Starting phenix.real_space_refine
on Thu Jul  2 08:09:35 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8gkh_40184/07_2026/8gkh_40184_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8gkh_40184/07_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_40184/07_2026/8gkh_40184_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8gkh_40184/07_2026/8gkh_40184_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8gkh_40184/07_2026/8gkh_40184.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8gkh_40184/07_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-dev-6108/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: 1.24, per 1000 atoms: 0.16
  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: 0.49
  Conformation dependent library (CDL) restraints added in 218.4 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: 0.74
  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: 1.21

  Time building geometry restraints manager: 0.70 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=" 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=" O3'   C W  19 "
        pdb=" C3'   C W  19 "
        pdb=" C2'   C W  19 "
      ideal   model   delta    sigma   weight residual
     109.50  116.88   -7.38 1.50e+00 4.44e-01 2.42e+01
  angle pdb=" C4'   U W  76 "
        pdb=" C3'   U W  76 "
        pdb=" O3'   U W  76 "
      ideal   model   delta    sigma   weight residual
     109.40  116.64   -7.24 1.50e+00 4.44e-01 2.33e+01
  angle pdb=" N3   DT T -10 "
        pdb=" C4   DT T -10 "
        pdb=" O4   DT T -10 "
      ideal   model   delta    sigma   weight residual
     119.90  122.60   -2.70 6.00e-01 2.78e+00 2.02e+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: 1211
       0.151 -    0.303: 44
       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:             1.690
  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:         0.020
  Set scattering table:                    0.030
  Process input model:                     7.480
  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:6.080
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.480
-------------------------------------------------------------------------------
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= 0.279
  Angle     :  1.298  23.219  11376  Z= 0.612
  Chirality :  0.100   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        0.00315 /  0.28 ( 7991)
  covalent geometry    : angle       1.29829 /  0.61 (11370)
  hydrogen bonds       : bond        0.13323 / 14.40 (  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  : 0.226 
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: 0.7050 (m-30)
REVERT: P  574 GLU cc_start: 0.7050 (tp30) cc_final: 0.6738 (tp30)
  outliers start: 0
  outliers final: 1
  residues processed: 128
  average time/residue: 0.6931
  time to fit residues: 92.8708
Evaluate side-chains
  121 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 120
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
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:    0.8980
   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:    0.6980
   chunk 27 optimal weight:    0.5980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
P  35 ASN
P 129 GLN
P 259 GLN
P 378 ASN
P 393 GLN
P 396 ASN
P 482 GLN
P 517 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4448 r_free = 0.4448 target = 0.193972 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4210 r_free = 0.4210 target = 0.170853 restraints weight = 11458.843|
|-----------------------------------------------------------------------------|
r_work (start): 0.4204 rms_B_bonded: 1.32
r_work: 0.4111 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3999 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.3999
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7249
moved from start:          0.1620

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063   7995  Z= 0.197
  Angle     :  0.692   8.449  11376  Z= 0.401
  Chirality :  0.047   0.297   1307
  Planarity :  0.005   0.038   1000
  Dihedral  : 25.805 177.909   2411
  Min Nonbonded Distance : 1.799

