P' and resid 151 through 164
    Processing helix  chain 'P' and resid 164 through 172
    Processing helix  chain 'P' and resid 176 through 194
      removed outlier: 3.630A  pdb=" N   PHE P 182 " --> pdb=" O   ALA P 178 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   SER P 191 " --> pdb=" O   ARG P 187 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   VAL P 192 " --> pdb=" O   TYR P 188 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 200 through 207
    Processing helix  chain 'P' and resid 208 through 220
    Processing helix  chain 'P' and resid 230 through 238
    Processing helix  chain 'P' and resid 239 through 241
      No H-bonds generated for 'chain 'P' and resid 239 through 241'
    Processing helix  chain 'P' and resid 242 through 257
    Processing helix  chain 'P' and resid 279 through 286
    Processing helix  chain 'P' and resid 290 through 296
      removed outlier: 3.847A  pdb=" N   THR P 296 " --> pdb=" O   ARG P 292 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 298 through 305
      removed outlier: 3.601A  pdb=" N   ARG P 305 " --> pdb=" O   ASP P 301 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 311 through 315
    Processing helix  chain 'P' and resid 365 through 368
    Processing helix  chain 'P' and resid 369 through 376
    Processing helix  chain 'P' and resid 403 through 412
    Processing helix  chain 'P' and resid 412 through 428
    Processing helix  chain 'P' and resid 428 through 435
      removed outlier: 3.730A  pdb=" N   ARG P 435 " --> pdb=" O   LEU P 431 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 443 through 457
      removed outlier: 3.741A  pdb=" N   ASP P 457 " --> pdb=" O   VAL P 453 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 457 through 466
    Processing helix  chain 'P' and resid 468 through 497
    Processing helix  chain 'P' and resid 523 through 532
      removed outlier: 4.036A  pdb=" N   THR P 527 " --> pdb=" O   LYS P 523 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 568 through 575
    Processing helix  chain 'P' and resid 588 through 592
    Processing helix  chain 'P' and resid 605 through 622
    Processing sheet with id=AA1, first strand: chain 'P' and resid 21 through 27
      removed outlier: 4.929A  pdb=" N   SER P 325 " --> pdb=" O   TYR P 336 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'P' and resid 400 through 402
    Processing sheet with id=AA3, first strand: chain 'P' and resid 557 through 559
      removed outlier: 3.642A  pdb=" N   GLY P 585 " --> pdb=" O   GLU P 558 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'P' and resid 563 through 565

    271 hydrogen bonds defined for protein.
    786 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      132 hydrogen bonds
      248 hydrogen bond angles
      0 basepair planarities
      52 basepair parallelities
      76 stacking parallelities
  Total time for adding SS restraints: 1.27

  Time building geometry restraints manager: 0.71 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1900
        1.34 -     1.45: 2153
        1.45 -     1.57: 3645
        1.57 -     1.69: 245
        1.69 -     1.81: 48
  Bond restraints: 7991
  Sorted by residual:
  bond pdb=" C3'  DG N  -7 "
       pdb=" C2'  DG N  -7 "
    ideal  model  delta    sigma   weight residual
    1.516  1.539 -0.023 8.00e-03 1.56e+04 8.27e+00
  bond pdb=" C1'  DC N  -8 "
       pdb=" N1   DC N  -8 "
    ideal  model  delta    sigma   weight residual
    1.468  1.508 -0.040 1.40e-02 5.10e+03 7.99e+00
  bond pdb=" C3'  DG N -14 "
       pdb=" C2'  DG N -14 "
    ideal  model  delta    sigma   weight residual
    1.516  1.539 -0.023 8.00e-03 1.56e+04 7.93e+00
  bond pdb=" C1'  DC N  -9 "
       pdb=" N1   DC N  -9 "
    ideal  model  delta    sigma   weight residual
    1.468  1.507 -0.039 1.40e-02 5.10e+03 7.89e+00
  bond pdb=" C3'  DC T  14 "
       pdb=" C2'  DC T  14 "
    ideal  model  delta    sigma   weight residual
    1.516  1.538 -0.022 8.00e-03 1.56e+04 7.48e+00
  ... (remaining 7986 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.64: 11204
        4.64 -     9.29: 54
        9.29 -    13.93: 110
       13.93 -    18.58: 1
       18.58 -    23.22: 1
  Bond angle restraints: 11370
  Sorted by residual:
  angle pdb=" O3'  DG T -17 "
        pdb=" P    DA T -16 "
        pdb=" OP1  DA T -16 "
      ideal   model   delta    sigma   weight residual
     108.00  131.22  -23.22 3.00e+00 1.11e-01 5.99e+01
  angle pdb=" O4'   U W  76 "
        pdb=" C1'   U W  76 "
        pdb=" N1    U W  76 "
      ideal   model   delta    sigma   weight residual
     108.20  114.13   -5.93 8.00e-01 1.56e+00 5.50e+01
  angle pdb=" OP1  DA T -16 "
        pdb=" P    DA T -16 "
        pdb=" OP2  DA T -16 "
      ideal   model   delta    sigma   weight residual
     120.00  103.13   16.87 3.00e+00 1.11e-01 3.16e+01
  angle pdb=" O4'   C W  21 "
        pdb=" C1'   C W  21 "
        pdb=" N1    C W  21 "
      ideal   model   delta    sigma   weight residual
     108.50  112.03   -3.53 7.00e-01 2.04e+00 2.55e+01
  angle pdb=" O5'   U W  84 "
        pdb=" C5'   U W  84 "
        pdb=" C4'   U W  84 "
      ideal   model   delta    sigma   weight residual
     109.40  113.05   -3.65 8.00e-01 1.56e+00 2.08e+01
  ... (remaining 11365 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.94: 4417
       35.94 -    71.88: 334
       71.88 -   107.82: 31
      107.82 -   143.76: 8
      143.76 -   179.70: 11
  Dihedral angle restraints: 4801
    sinusoidal: 3023
      harmonic: 1778
  Sorted by residual:
  dihedral pdb=" C4'   U W  76 "
           pdb=" C3'   U W  76 "
           pdb=" C2'   U W  76 "
           pdb=" C1'   U W  76 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -35.00   36.12  -71.12     1      8.00e+00 1.56e-02 1.01e+02
  dihedral pdb=" C4'   A W  16 "
           pdb=" C3'   A W  16 "
           pdb=" C2'   A W  16 "
           pdb=" C1'   A W  16 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -35.00   35.70  -70.70     1      8.00e+00 1.56e-02 1.00e+02
  dihedral pdb=" C4'   C W  19 "
           pdb=" C3'   C W  19 "
           pdb=" C2'   C W  19 "
           pdb=" C1'   C W  19 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -35.00   35.27  -70.27     1      8.00e+00 1.56e-02 9.94e+01
  ... (remaining 4798 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.151: 1216
       0.151 -    0.303: 39
       0.303 -    0.454: 51
       0.454 -    0.606: 0
       0.606 -    0.757: 1
  Chirality restraints: 1307
  Sorted by residual:
  chirality pdb=" P    DA T -16 "
            pdb=" OP1  DA T -16 "
            pdb=" OP2  DA T -16 "
            pdb=" O5'  DA T -16 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.34   -3.09   -0.76 2.00e-01 2.50e+01 1.43e+01
  chirality pdb=" P    DC T   7 "
            pdb=" OP1  DC T   7 "
            pdb=" OP2  DC T   7 "
            pdb=" O5'  DC T   7 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.34   -2.79   -0.45 2.00e-01 2.50e+01 5.14e+00
  chirality pdb=" P    DA T  -4 "
            pdb=" OP1  DA T  -4 "
            pdb=" OP2  DA T  -4 "
            pdb=" O5'  DA T  -4 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.34   -2.76   -0.43 2.00e-01 2.50e+01 4.54e+00
  ... (remaining 1304 not shown)