Molprobity Statistics.
  All-atom Clashscore : 6.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.67 %
    Favored  : 99.33 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  :  9.21 %
    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:  2.21 (0.35), residues: 596
  helix:  2.11 (0.28), residues: 337
  sheet:  0.31 (0.80), residues: 41
  loop :  0.81 (0.43), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG P 564 
 TYR   0.015   0.002   TYR P 283 
 PHE   0.016   0.002   PHE P 400 
 TRP   0.010   0.002   TRP P 570 
 HIS   0.007   0.001   HIS P 566 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00389 /  0.20 ( 7991)
  covalent geometry    : angle       0.68586 /  0.40 (11370)
  hydrogen bonds       : bond        0.05968 /  6.35 (  403)
  hydrogen bonds       : angle       4.36837 /  4.27 ( 1034)
  metal coordination   : bond        0.00859 /  0.73 (    4)
  metal coordination   : angle       4.17932 /  7.48 (    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
  135 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 121
  time to evaluate  : 0.218 
Fit side-chains
   revert: symmetry clash
REVERT: P  238 ASP cc_start: 0.7259 (t0) cc_final: 0.6940 (t0)
REVERT: P  362 LYS cc_start: 0.7280 (OUTLIER) cc_final: 0.6973 (mtmt)
REVERT: P  445 MET cc_start: 0.4108 (OUTLIER) cc_final: 0.3784 (tmm)
REVERT: P  483 LYS cc_start: 0.8132 (tppt) cc_final: 0.7658 (tppt)
REVERT: P  574 GLU cc_start: 0.7186 (tp30) cc_final: 0.6852 (tp30)
  outliers start: 14
  outliers final: 6
  residues processed: 123
  average time/residue: 0.6076
  time to fit residues: 78.6365
Evaluate side-chains
  127 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 119
  time to evaluate  : 0.249 
-------------------------------------------------------------------------------
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  382 ILE
Chi-restraints excluded: chain P residue  445 MET
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:    0.5980
   chunk 66 optimal weight:    5.9990
   chunk 69 optimal weight:    6.9990
   chunk 60 optimal weight:    0.7980
   chunk 46 optimal weight:    1.9990
   chunk 12 optimal weight:    0.8980
   chunk 0 optimal weight:   10.0000
   chunk 43 optimal weight:    0.9980
   chunk 44 optimal weight:    0.6980
   chunk 58 optimal weight:    0.5980
   chunk 19 optimal weight:    4.9990
   overall best weight:    0.7180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
P  35 ASN
P 321 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 = 0.4422 r_free = 0.4422 target = 0.191445 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4177 r_free = 0.4177 target = 0.167911 restraints weight = 11278.677|
|-----------------------------------------------------------------------------|
r_work (start): 0.4168 rms_B_bonded: 1.30
r_work: 0.4076 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.3966 rms_B_bonded: 3.93 restraints_weight: 0.2500
r_work (final): 0.3966
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7304
moved from start:          0.2048

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   7995  Z= 0.179
  Angle     :  0.629  10.411  11376  Z= 0.362
  Chirality :  0.045   0.284   1307
  Planarity :  0.005   0.039   1000
  Dihedral  : 25.485 179.209   2411
  Min Nonbonded Distance : 1.820

Molprobity Statistics.
  All-atom Clashscore : 6.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.84 %
    Favored  : 99.16 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 10.87 %
    Favored  : 86.56 %
  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:  1.79 (0.34), residues: 596
  helix:  1.82 (0.28), residues: 337
  sheet:  0.07 (0.80), residues: 41
  loop :  0.56 (0.42), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG P 564 
 TYR   0.019   0.002   TYR P 134 
 PHE   0.015   0.002   PHE P  62 
 TRP   0.011   0.001   TRP P 570 
 HIS   0.007   0.001   HIS P 566 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00355 /  0.18 ( 7991)
  covalent geometry    : angle       0.62664 /  0.36 (11370)
  hydrogen bonds       : bond        0.05550 /  6.05 (  403)
  hydrogen bonds       : angle       4.31308 /  4.22 ( 1034)
  metal coordination   : bond        0.00515 /  0.44 (    4)
  metal coordination   : angle       2.60812 /  6.07 (    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
  134 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 120
  time to evaluate  : 0.216 
Fit side-chains
   revert: symmetry clash
REVERT: P  238 ASP cc_start: 0.7358 (t0) cc_final: 0.7028 (t0)
REVERT: P  284 GLN cc_start: 0.8209 (mt0) cc_final: 0.7813 (mt0)
REVERT: P  362 LYS cc_start: 0.7449 (OUTLIER) cc_final: 0.7166 (mtmt)
REVERT: P  388 ASP cc_start: 0.7788 (m-30) cc_final: 0.7529 (m-30)
REVERT: P  445 MET cc_start: 0.4277 (OUTLIER) cc_final: 0.3918 (tmm)
REVERT: P  483 LYS cc_start: 0.8051 (tppt) cc_final: 0.7751 (tppt)
REVERT: P  574 GLU cc_start: 0.7197 (tp30) cc_final: 0.6890 (tp30)
REVERT: P  580 VAL cc_start: 0.8130 (t) cc_final: 0.7923 (t)
  outliers start: 14
  outliers final: 7
  residues processed: 123
  average time/residue: 0.6322
  time to fit residues: 81.7477
Evaluate side-chains
  119 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 110
  time to evaluate  : 0.208 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue   80 ILE
Chi-restraints excluded: chain P residue  129 GLN
Chi-restraints excluded: chain P residue  327 THR
Chi-restraints excluded: chain P residue  362 LYS
Chi-restraints excluded: chain P residue  419 ARG
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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 13 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 59 optimal weight:    0.9980
   chunk 19 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9980
   chunk 28 optimal weight:    1.9990
   chunk 30 optimal weight:    0.7980
   chunk 53 optimal weight:    0.0470
   chunk 27 optimal weight:    0.8980
   chunk 8 optimal weight:    0.0020
   chunk 1 optimal weight:    1.9990
   overall best weight:    0.5486

-------------------------------------------------------------------------------
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 = 0.4421 r_free = 0.4421 target = 0.191553 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4175 r_free = 0.4175 target = 0.167822 restraints weight = 11451.524|
|-----------------------------------------------------------------------------|
r_work (start): 0.4167 rms_B_bonded: 1.31
r_work: 0.4076 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.3965 rms_B_bonded: 3.94 restraints_weight: 0.2500
r_work (final): 0.3965
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7308
moved from start:          0.2292

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= 0.155
  Angle     :  0.596   7.031  11376  Z= 0.343
  Chirality :  0.042   0.223   1307
  Planarity :  0.005   0.041   1000
  Dihedral  : 25.254 171.472   2411
  Min Nonbonded Distance : 1.837

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.84 %
    Favored  : 99.16 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 12.34 %
    Favored  : 85.08 %
  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:  1.63 (0.34), residues: 596
  helix:  1.78 (0.28), residues: 338
  sheet: -0.06 (0.80), residues: 41
  loop :  0.33 (0.41), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG P 374 
 TYR   0.020   0.002   TYR P 134 
 PHE   0.016   0.002   PHE P 630 
 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        0.00300 /  0.15 ( 7991)
  covalent geometry    : angle       0.59229 /  0.34 (11370)
  hydrogen bonds       : bond        0.05166 /  5.52 (  403)
  hydrogen bonds       : angle       4.16584 /  4.09 ( 1034)
  metal coordination   : bond        0.00557 /  0.51 (    4)
  metal coordination   : angle       2.86006 /  6.74 (    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
  128 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 114
  time to evaluate  : 0.237 
Fit side-chains
REVERT: P  238 ASP cc_start: 0.7356 (t0) cc_final: 0.7060 (t0)
REVERT: P  362 LYS cc_start: 0.7511 (OUTLIER) cc_final: 0.7238 (mtmt)
REVERT: P  445 MET cc_start: 0.4346 (OUTLIER) cc_final: 0.3955 (tmm)
REVERT: P  483 LYS cc_start: 0.8101 (tppt) cc_final: 0.7840 (tppt)
REVERT: P  574 GLU cc_start: 0.7219 (tp30) cc_final: 0.6716 (tp30)
  outliers start: 14
  outliers final: 7
  residues processed: 117
  average time/residue: 0.6486
  time to fit residues: 79.7300
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  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  419 ARG
Chi-restraints excluded: chain P residue  445 MET
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 10 optimal weight:    0.8980
   chunk 51 optimal weight:    0.5980
   chunk 47 optimal weight:    0.2980
   chunk 22 optimal weight:    0.3980
   chunk 28 optimal weight:    0.0980
   chunk 58 optimal weight:    1.9990
   chunk 26 optimal weight:    3.9990
   chunk 1 optimal weight:    1.9990
   chunk 21 optimal weight:    2.9990
   chunk 69 optimal weight:    6.9990
   chunk 25 optimal weight:    4.9990
   overall best weight:    0.4580

-------------------------------------------------------------------------------
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 = 0.4422 r_free = 0.4422 target = 0.191602 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4175 r_free = 0.4175 target = 0.167851 restraints weight = 11381.022|
|-----------------------------------------------------------------------------|
r_work (start): 0.4168 rms_B_bonded: 1.31
r_work: 0.4077 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.3966 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.3966
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7307
moved from start:          0.2428