  Planarity restraints: 1000
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G W  20 "    0.014 2.00e-02 2.50e+03   7.39e-03 1.64e+00
        pdb=" N9    G W  20 "   -0.020 2.00e-02 2.50e+03
        pdb=" C8    G W  20 "    0.000 2.00e-02 2.50e+03
        pdb=" N7    G W  20 "    0.000 2.00e-02 2.50e+03
        pdb=" C5    G W  20 "    0.002 2.00e-02 2.50e+03
        pdb=" C6    G W  20 "   -0.003 2.00e-02 2.50e+03
        pdb=" O6    G W  20 "    0.006 2.00e-02 2.50e+03
        pdb=" N1    G W  20 "    0.000 2.00e-02 2.50e+03
        pdb=" C2    G W  20 "    0.001 2.00e-02 2.50e+03
        pdb=" N2    G W  20 "   -0.003 2.00e-02 2.50e+03
        pdb=" N3    G W  20 "    0.001 2.00e-02 2.50e+03
        pdb=" C4    G W  20 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G W  70 "   -0.016 2.00e-02 2.50e+03   7.29e-03 1.59e+00
        pdb=" N9    G W  70 "    0.018 2.00e-02 2.50e+03
        pdb=" C8    G W  70 "    0.001 2.00e-02 2.50e+03
        pdb=" N7    G W  70 "   -0.001 2.00e-02 2.50e+03
        pdb=" C5    G W  70 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6    G W  70 "    0.001 2.00e-02 2.50e+03
        pdb=" O6    G W  70 "   -0.006 2.00e-02 2.50e+03
        pdb=" N1    G W  70 "   -0.001 2.00e-02 2.50e+03
        pdb=" C2    G W  70 "    0.001 2.00e-02 2.50e+03
        pdb=" N2    G W  70 "    0.001 2.00e-02 2.50e+03
        pdb=" N3    G W  70 "    0.001 2.00e-02 2.50e+03
        pdb=" C4    G W  70 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   U W  27 "   -0.015 2.00e-02 2.50e+03   7.91e-03 1.41e+00
        pdb=" N1    U W  27 "    0.017 2.00e-02 2.50e+03
        pdb=" C2    U W  27 "    0.001 2.00e-02 2.50e+03
        pdb=" O2    U W  27 "    0.002 2.00e-02 2.50e+03
        pdb=" N3    U W  27 "   -0.001 2.00e-02 2.50e+03
        pdb=" C4    U W  27 "   -0.002 2.00e-02 2.50e+03
        pdb=" O4    U W  27 "   -0.004 2.00e-02 2.50e+03
        pdb=" C5    U W  27 "    0.000 2.00e-02 2.50e+03
        pdb=" C6    U W  27 "    0.003 2.00e-02 2.50e+03
  ... (remaining 997 not shown)

  Histogram of nonbonded interaction distances:
        1.88 -     2.48: 63
        2.48 -     3.09: 5215
        3.09 -     3.69: 12649
        3.69 -     4.30: 18239
        4.30 -     4.90: 28379
  Nonbonded interactions: 64545
  Sorted by model distance:
  nonbonded pdb="MG    MG P 702 "
            pdb=" O   HOH P 801 "
     model   vdw
     1.881 2.170
  nonbonded pdb=" OD1 ASN P 385 "
            pdb="MG    MG P 701 "
     model   vdw
     1.886 2.170
  nonbonded pdb=" OP1  DT T -19 "
            pdb="MG    MG P 701 "
     model   vdw
     1.900 2.170
  nonbonded pdb=" OP2  DT T -19 "
            pdb="MG    MG P 702 "
     model   vdw
     1.902 2.170
  nonbonded pdb=" O2'   G W  20 "
            pdb=" OP1   C W  21 "
     model   vdw
     1.902 3.040
  ... (remaining 64540 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.040
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.030
  Set scattering table:                    0.010
  Process input model:                     8.350
  Find NCS groups from input model:        0.020
  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:7.480
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.070
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7032
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      :  0.003   0.040   7995  Z= 0.284
  Angle     :  1.325  23.219  11376  Z= 0.670
  Chirality :  0.102   0.757   1307
  Planarity :  0.002   0.025   1000
  Dihedral  : 22.525 179.701   3645
  Min Nonbonded Distance : 1.881

Molprobity Statistics.
  All-atom Clashscore : 5.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.17 %
    Favored  : 98.83 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.74 %
    Favored  : 99.26 %
  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:  3.05 (0.36), residues: 596
  helix:  2.95 (0.29), residues: 331
  sheet:  0.24 (0.83), residues: 41
  loop :  1.06 (0.44), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG P 461 
 TYR   0.016   0.001   TYR P 283 
 PHE   0.005   0.001   PHE P 151 
 TRP   0.005   0.001   TRP P  93 
 HIS   0.002   0.001   HIS P  55 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00317 /  0.28 ( 7991)
  covalent geometry    : angle       1.32507 /  0.67 (11370)
  hydrogen bonds       : bond        0.13323 / 14.41 (  403)
  hydrogen bonds       : angle       5.40211 /  5.14 ( 1034)
  metal coordination   : bond        0.00177 /  0.11 (    4)
  metal coordination   : angle       1.14425 /  2.74 (    6)

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

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

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 128
  time to evaluate  : 0.139 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: P  238 ASP cc_start: 0.7088 (t0) cc_final: 0.6786 (t0)
REVERT: P  487 ASP cc_start: 0.7283 (m-30) cc_final: 0.7036 (m-30)
REVERT: P  574 GLU cc_start: 0.7050 (tp30) cc_final: 0.6737 (tp30)
  outliers start: 0
  outliers final: 1
  residues processed: 128
  average time/residue: 0.5359
  time to fit residues: 71.9650
Evaluate side-chains
  119 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 118
  time to evaluate  : 0.126 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue  577 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    0.2980
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    6.9990
   chunk 45 optimal weight:    0.7980
   chunk 27 optimal weight:    0.5980
   overall best weight:    0.9182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
P  35 ASN
P 129 GLN
P 378 ASN
P 393 GLN
P 396 ASN
P 482 GLN
P 517 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4431 r_free = 0.4431 target = 0.192373 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4188 r_free = 0.4188 target = 0.169007 restraints weight = 11401.191|
|-----------------------------------------------------------------------------|
r_work (start): 0.4182 rms_B_bonded: 1.33
r_work: 0.4088 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3975 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.3975
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7291
moved from start:          0.1636

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   7995  Z= 0.224
  Angle     :  0.779  16.344  11376  Z= 0.425
  Chirality :  0.057   0.577   1307
  Planarity :  0.005   0.038   1000
  Dihedral  : 25.678 175.034   2411
  Min Nonbonded Distance : 1.806

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.67 %
    Favored  : 99.33 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  :  9.39 %
    Favored  : 88.21 %
  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:  2.02 (0.34), residues: 596
  helix:  1.96 (0.28), residues: 339
  sheet:  0.31 (0.80), residues: 41
  loop :  0.70 (0.43), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG P 407 
 TYR   0.015   0.002   TYR P 283 
 PHE   0.017   0.002   PHE P  62 
 TRP   0.011   0.002   TRP P 570 
 HIS   0.008   0.002   HIS P 566 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00445 /  0.22 ( 7991)
  covalent geometry    : angle       0.77385 /  0.42 (11370)
  hydrogen bonds       : bond        0.06122 /  6.55 (  403)
  hydrogen bonds       : angle       4.45974 /  4.36 ( 1034)
  metal coordination   : bond        0.01018 /  0.88 (    4)
  metal coordination   : angle       4.01363 /  7.72 (    6)

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

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

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 120
  time to evaluate  : 0.214 
Fit side-chains
   revert: symmetry clash
REVERT: P   32 PHE cc_start: 0.8211 (m-80) cc_final: 0.7942 (m-80)
REVERT: P  238 ASP cc_start: 0.7276 (t0) cc_final: 0.6952 (t0)
REVERT: P  284 GLN cc_start: 0.8161 (mt0) cc_final: 0.7778 (mt0)
REVERT: P  362 LYS cc_start: 0.7326 (OUTLIER) cc_final: 0.7011 (mtmt)
REVERT: P  487 ASP cc_start: 0.7452 (m-30) cc_final: 0.7176 (m-30)
REVERT: P  574 GLU cc_start: 0.7208 (tp30) cc_final: 0.6861 (tp30)
REVERT: P  602 TYR cc_start: 0.8082 (m-80) cc_final: 0.7871 (m-80)
  outliers start: 13
  outliers final: 5
  residues processed: 122
  average time/residue: 0.5000
  time to fit residues: 64.2988
Evaluate side-chains
  123 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 117
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue  327 THR
Chi-restraints excluded: chain P residue  362 LYS
Chi-restraints excluded: chain P residue  545 SER
Chi-restraints excluded: chain P residue  563 THR
Chi-restraints excluded: chain P residue  577 ILE
Chi-restraints excluded: chain P residue  629 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 36 optimal weight:    0.0970
   chunk 66 optimal weight:    7.9990
   chunk 69 optimal weight:    8.9990
   chunk 60 optimal weight:    0.2980
   chunk 46 optimal weight:    0.7980
   chunk 12 optimal weight:    0.5980
   chunk 0 optimal weight:   10.0000
   chunk 43 optimal weight:    0.0040
   chunk 44 optimal weight:    0.9980
   chunk 58 optimal weight:    0.7980
   chunk 19 optimal weight:    3.9990
   overall best weight:    0.3590

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
P  35 ASN
P 378 ASN
P 393 GLN
P 396 ASN
P 482 GLN
P 517 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4445 r_free = 0.4445 target = 0.193714 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4208 r_free = 0.4208 target = 0.170649 restraints weight = 11317.174|
|-----------------------------------------------------------------------------|
r_work (start): 0.4196 rms_B_bonded: 1.29
r_work: 0.4105 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3995 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.3995
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7250
moved from start:          0.1846

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7995  Z= 0.142
  Angle     :  0.629   8.711  11376  Z= 0.353
  Chirality :  0.048   0.550   1307
  Planarity :  0.004   0.042   1000
  Dihedral  : 25.360 177.595   2411
  Min Nonbonded Distance : 1.877