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= 0.142
  Angle     :  0.578   6.943  11376  Z= 0.333
  Chirality :  0.041   0.220   1307
  Planarity :  0.004   0.040   1000
  Dihedral  : 25.226 172.912   2411
  Min Nonbonded Distance : 1.858

Molprobity Statistics.
  All-atom Clashscore : 8.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.67 %
    Favored  : 99.33 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 11.79 %
    Favored  : 85.08 %
  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:  1.56 (0.34), residues: 596
  helix:  1.77 (0.28), residues: 338
  sheet: -0.00 (0.82), residues: 41
  loop :  0.18 (0.41), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG P 374 
 TYR   0.019   0.002   TYR P 134 
 PHE   0.016   0.001   PHE P 630 
 TRP   0.010   0.001   TRP P 570 
 HIS   0.004   0.001   HIS P  21 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00267 /  0.14 ( 7991)
  covalent geometry    : angle       0.57589 /  0.33 (11370)
  hydrogen bonds       : bond        0.04973 /  5.28 (  403)
  hydrogen bonds       : angle       4.17318 /  4.10 ( 1034)
  metal coordination   : bond        0.00555 /  0.51 (    4)
  metal coordination   : angle       2.05489 /  4.92 (    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
  135 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 118
  time to evaluate  : 0.241 
Fit side-chains
REVERT: P   62 PHE cc_start: 0.5523 (t80) cc_final: 0.3937 (t80)
REVERT: P  238 ASP cc_start: 0.7422 (t0) cc_final: 0.7151 (t0)
REVERT: P  362 LYS cc_start: 0.7517 (OUTLIER) cc_final: 0.7268 (mtmt)
REVERT: P  388 ASP cc_start: 0.7809 (m-30) cc_final: 0.7604 (m-30)
REVERT: P  445 MET cc_start: 0.4353 (OUTLIER) cc_final: 0.3966 (tmm)
REVERT: P  483 LYS cc_start: 0.8058 (tppt) cc_final: 0.7843 (tppt)
REVERT: P  574 GLU cc_start: 0.7171 (tp30) cc_final: 0.6792 (tp30)
  outliers start: 17
  outliers final: 6
  residues processed: 120
  average time/residue: 0.6107
  time to fit residues: 77.2473
Evaluate side-chains
  122 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 114
  time to evaluate  : 0.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue  141 THR
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  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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 8 optimal weight:    1.9990
   chunk 51 optimal weight:    0.7980
   chunk 1 optimal weight:    2.9990
   chunk 12 optimal weight:    0.6980
   chunk 47 optimal weight:    0.5980
   chunk 56 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9990
   chunk 26 optimal weight:    1.9990
   chunk 61 optimal weight:    6.9990
   chunk 3 optimal weight:    0.7980
   chunk 33 optimal weight:    0.9980
   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 = 0.4403 r_free = 0.4403 target = 0.189378 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4144 r_free = 0.4144 target = 0.164942 restraints weight = 11229.283|
|-----------------------------------------------------------------------------|
r_work (start): 0.4136 rms_B_bonded: 1.28
r_work: 0.4041 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.3927 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.3927
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7367
moved from start:          0.2640

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= 0.183
  Angle     :  0.639  17.078  11376  Z= 0.354
  Chirality :  0.044   0.233   1307
  Planarity :  0.005   0.042   1000
  Dihedral  : 25.223 170.221   2411
  Min Nonbonded Distance : 1.817