Molprobity Statistics.
  All-atom Clashscore : 7.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.67 %
    Favored  : 99.33 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 10.68 %
    Favored  : 86.74 %
  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:  2.02 (0.34), residues: 596
  helix:  2.00 (0.28), residues: 337
  sheet:  0.19 (0.81), residues: 41
  loop :  0.67 (0.42), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG P 407 
 TYR   0.016   0.002   TYR P 283 
 PHE   0.012   0.001   PHE P 630 
 TRP   0.009   0.001   TRP P 570 
 HIS   0.005   0.001   HIS P 566 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00258 /  0.14 ( 7991)
  covalent geometry    : angle       0.62712 /  0.35 (11370)
  hydrogen bonds       : bond        0.05349 /  5.70 (  403)
  hydrogen bonds       : angle       4.26677 /  4.15 ( 1034)
  metal coordination   : bond        0.00472 /  0.43 (    4)
  metal coordination   : angle       2.36177 /  4.92 (    6)

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

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

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 115
  time to evaluate  : 0.135 
Fit side-chains
   revert: symmetry clash
REVERT: P  238 ASP cc_start: 0.7277 (t0) cc_final: 0.6947 (t0)
REVERT: P  362 LYS cc_start: 0.7287 (OUTLIER) cc_final: 0.6953 (mtmt)
REVERT: P  445 MET cc_start: 0.4125 (OUTLIER) cc_final: 0.3783 (tmm)
REVERT: P  483 LYS cc_start: 0.8089 (OUTLIER) cc_final: 0.7404 (tppt)
REVERT: P  487 ASP cc_start: 0.7362 (m-30) cc_final: 0.7126 (m-30)
REVERT: P  574 GLU cc_start: 0.7195 (tp30) cc_final: 0.6841 (tp30)
REVERT: P  602 TYR cc_start: 0.8101 (m-80) cc_final: 0.7849 (m-80)
REVERT: P  606 ASP cc_start: 0.7489 (m-30) cc_final: 0.7231 (m-30)
  outliers start: 14
  outliers final: 6
  residues processed: 119
  average time/residue: 0.5275
  time to fit residues: 66.0637
Evaluate side-chains
  118 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 109
  time to evaluate  : 0.188 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue   80 ILE
Chi-restraints excluded: chain P residue  323 GLU
Chi-restraints excluded: chain P residue  327 THR
Chi-restraints excluded: chain P residue  362 LYS
Chi-restraints excluded: chain P residue  389 ILE
Chi-restraints excluded: chain P residue  445 MET
Chi-restraints excluded: chain P residue  483 LYS
Chi-restraints excluded: chain P residue  577 ILE
Chi-restraints excluded: chain P residue  629 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 13 optimal weight:    0.7980
   chunk 29 optimal weight:    1.9990
   chunk 59 optimal weight:    0.5980
   chunk 19 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9990
   chunk 28 optimal weight:    0.5980
   chunk 30 optimal weight:    0.5980
   chunk 53 optimal weight:    0.0980
   chunk 27 optimal weight:    0.0020
   chunk 8 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   overall best weight:    0.3788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
P  35 ASN
P 378 ASN
P 393 GLN
P 396 ASN
P 482 GLN
P 517 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4441 r_free = 0.4441 target = 0.193481 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4202 r_free = 0.4202 target = 0.170230 restraints weight = 11515.613|
|-----------------------------------------------------------------------------|
r_work (start): 0.4193 rms_B_bonded: 1.31
r_work: 0.4102 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3993 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.3993
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7257
moved from start:          0.2044

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   7995  Z= 0.137
  Angle     :  0.598   8.968  11376  Z= 0.336
  Chirality :  0.045   0.424   1307
  Planarity :  0.004   0.042   1000
  Dihedral  : 25.200 175.021   2411
  Min Nonbonded Distance : 1.863

Molprobity Statistics.
  All-atom Clashscore : 7.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.84 %
    Favored  : 99.16 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 12.15 %
    Favored  : 85.27 %
  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:  1.92 (0.34), residues: 596
  helix:  2.02 (0.28), residues: 337
  sheet: -0.09 (0.81), residues: 41
  loop :  0.48 (0.41), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG P 374 
 TYR   0.019   0.001   TYR P 134 
 PHE   0.014   0.001   PHE P 630 
 TRP   0.009   0.001   TRP P 570 
 HIS   0.005   0.001   HIS P 566 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00245 /  0.14 ( 7991)
  covalent geometry    : angle       0.59530 /  0.34 (11370)
  hydrogen bonds       : bond        0.05061 /  5.37 (  403)
  hydrogen bonds       : angle       4.15302 /  4.06 ( 1034)
  metal coordination   : bond        0.00485 /  0.44 (    4)
  metal coordination   : angle       2.42343 /  5.61 (    6)

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

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

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 113
  time to evaluate  : 0.209 
Fit side-chains
   revert: symmetry clash
REVERT: P  238 ASP cc_start: 0.7335 (t0) cc_final: 0.7027 (t0)
REVERT: P  362 LYS cc_start: 0.7442 (OUTLIER) cc_final: 0.7165 (mtmt)
REVERT: P  445 MET cc_start: 0.4211 (OUTLIER) cc_final: 0.3853 (tmm)
REVERT: P  483 LYS cc_start: 0.8127 (tppt) cc_final: 0.7464 (tppt)
REVERT: P  487 ASP cc_start: 0.7366 (m-30) cc_final: 0.7128 (m-30)
REVERT: P  574 GLU cc_start: 0.7185 (tp30) cc_final: 0.6806 (tp30)
REVERT: P  602 TYR cc_start: 0.8129 (m-80) cc_final: 0.7829 (m-80)
  outliers start: 14
  outliers final: 5
  residues processed: 116
  average time/residue: 0.5167
  time to fit residues: 63.0902
Evaluate side-chains
  117 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 110
  time to evaluate  : 0.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue   80 ILE
Chi-restraints excluded: chain P residue  327 THR
Chi-restraints excluded: chain P residue  362 LYS
Chi-restraints excluded: chain P residue  445 MET
Chi-restraints excluded: chain P residue  545 SER
Chi-restraints excluded: chain P residue  577 ILE
Chi-restraints excluded: chain P residue  629 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 10 optimal weight:    0.5980
   chunk 51 optimal weight:    0.9980
   chunk 47 optimal weight:    0.9990
   chunk 22 optimal weight:    0.9990
   chunk 28 optimal weight:    0.0470
   chunk 58 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 1 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   chunk 69 optimal weight:    9.9990
   chunk 25 optimal weight:    3.9990
   overall best weight:    0.7282