Molprobity Statistics.
  All-atom Clashscore : 8.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.17 %
    Favored  : 98.83 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 13.08 %
    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:  1.29 (0.34), residues: 596
  helix:  1.51 (0.28), residues: 338
  sheet:  0.10 (0.81), residues: 41
  loop :  0.09 (0.41), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG P 374 
 TYR   0.019   0.002   TYR P 283 
 PHE   0.018   0.002   PHE P  62 
 TRP   0.012   0.001   TRP P 570 
 HIS   0.005   0.001   HIS P 566 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00365 /  0.18 ( 7991)
  covalent geometry    : angle       0.63608 /  0.35 (11370)
  hydrogen bonds       : bond        0.05372 /  5.75 (  403)
  hydrogen bonds       : angle       4.31528 /  4.22 ( 1034)
  metal coordination   : bond        0.00733 /  0.62 (    4)
  metal coordination   : angle       2.92614 /  7.17 (    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
  126 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 110
  time to evaluate  : 0.221 
Fit side-chains
   revert: symmetry clash
REVERT: P   62 PHE cc_start: 0.5643 (t80) cc_final: 0.3896 (t80)
REVERT: P  238 ASP cc_start: 0.7526 (t0) cc_final: 0.7259 (t0)
REVERT: P  277 ILE cc_start: 0.8416 (OUTLIER) cc_final: 0.8071 (mp)
REVERT: P  362 LYS cc_start: 0.7506 (OUTLIER) cc_final: 0.7265 (mtmt)
REVERT: P  442 MET cc_start: 0.4671 (OUTLIER) cc_final: 0.0516 (mpt)
REVERT: P  483 LYS cc_start: 0.8091 (tppt) cc_final: 0.7868 (tppt)
REVERT: P  574 GLU cc_start: 0.7228 (tp30) cc_final: 0.6883 (tp30)
REVERT: P  580 VAL cc_start: 0.8213 (t) cc_final: 0.7985 (t)
  outliers start: 16
  outliers final: 7
  residues processed: 113
  average time/residue: 0.6436
  time to fit residues: 76.5463
Evaluate side-chains
  124 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 114
  time to evaluate  : 0.178 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue  141 THR
Chi-restraints excluded: chain P residue  277 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  442 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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 37 optimal weight:    0.5980
   chunk 34 optimal weight:    0.8980
   chunk 61 optimal weight:    5.9990
   chunk 56 optimal weight:    1.9990
   chunk 20 optimal weight:    0.5980
   chunk 48 optimal weight:    0.6980
   chunk 70 optimal weight:    3.9990
   chunk 66 optimal weight:    5.9990
   chunk 16 optimal weight:    0.4980
   chunk 5 optimal weight:    0.9980
   chunk 38 optimal weight:    1.9990
   overall best weight:    0.6580

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

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4408 r_free = 0.4408 target = 0.189804 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4148 r_free = 0.4148 target = 0.165347 restraints weight = 11135.555|
|-----------------------------------------------------------------------------|
r_work (start): 0.4133 rms_B_bonded: 1.28
r_work: 0.4040 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.3925 rms_B_bonded: 3.93 restraints_weight: 0.2500
r_work (final): 0.3925
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7361
moved from start:          0.2767

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= 0.167
  Angle     :  0.636  18.826  11376  Z= 0.351
  Chirality :  0.043   0.235   1307
  Planarity :  0.005   0.045   1000
  Dihedral  : 25.221 170.454   2411
  Min Nonbonded Distance : 1.836