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
P  35 ASN
P 129 GLN
P 378 ASN
P 393 GLN
P 396 ASN
P 482 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4406 r_free = 0.4406 target = 0.190022 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4160 r_free = 0.4160 target = 0.166466 restraints weight = 11260.679|
|-----------------------------------------------------------------------------|
r_work (start): 0.4151 rms_B_bonded: 1.29
r_work: 0.4060 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3950 rms_B_bonded: 3.91 restraints_weight: 0.2500
r_work (final): 0.3950
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7342
moved from start:          0.2400

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7995  Z= 0.175
  Angle     :  0.642   8.348  11376  Z= 0.353
  Chirality :  0.047   0.313   1307
  Planarity :  0.005   0.041   1000
  Dihedral  : 25.226 172.083   2411
  Min Nonbonded Distance : 1.832

Molprobity Statistics.
  All-atom Clashscore : 7.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.50 %
    Favored  : 99.50 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 12.89 %
    Favored  : 84.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.49 (0.34), residues: 596
  helix:  1.69 (0.28), residues: 338
  sheet: -0.02 (0.80), residues: 41
  loop :  0.21 (0.41), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG P 292 
 TYR   0.022   0.002   TYR P 134 
 PHE   0.019   0.002   PHE P  62 
 TRP   0.013   0.001   TRP P 570 
 HIS   0.006   0.001   HIS P 566 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00345 /  0.17 ( 7991)
  covalent geometry    : angle       0.63935 /  0.35 (11370)
  hydrogen bonds       : bond        0.05405 /  5.89 (  403)
  hydrogen bonds       : angle       4.20946 /  4.18 ( 1034)
  metal coordination   : bond        0.00664 /  0.52 (    4)
  metal coordination   : angle       2.62195 /  6.35 (    6)

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

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

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 119
  time to evaluate  : 0.160 
Fit side-chains
REVERT: P   62 PHE cc_start: 0.5688 (t80) cc_final: 0.4075 (t80)
REVERT: P  238 ASP cc_start: 0.7464 (t0) cc_final: 0.7247 (t0)
REVERT: P  388 ASP cc_start: 0.7779 (m-30) cc_final: 0.7576 (m-30)
REVERT: P  483 LYS cc_start: 0.8183 (tppt) cc_final: 0.7493 (tppt)
REVERT: P  487 ASP cc_start: 0.7372 (m-30) cc_final: 0.7124 (m-30)
REVERT: P  574 GLU cc_start: 0.7214 (tp30) cc_final: 0.6882 (tp30)
REVERT: P  602 TYR cc_start: 0.8176 (m-80) cc_final: 0.7880 (m-80)
  outliers start: 15
  outliers final: 8
  residues processed: 124
  average time/residue: 0.5041
  time to fit residues: 65.7223
Evaluate side-chains
  125 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 117
  time to evaluate  : 0.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue   80 ILE
Chi-restraints excluded: chain P residue  327 THR
Chi-restraints excluded: chain P residue  419 ARG
Chi-restraints excluded: chain P residue  486 SER
Chi-restraints excluded: chain P residue  534 ILE
Chi-restraints excluded: chain P residue  545 SER
Chi-restraints excluded: chain P residue  577 ILE
Chi-restraints excluded: chain P residue  629 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 8 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9980
   chunk 1 optimal weight:    2.9990
   chunk 12 optimal weight:    0.7980
   chunk 47 optimal weight:    0.6980
   chunk 56 optimal weight:    1.9990
   chunk 22 optimal weight:    0.6980
   chunk 26 optimal weight:    1.9990
   chunk 61 optimal weight:    6.9990
   chunk 3 optimal weight:    0.7980
   chunk 33 optimal weight:    0.8980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
P  35 ASN
P 378 ASN
P 393 GLN
P 396 ASN
P 482 GLN
P 517 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4396 r_free = 0.4396 target = 0.189157 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4149 r_free = 0.4149 target = 0.165531 restraints weight = 11255.519|
|-----------------------------------------------------------------------------|
r_work (start): 0.4138 rms_B_bonded: 1.28
r_work: 0.4048 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.3938 rms_B_bonded: 3.88 restraints_weight: 0.2500
r_work (final): 0.3938
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7355
moved from start:          0.2585

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   7995  Z= 0.179
  Angle     :  0.635   8.045  11376  Z= 0.351
  Chirality :  0.046   0.312   1307
  Planarity :  0.005   0.045   1000
  Dihedral  : 25.214 171.493   2411
  Min Nonbonded Distance : 1.825

Molprobity Statistics.
  All-atom Clashscore : 8.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.84 %
    Favored  : 99.16 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 14.00 %
    Favored  : 83.98 %
  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:  1.31 (0.34), residues: 596
  helix:  1.56 (0.28), residues: 338
  sheet: -0.08 (0.82), residues: 41
  loop :  0.09 (0.40), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG P 407 
 TYR   0.019   0.002   TYR P 283 
 PHE   0.018   0.002   PHE P  62 
 TRP   0.011   0.001   TRP P 570 
 HIS   0.005   0.001   HIS P 566 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00356 /  0.18 ( 7991)
  covalent geometry    : angle       0.63188 /  0.35 (11370)
  hydrogen bonds       : bond        0.05278 /  5.68 (  403)
  hydrogen bonds       : angle       4.25125 /  4.18 ( 1034)
  metal coordination   : bond        0.00729 /  0.61 (    4)
  metal coordination   : angle       2.84894 /  7.01 (    6)

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

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

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 113
  time to evaluate  : 0.213 
Fit side-chains
REVERT: P   62 PHE cc_start: 0.5646 (t80) cc_final: 0.3944 (t80)
REVERT: P  238 ASP cc_start: 0.7522 (t0) cc_final: 0.7253 (t0)
REVERT: P  362 LYS cc_start: 0.7504 (OUTLIER) cc_final: 0.7273 (mtmt)
REVERT: P  388 ASP cc_start: 0.7789 (m-30) cc_final: 0.7573 (m-30)
REVERT: P  483 LYS cc_start: 0.8182 (tppt) cc_final: 0.7480 (tppt)
REVERT: P  487 ASP cc_start: 0.7384 (m-30) cc_final: 0.7124 (m-30)
REVERT: P  574 GLU cc_start: 0.7205 (tp30) cc_final: 0.6866 (tp30)
REVERT: P  602 TYR cc_start: 0.8198 (m-80) cc_final: 0.7907 (m-80)
  outliers start: 11
  outliers final: 5
  residues processed: 117
  average time/residue: 0.4751
  time to fit residues: 58.6422
Evaluate side-chains
  120 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 114
  time to evaluate  : 0.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue  327 THR
Chi-restraints excluded: chain P residue  362 LYS
Chi-restraints excluded: chain P residue  486 SER
Chi-restraints excluded: chain P residue  545 SER
Chi-restraints excluded: chain P residue  577 ILE
Chi-restraints excluded: chain P residue  629 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 37 optimal weight:    0.3980
   chunk 34 optimal weight:    0.9980
   chunk 61 optimal weight:    6.9990
   chunk 56 optimal weight:    0.8980
   chunk 20 optimal weight:    0.5980
   chunk 48 optimal weight:    1.9990
   chunk 70 optimal weight:    5.9990
   chunk 66 optimal weight:    7.9990
   chunk 16 optimal weight:    0.4980
   chunk 5 optimal weight:    0.9980
   chunk 38 optimal weight:    0.5980
   overall best weight:    0.5980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
P  35 ASN
P 378 ASN
P 396 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4406 r_free = 0.4406 target = 0.189662 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.165781 restraints weight = 11123.084|
|-----------------------------------------------------------------------------|
r_work (start): 0.4140 rms_B_bonded: 1.26
r_work: 0.4046 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3932 rms_B_bonded: 3.91 restraints_weight: 0.2500
r_work (final): 0.3932
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7352
moved from start:          0.2670

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7995  Z= 0.159
  Angle     :  0.646  14.574  11376  Z= 0.350
  Chirality :  0.045   0.311   1307
  Planarity :  0.005   0.045   1000
  Dihedral  : 25.200 171.970   2411
  Min Nonbonded Distance : 1.836

Molprobity Statistics.
  All-atom Clashscore : 8.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.84 %
    Favored  : 99.16 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 14.36 %
    Favored  : 83.43 %
  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:  1.15 (0.33), residues: 596
  helix:  1.38 (0.28), residues: 338
  sheet: -0.05 (0.82), residues: 41
  loop :  0.08 (0.41), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG P 374 
 TYR   0.018   0.002   TYR P 283 
 PHE   0.020   0.002   PHE P 516 
 TRP   0.011   0.001   TRP P 570 
 HIS   0.004   0.001   HIS P  21 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00308 /  0.16 ( 7991)
  covalent geometry    : angle       0.64345 /  0.35 (11370)
  hydrogen bonds       : bond        0.05148 /  5.50 (  403)
  hydrogen bonds       : angle       4.35567 /  4.26 ( 1034)
  metal coordination   : bond        0.00635 /  0.55 (    4)
  metal coordination   : angle       2.66984 /  6.57 (    6)

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

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

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 114
  time to evaluate  : 0.175 
Fit side-chains
REVERT: P   62 PHE cc_start: 0.5626 (t80) cc_final: 0.3877 (t80)
REVERT: P  238 ASP cc_start: 0.7542 (t0) cc_final: 0.7255 (t0)
REVERT: P  362 LYS cc_start: 0.7460 (OUTLIER) cc_final: 0.7235 (mtmt)
REVERT: P  442 MET cc_start: 0.4542 (OUTLIER) cc_final: 0.0469 (mpt)
REVERT: P  445 MET cc_start: 0.4445 (OUTLIER) cc_final: 0.4017 (tmm)
REVERT: P  483 LYS cc_start: 0.8185 (tppt) cc_final: 0.7488 (tppt)
REVERT: P  487 ASP cc_start: 0.7332 (m-30) cc_final: 0.7089 (m-30)
REVERT: P  574 GLU cc_start: 0.7200 (tp30) cc_final: 0.6651 (tp30)
REVERT: P  602 TYR cc_start: 0.8201 (m-80) cc_final: 0.7917 (m-80)
  outliers start: 12
  outliers final: 6
  residues processed: 114
  average time/residue: 0.5080
  time to fit residues: 60.7954
Evaluate side-chains
  116 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 107
  time to evaluate  : 0.177 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue   33 LEU
Chi-restraints excluded: chain P residue  327 THR
Chi-restraints excluded: chain P residue  362 LYS
Chi-restraints excluded: chain P residue  442 MET
Chi-restraints excluded: chain P residue  445 MET
Chi-restraints excluded: chain P residue  545 SER
Chi-restraints excluded: chain P residue  558 GLU
Chi-restraints excluded: chain P residue  577 ILE
Chi-restraints excluded: chain P residue  629 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 30 optimal weight:    0.0670
   chunk 36 optimal weight:    0.9980
   chunk 23 optimal weight:    0.0270
   chunk 40 optimal weight:    0.9990
   chunk 4 optimal weight:    0.5980
   chunk 59 optimal weight:    0.7980
   chunk 69 optimal weight:    8.9990
   chunk 45 optimal weight:    1.9990
   chunk 41 optimal weight:    1.9990
   chunk 67 optimal weight:    6.9990
   chunk 55 optimal weight:    0.7980
   overall best weight:    0.4576

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
P  35 ASN
P 378 ASN
P 393 GLN
P 396 ASN
P 482 GLN
P 517 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4420 r_free = 0.4420 target = 0.190892 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4165 r_free = 0.4165 target = 0.166679 restraints weight = 11254.889|
|-----------------------------------------------------------------------------|
r_work (start): 0.4158 rms_B_bonded: 1.28
r_work: 0.4063 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.3948 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.3948
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7345
moved from start:          0.2763