Molprobity Statistics.
  All-atom Clashscore : 8.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.01 %
    Favored  : 98.99 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 13.81 %
    Favored  : 83.06 %
  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 (0.34), residues: 596
  helix:  1.39 (0.28), residues: 338
  sheet:  0.02 (0.82), residues: 41
  loop :  0.04 (0.41), 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   0.018   0.002   PHE P 630 
 TRP   0.011   0.001   TRP P 570 
 HIS   0.004   0.001   HIS P 566 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00324 /  0.17 ( 7991)
  covalent geometry    : angle       0.63298 /  0.35 (11370)
  hydrogen bonds       : bond        0.05153 /  5.45 (  403)
  hydrogen bonds       : angle       4.33005 /  4.22 ( 1034)
  metal coordination   : bond        0.00666 /  0.57 (    4)
  metal coordination   : angle       2.75813 /  6.80 (    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
  127 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 110
  time to evaluate  : 0.146 
Fit side-chains
   revert: symmetry clash
REVERT: P   62 PHE cc_start: 0.5679 (t80) cc_final: 0.3932 (t80)
REVERT: P  238 ASP cc_start: 0.7545 (t0) cc_final: 0.7258 (t0)
REVERT: P  362 LYS cc_start: 0.7504 (OUTLIER) cc_final: 0.7284 (mtmt)
REVERT: P  442 MET cc_start: 0.4624 (OUTLIER) cc_final: 0.0497 (mpt)
REVERT: P  445 MET cc_start: 0.4478 (OUTLIER) cc_final: 0.4053 (tmm)
REVERT: P  483 LYS cc_start: 0.8115 (tppt) cc_final: 0.7889 (tppt)
REVERT: P  574 GLU cc_start: 0.7224 (tp30) cc_final: 0.6885 (tp30)
  outliers start: 17
  outliers final: 8
  residues processed: 113
  average time/residue: 0.6845
  time to fit residues: 81.1521
Evaluate side-chains
  117 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 106
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
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  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  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
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 30 optimal weight:    0.5980
   chunk 36 optimal weight:    0.6980
   chunk 23 optimal weight:    0.9980
   chunk 40 optimal weight:    0.0050
   chunk 4 optimal weight:    0.6980
   chunk 59 optimal weight:    0.7980
   chunk 69 optimal weight:    6.9990
   chunk 45 optimal weight:    0.4980
   chunk 41 optimal weight:    0.4980
   chunk 67 optimal weight:    4.9990
   chunk 55 optimal weight:    0.6980
   overall best weight:    0.4594

-------------------------------------------------------------------------------
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 = 0.4410 r_free = 0.4410 target = 0.190326 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4164 r_free = 0.4164 target = 0.166561 restraints weight = 11314.938|
|-----------------------------------------------------------------------------|
r_work (start): 0.4153 rms_B_bonded: 1.28
r_work: 0.4064 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.3953 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.3953
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7333
moved from start:          0.2809

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7995  Z= 0.143
  Angle     :  0.606  16.724  11376  Z= 0.338
  Chirality :  0.042   0.236   1307
  Planarity :  0.005   0.045   1000
  Dihedral  : 25.212 171.119   2411
  Min Nonbonded Distance : 1.852

Molprobity Statistics.
  All-atom Clashscore : 8.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.84 %
    Favored  : 99.16 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 14.00 %
    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:  1.24 (0.34), residues: 596
  helix:  1.51 (0.28), residues: 338
  sheet: -0.07 (0.82), residues: 41
  loop :  0.03 (0.41), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG P 374 
 TYR   0.017   0.002   TYR P 283 
 PHE   0.018   0.002   PHE P 630 
 TRP   0.011   0.001   TRP P 570 
 HIS   0.004   0.001   HIS P 566 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00270 /  0.14 ( 7991)
  covalent geometry    : angle       0.60371 /  0.34 (11370)
  hydrogen bonds       : bond        0.04965 /  5.21 (  403)
  hydrogen bonds       : angle       4.27683 /  4.17 ( 1034)
  metal coordination   : bond        0.00536 /  0.48 (    4)
  metal coordination   : angle       2.50262 /  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
  126 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 112
  time to evaluate  : 0.183 
Fit side-chains
   revert: symmetry clash
REVERT: P   62 PHE cc_start: 0.5632 (t80) cc_final: 0.3946 (t80)
REVERT: P  238 ASP cc_start: 0.7461 (t0) cc_final: 0.7214 (t0)
REVERT: P  362 LYS cc_start: 0.7500 (OUTLIER) cc_final: 0.7276 (mtmt)
REVERT: P  442 MET cc_start: 0.4661 (OUTLIER) cc_final: 0.0542 (mpt)
REVERT: P  445 MET cc_start: 0.4464 (OUTLIER) cc_final: 0.4031 (tmm)
REVERT: P  483 LYS cc_start: 0.8106 (tppt) cc_final: 0.7901 (tppt)
REVERT: P  574 GLU cc_start: 0.7134 (tp30) cc_final: 0.6768 (tp30)
  outliers start: 14
  outliers final: 11
  residues processed: 113
  average time/residue: 0.6613
  time to fit residues: 78.4096
Evaluate side-chains
  123 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 109
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
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  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  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  559 LYS
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:    0.9990
   chunk 9 optimal weight:    1.9990
   chunk 10 optimal weight:    2.9990
   chunk 64 optimal weight:    3.9990
   chunk 50 optimal weight:    0.8980
   chunk 12 optimal weight:    0.9980
   chunk 57 optimal weight:    0.6980
   chunk 30 optimal weight:    0.0060
   chunk 25 optimal weight:    0.9990
   chunk 43 optimal weight:    0.6980
   chunk 51 optimal weight:    0.5980
   overall best weight:    0.5796