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   7995  Z= 0.149
  Angle     :  0.637  12.400  11376  Z= 0.347
  Chirality :  0.044   0.311   1307
  Planarity :  0.005   0.044   1000
  Dihedral  : 25.182 172.746   2411
  Min Nonbonded Distance : 1.849

Molprobity Statistics.
  All-atom Clashscore : 8.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.01 %
    Favored  : 98.99 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 14.36 %
    Favored  : 83.61 %
  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:  1.12 (0.34), residues: 596
  helix:  1.35 (0.28), residues: 338
  sheet: -0.08 (0.81), residues: 41
  loop :  0.10 (0.40), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG P 374 
 TYR   0.020   0.002   TYR P 253 
 PHE   0.018   0.002   PHE P 630 
 TRP   0.011   0.001   TRP P 570 
 HIS   0.004   0.001   HIS P  21 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00287 /  0.15 ( 7991)
  covalent geometry    : angle       0.63417 /  0.35 (11370)
  hydrogen bonds       : bond        0.05005 /  5.30 (  403)
  hydrogen bonds       : angle       4.35381 /  4.23 ( 1034)
  metal coordination   : bond        0.00526 /  0.46 (    4)
  metal coordination   : angle       2.50933 /  6.14 (    6)

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

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

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 110
  time to evaluate  : 0.137 
Fit side-chains
REVERT: P   62 PHE cc_start: 0.5633 (t80) cc_final: 0.3932 (t80)
REVERT: P  238 ASP cc_start: 0.7530 (t0) cc_final: 0.7246 (t0)
REVERT: P  442 MET cc_start: 0.4497 (OUTLIER) cc_final: 0.0389 (mpt)
REVERT: P  445 MET cc_start: 0.4435 (OUTLIER) cc_final: 0.4018 (tmm)
REVERT: P  483 LYS cc_start: 0.8194 (tppt) cc_final: 0.7509 (tppt)
REVERT: P  487 ASP cc_start: 0.7343 (m-30) cc_final: 0.7100 (m-30)
REVERT: P  574 GLU cc_start: 0.7180 (tp30) cc_final: 0.6765 (tp30)
REVERT: P  602 TYR cc_start: 0.8191 (m-80) cc_final: 0.7916 (m-80)
  outliers start: 11
  outliers final: 7
  residues processed: 111
  average time/residue: 0.5525
  time to fit residues: 64.4250
Evaluate side-chains
  115 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 106
  time to evaluate  : 0.186 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue   33 LEU
Chi-restraints excluded: chain P residue  327 THR
Chi-restraints excluded: chain P residue  395 SER
Chi-restraints excluded: chain P residue  442 MET
Chi-restraints excluded: chain P residue  445 MET
Chi-restraints excluded: chain P residue  545 SER
Chi-restraints excluded: chain P residue  558 GLU
Chi-restraints excluded: chain P residue  577 ILE
Chi-restraints excluded: chain P residue  629 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 17 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 10 optimal weight:    2.9990
   chunk 64 optimal weight:    5.9990
   chunk 50 optimal weight:    0.5980
   chunk 12 optimal weight:    0.9980
   chunk 57 optimal weight:    0.8980
   chunk 30 optimal weight:    1.9990
   chunk 25 optimal weight:    2.9990
   chunk 43 optimal weight:    0.9990
   chunk 51 optimal weight:    0.6980
   overall best weight:    0.8382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
P  35 ASN
P 378 ASN
P 393 GLN
P 396 ASN
P 482 GLN
P 517 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4389 r_free = 0.4389 target = 0.188029 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4130 r_free = 0.4130 target = 0.163692 restraints weight = 11047.723|
|-----------------------------------------------------------------------------|
r_work (start): 0.4123 rms_B_bonded: 1.25
r_work: 0.4027 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.3912 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.3912
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7402
moved from start:          0.2980

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.081   7995  Z= 0.198
  Angle     :  0.684  11.187  11376  Z= 0.370
  Chirality :  0.047   0.311   1307
  Planarity :  0.005   0.055   1000
  Dihedral  : 25.127 169.885   2411
  Min Nonbonded Distance : 1.814

Molprobity Statistics.
  All-atom Clashscore : 9.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 14.92 %
    Favored  : 82.87 %
  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:  0.79 (0.33), residues: 596
  helix:  1.03 (0.27), residues: 338
  sheet:  0.13 (0.81), residues: 41
  loop : -0.04 (0.40), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG P 407 
 TYR   0.019   0.002   TYR P 283 
 PHE   0.020   0.002   PHE P 516 
 TRP   0.014   0.001   TRP P 570 
 HIS   0.006   0.001   HIS P 566 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00407 /  0.20 ( 7991)
  covalent geometry    : angle       0.68016 /  0.37 (11370)
  hydrogen bonds       : bond        0.05601 /  6.08 (  403)
  hydrogen bonds       : angle       4.51657 /  4.42 ( 1034)
  metal coordination   : bond        0.00803 /  0.63 (    4)
  metal coordination   : angle       3.29554 /  8.08 (    6)

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

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

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 110
  time to evaluate  : 0.169 
Fit side-chains
REVERT: P  238 ASP cc_start: 0.7539 (t0) cc_final: 0.7259 (t0)
REVERT: P  442 MET cc_start: 0.4656 (OUTLIER) cc_final: 0.0516 (mpt)
REVERT: P  483 LYS cc_start: 0.8173 (tppt) cc_final: 0.7491 (tppt)
REVERT: P  487 ASP cc_start: 0.7369 (m-30) cc_final: 0.7117 (m-30)
REVERT: P  574 GLU cc_start: 0.7224 (tp30) cc_final: 0.6866 (tp30)
REVERT: P  602 TYR cc_start: 0.8203 (m-80) cc_final: 0.7965 (m-80)
  outliers start: 12
  outliers final: 8
  residues processed: 114
  average time/residue: 0.5395
  time to fit residues: 64.5942
Evaluate side-chains
  115 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 106
  time to evaluate  : 0.129 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue   33 LEU
Chi-restraints excluded: chain P residue  141 THR
Chi-restraints excluded: chain P residue  327 THR
Chi-restraints excluded: chain P residue  395 SER
Chi-restraints excluded: chain P residue  442 MET
Chi-restraints excluded: chain P residue  486 SER
Chi-restraints excluded: chain P residue  545 SER
Chi-restraints excluded: chain P residue  558 GLU
Chi-restraints excluded: chain P residue  577 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 65 optimal weight:    4.9990
   chunk 2 optimal weight:    0.0670
   chunk 54 optimal weight:    0.6980
   chunk 28 optimal weight:    1.9990
   chunk 56 optimal weight:    1.9990
   chunk 42 optimal weight:    0.8980
   chunk 48 optimal weight:    0.9980
   chunk 22 optimal weight:    0.0770
   chunk 70 optimal weight:    5.9990
   chunk 10 optimal weight:    2.9990
   overall best weight:    0.5476

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
P  35 ASN
P 378 ASN
P 396 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4405 r_free = 0.4405 target = 0.189556 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.4146 r_free = 0.4146 target = 0.165156 restraints weight = 11244.207|
|-----------------------------------------------------------------------------|
r_work (start): 0.4139 rms_B_bonded: 1.28
r_work: 0.4042 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3927 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.3927
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7376
moved from start:          0.3033

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   7995  Z= 0.157
  Angle     :  0.642  11.423  11376  Z= 0.351
  Chirality :  0.045   0.309   1307
  Planarity :  0.005   0.044   1000
  Dihedral  : 24.984 171.247   2411
  Min Nonbonded Distance : 1.858

Molprobity Statistics.
  All-atom Clashscore : 8.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.67 %
    Favored  : 99.33 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  : 16.76 %
    Favored  : 82.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.98 (0.33), residues: 596
  helix:  1.25 (0.28), residues: 338
  sheet:  0.13 (0.82), residues: 41
  loop : -0.06 (0.40), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG P 374 
 TYR   0.018   0.002   TYR P 283 
 PHE   0.021   0.002   PHE P 630 
 TRP   0.010   0.001   TRP P 570 
 HIS   0.005   0.001   HIS P  21 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00308 /  0.16 ( 7991)
  covalent geometry    : angle       0.63876 /  0.35 (11370)
  hydrogen bonds       : bond        0.05084 /  5.34 (  403)
  hydrogen bonds       : angle       4.35667 /  4.29 ( 1034)
  metal coordination   : bond        0.00597 /  0.52 (    4)
  metal coordination   : angle       2.96642 /  7.32 (    6)

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

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

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 108
  time to evaluate  : 0.216 
Fit side-chains
REVERT: P  238 ASP cc_start: 0.7543 (t0) cc_final: 0.7265 (t0)
REVERT: P  442 MET cc_start: 0.4568 (OUTLIER) cc_final: 0.0474 (mpt)
REVERT: P  483 LYS cc_start: 0.8181 (tppt) cc_final: 0.7508 (tppt)
REVERT: P  487 ASP cc_start: 0.7350 (m-30) cc_final: 0.7105 (m-30)
REVERT: P  574 GLU cc_start: 0.7204 (tp30) cc_final: 0.6999 (tp30)
REVERT: P  602 TYR cc_start: 0.8199 (m-80) cc_final: 0.7975 (m-80)
  outliers start: 6
  outliers final: 4
  residues processed: 109
  average time/residue: 0.5240
  time to fit residues: 60.1252
Evaluate side-chains
  110 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 105
  time to evaluate  : 0.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue  327 THR
Chi-restraints excluded: chain P residue  442 MET
Chi-restraints excluded: chain P residue  486 SER
Chi-restraints excluded: chain P residue  545 SER
Chi-restraints excluded: chain P residue  577 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 12 optimal weight:    0.7980
   chunk 35 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 6 optimal weight:    3.9990
   chunk 1 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9990
   chunk 40 optimal weight:    0.8980
   chunk 2 optimal weight:    0.0770
   chunk 68 optimal weight:   50.0000
   chunk 16 optimal weight:    6.9990
   chunk 17 optimal weight:    1.9990
   overall best weight:    0.9542

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
P  35 ASN
P  58 HIS
P 378 ASN
P 393 GLN
P 396 ASN
P 482 GLN
P 517 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4380 r_free = 0.4380 target = 0.187108 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.4118 r_free = 0.4118 target = 0.162623 restraints weight = 11106.342|
|-----------------------------------------------------------------------------|
r_work (start): 0.4110 rms_B_bonded: 1.27
r_work: 0.4012 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.3896 rms_B_bonded: 3.91 restraints_weight: 0.2500
r_work (final): 0.3896
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7432
moved from start:          0.3240

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   7995  Z= 0.215
  Angle     :  0.687  11.048  11376  Z= 0.374
  Chirality :  0.048   0.312   1307
  Planarity :  0.005   0.046   1000
  Dihedral  : 24.908 168.635   2411
  Min Nonbonded Distance : 1.845

Molprobity Statistics.
  All-atom Clashscore : 9.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.34 %
    Favored  : 98.66 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 17.13 %
    Favored  : 81.58 %
  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:  0.67 (0.33), residues: 596
  helix:  0.95 (0.27), residues: 339
  sheet:  0.15 (0.83), residues: 41
  loop : -0.15 (0.41), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG P 374 
 TYR   0.019   0.003   TYR P 283 
 PHE   0.021   0.002   PHE P 630 
 TRP   0.015   0.002   TRP P 570 
 HIS   0.006   0.001   HIS P 566 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00443 /  0.21 ( 7991)
  covalent geometry    : angle       0.68314 /  0.37 (11370)
  hydrogen bonds       : bond        0.05657 /  6.09 (  403)
  hydrogen bonds       : angle       4.48362 /  4.44 ( 1034)
  metal coordination   : bond        0.00808 /  0.64 (    4)
  metal coordination   : angle       3.40967 /  8.42 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2682.88 seconds
wall clock time: 46 minutes 13.73 seconds (2773.73 seconds total)