-------------------------------------------------------------------------------
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 = 0.4409 r_free = 0.4409 target = 0.189973 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4150 r_free = 0.4150 target = 0.165619 restraints weight = 11093.472|
|-----------------------------------------------------------------------------|
r_work (start): 0.4144 rms_B_bonded: 1.26
r_work: 0.4049 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.3936 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.3936
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7358
moved from start:          0.2951

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= 0.157
  Angle     :  0.608  14.504  11376  Z= 0.341
  Chirality :  0.042   0.236   1307
  Planarity :  0.005   0.039   1000
  Dihedral  : 25.058 170.520   2411
  Min Nonbonded Distance : 1.838

Molprobity Statistics.
  All-atom Clashscore : 8.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.34 %
    Favored  : 98.66 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 14.73 %
    Favored  : 83.06 %
  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 (0.34), residues: 596
  helix:  1.44 (0.28), residues: 338
  sheet: -0.11 (0.83), residues: 41
  loop : -0.01 (0.41), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG P 374 
 TYR   0.018   0.002   TYR P 283 
 PHE   0.018   0.002   PHE P 630 
 TRP   0.010   0.001   TRP P 570 
 HIS   0.004   0.001   HIS P 566 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00306 /  0.16 ( 7991)
  covalent geometry    : angle       0.60529 /  0.34 (11370)
  hydrogen bonds       : bond        0.05095 /  5.40 (  403)
  hydrogen bonds       : angle       4.28143 /  4.19 ( 1034)
  metal coordination   : bond        0.00606 /  0.52 (    4)
  metal coordination   : angle       2.72160 /  6.74 (    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
  123 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 111
  time to evaluate  : 0.226 
Fit side-chains
REVERT: P   62 PHE cc_start: 0.5676 (t80) cc_final: 0.3957 (t80)
REVERT: P  238 ASP cc_start: 0.7546 (t0) cc_final: 0.7262 (t0)
REVERT: P  442 MET cc_start: 0.4635 (OUTLIER) cc_final: 0.0509 (mpt)
REVERT: P  483 LYS cc_start: 0.8104 (tppt) cc_final: 0.7893 (tppt)
REVERT: P  506 ASP cc_start: 0.6942 (p0) cc_final: 0.6713 (p0)
REVERT: P  574 GLU cc_start: 0.7210 (tp30) cc_final: 0.6993 (tp30)
  outliers start: 12
  outliers final: 7
  residues processed: 112
  average time/residue: 0.6816
  time to fit residues: 80.0897
Evaluate side-chains
  119 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 111
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
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  389 ILE
Chi-restraints excluded: chain P residue  442 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
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:    3.9990
   chunk 2 optimal weight:    0.5980
   chunk 54 optimal weight:    0.4980
   chunk 28 optimal weight:    1.9990
   chunk 56 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9980
   chunk 48 optimal weight:    0.0470
   chunk 22 optimal weight:    0.7980
   chunk 70 optimal weight:    3.9990
   chunk 10 optimal weight:    3.9990
   overall best weight:    0.5878

-------------------------------------------------------------------------------
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 = 0.4404 r_free = 0.4404 target = 0.189686 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4157 r_free = 0.4157 target = 0.166164 restraints weight = 11331.272|
|-----------------------------------------------------------------------------|
r_work (start): 0.4143 rms_B_bonded: 1.27
r_work: 0.4055 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.3947 rms_B_bonded: 3.86 restraints_weight: 0.2500
r_work (final): 0.3947
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7348
moved from start:          0.3030

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7995  Z= 0.155
  Angle     :  0.602  14.312  11376  Z= 0.338
  Chirality :  0.042   0.224   1307
  Planarity :  0.005   0.040   1000
  Dihedral  : 24.954 170.372   2411
  Min Nonbonded Distance : 1.858

Molprobity Statistics.
  All-atom Clashscore : 8.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.01 %
    Favored  : 98.99 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 15.47 %
    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:  1.13 (0.34), residues: 596
  helix:  1.44 (0.28), residues: 338
  sheet: -0.18 (0.82), residues: 41
  loop : -0.04 (0.41), 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   0.018   0.002   PHE P 630 
 TRP   0.011   0.001   TRP P 570 
 HIS   0.004   0.001   HIS P 566 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00300 /  0.15 ( 7991)
  covalent geometry    : angle       0.59893 /  0.34 (11370)
  hydrogen bonds       : bond        0.04987 /  5.23 (  403)
  hydrogen bonds       : angle       4.31080 /  4.26 ( 1034)
  metal coordination   : bond        0.00633 /  0.53 (    4)
  metal coordination   : angle       2.72839 /  6.76 (    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
  115 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 106
  time to evaluate  : 0.233 
Fit side-chains
REVERT: P   62 PHE cc_start: 0.5692 (t80) cc_final: 0.3975 (t80)
REVERT: P  238 ASP cc_start: 0.7461 (t0) cc_final: 0.7200 (t0)
REVERT: P  362 LYS cc_start: 0.7515 (OUTLIER) cc_final: 0.7314 (mtmt)
REVERT: P  442 MET cc_start: 0.4642 (OUTLIER) cc_final: 0.0526 (mpt)
REVERT: P  483 LYS cc_start: 0.8104 (tppt) cc_final: 0.7898 (tppt)
  outliers start: 9
  outliers final: 7
  residues processed: 108
  average time/residue: 0.6634
  time to fit residues: 75.2221
Evaluate side-chains
  120 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 111
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
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  362 LYS
Chi-restraints excluded: chain P residue  389 ILE
Chi-restraints excluded: chain P residue  442 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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 12 optimal weight:    0.3980
   chunk 35 optimal weight:    2.9990
   chunk 53 optimal weight:    0.6980
   chunk 6 optimal weight:    0.0020
   chunk 1 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9980
   chunk 40 optimal weight:    0.9990
   chunk 2 optimal weight:    0.0670
   chunk 68 optimal weight:   40.0000
   chunk 16 optimal weight:    1.9990
   chunk 17 optimal weight:    0.7980
   overall best weight:    0.3926

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

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4421 r_free = 0.4421 target = 0.190958 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4163 r_free = 0.4163 target = 0.166637 restraints weight = 11242.132|
|-----------------------------------------------------------------------------|
r_work (start): 0.4157 rms_B_bonded: 1.27
r_work: 0.4063 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.3949 rms_B_bonded: 3.95 restraints_weight: 0.2500
r_work (final): 0.3949
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7337
moved from start:          0.3060

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7995  Z= 0.135
  Angle     :  0.594  13.782  11376  Z= 0.335
  Chirality :  0.041   0.220   1307
  Planarity :  0.005   0.045   1000
  Dihedral  : 24.877 171.452   2411
  Min Nonbonded Distance : 1.836

Molprobity Statistics.
  All-atom Clashscore : 8.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.17 %
    Favored  : 98.83 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  : 16.02 %
    Favored  : 82.50 %
  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:  1.27 (0.34), residues: 596
  helix:  1.57 (0.28), residues: 338
  sheet: -0.17 (0.84), residues: 41
  loop : -0.01 (0.40), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG P 374 
 TYR   0.017   0.001   TYR P 283 
 PHE   0.018   0.001   PHE P 630 
 TRP   0.011   0.001   TRP P 603 
 HIS   0.004   0.001   HIS P 566 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00254 /  0.14 ( 7991)
  covalent geometry    : angle       0.59123 /  0.33 (11370)
  hydrogen bonds       : bond        0.04798 /  4.95 (  403)
  hydrogen bonds       : angle       4.23556 /  4.20 ( 1034)
  metal coordination   : bond        0.00504 /  0.45 (    4)
  metal coordination   : angle       2.38494 /  5.79 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3307.47 seconds
wall clock time: 57 minutes 15.01 seconds (3435.01 seconds total)