Starting phenix.real_space_refine
on Fri Aug 22 20:39:23 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8gkh_40184/08_2025/8gkh_40184_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8gkh_40184/08_2025/8gkh_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_2025/8gkh_40184_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8gkh_40184/08_2025/8gkh_40184_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8gkh_40184/08_2025/8gkh_40184.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8gkh_40184/08_2025/8gkh_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-2.0-5787/lib/python3.9/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: 2.29, per 1000 atoms: 0.30
  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: 0.82
  Conformation dependent library (CDL) restraints added in 399.2 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  
  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: 0.98
  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: 1.04 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=" O3'  DG T -17 "
       pdb=" P    DA T -16 "
    ideal  model  delta    sigma   weight residual
    1.607  1.625 -0.018 1.50e-02 4.44e+03 1.37e+00
  bond pdb=" C1'   A W  16 "
       pdb=" N9    A W  16 "
    ideal  model  delta    sigma   weight residual
    1.465  1.480 -0.015 1.50e-02 4.44e+03 1.07e+00
  bond pdb=" C1'   U W  15 "
       pdb=" N1    U W  15 "
    ideal  model  delta    sigma   weight residual
    1.470  1.484 -0.014 1.50e-02 4.44e+03 8.77e-01
  bond pdb=" C3'  DC T  -6 "
       pdb=" O3'  DC T  -6 "
    ideal  model  delta    sigma   weight residual
    1.422  1.450 -0.028 3.00e-02 1.11e+03 8.52e-01
  bond pdb=" C3'  DA T  -8 "
       pdb=" O3'  DA T  -8 "
    ideal  model  delta    sigma   weight residual
    1.422  1.449 -0.027 3.00e-02 1.11e+03 7.82e-01
  ... (remaining 7986 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.64: 11205
        4.64 -     9.29: 53
        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=" C4'   U W  15 "
        pdb=" C3'   U W  15 "
        pdb=" O3'   U W  15 "
      ideal   model   delta    sigma   weight residual
     109.40  115.86   -6.46 1.50e+00 4.44e-01 1.85e+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 -    0.149: 1215
       0.149 -    0.299: 39
       0.299 -    0.448: 52
       0.448 -    0.598: 0
       0.598 -    0.747: 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       2.35   -3.09   -0.75 2.00e-01 2.50e+01 1.40e+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       2.35   -2.79   -0.44 2.00e-01 2.50e+01 4.91e+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       2.35   -2.76   -0.42 2.00e-01 2.50e+01 4.32e+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:             2.630
  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:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     11.370
  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:7.000
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.230
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6744
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   7995  Z= 0.115
  Angle     :  1.275  23.219  11376  Z= 0.504
  Chirality :  0.096   0.747   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 aren 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
  covalent geometry    : bond        0.00228 ( 7991)
  covalent geometry    : angle       1.27470 (11370)
  hydrogen bonds       : bond        0.13323 (  403)
  hydrogen bonds       : angle       5.40211 ( 1034)
  metal coordination   : bond        0.00177 (    4)
  metal coordination   : angle       1.14425 (    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  : 0.218 
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: 0.6283
  time to fit residues: 84.2386
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  : 0.219 
-------------------------------------------------------------------------------
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:    0.1980
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    0.3980
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    1.9990
   chunk 27 optimal weight:    0.5980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
P  35 ASN
P 129 GLN
P 378 ASN
P 393 GLN
P 396 ASN
P 482 GLN
P 517 GLN
P 581 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4426 r_free = 0.4426 target = 0.191874 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4182 r_free = 0.4182 target = 0.168432 restraints weight = 11379.448|
|-----------------------------------------------------------------------------|
r_work (start): 0.4175 rms_B_bonded: 1.31
r_work: 0.4084 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.3973 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.3973
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7024
moved from start:          0.1992

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   7995  Z= 0.176
  Angle     :  0.646  10.761  11376  Z= 0.345
  Chirality :  0.040   0.253   1307
  Planarity :  0.004   0.050   1000
  Dihedral  : 25.282 179.279   2411
  Min Nonbonded Distance : 1.811

Molprobity Statistics.
  All-atom Clashscore : 7.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.84 %
    Favored  : 99.16 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  :  9.21 %
    Favored  : 88.40 %
  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 aren not related in a simple way.
  whole:  2.23 (0.35), residues: 596
  helix:  2.19 (0.28), residues: 338
  sheet:  0.24 (0.80), residues: 41
  loop :  0.72 (0.43), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG P 374 
 TYR   0.017   0.002   TYR P 283 
 PHE   0.015   0.002   PHE P  62 
 TRP   0.010   0.001   TRP P 570 
 HIS   0.007   0.001   HIS P 566 

Details of bonding type rmsd
  covalent geometry    : bond        0.00375 ( 7991)
  covalent geometry    : angle       0.64327 (11370)
  hydrogen bonds       : bond        0.04923 (  403)
  hydrogen bonds       : angle       4.21337 ( 1034)
  metal coordination   : bond        0.00563 (    4)
  metal coordination   : angle       2.70331 (    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
  137 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 124
  time to evaluate  : 0.142 
Fit side-chains
   revert: symmetry clash
REVERT: P   62 PHE cc_start: 0.5523 (t80) cc_final: 0.4063 (t80)
REVERT: P  238 ASP cc_start: 0.7331 (t0) cc_final: 0.7004 (t0)
REVERT: P  314 PHE cc_start: 0.8136 (m-80) cc_final: 0.7923 (m-80)
REVERT: P  362 LYS cc_start: 0.7414 (OUTLIER) cc_final: 0.7164 (mtmt)
REVERT: P  388 ASP cc_start: 0.7756 (m-30) cc_final: 0.7545 (m-30)
REVERT: P  445 MET cc_start: 0.4270 (OUTLIER) cc_final: 0.3918 (tmm)
REVERT: P  483 LYS cc_start: 0.8101 (tppt) cc_final: 0.7467 (tppt)
REVERT: P  487 ASP cc_start: 0.7376 (m-30) cc_final: 0.7155 (m-30)
REVERT: P  574 GLU cc_start: 0.7213 (tp30) cc_final: 0.6846 (tp30)
REVERT: P  602 TYR cc_start: 0.8082 (m-80) cc_final: 0.7785 (m-80)
  outliers start: 13
  outliers final: 4
  residues processed: 125
  average time/residue: 0.5524
  time to fit residues: 72.8433
Evaluate side-chains
  124 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 118
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
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  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=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 36 optimal weight:    0.9980
   chunk 66 optimal weight:    2.9990
   chunk 69 optimal weight:    3.9990
   chunk 60 optimal weight:    0.2980
   chunk 46 optimal weight:    0.9980
   chunk 12 optimal weight:    0.5980
   chunk 0 optimal weight:    2.9990
   chunk 43 optimal weight:    0.8980
   chunk 44 optimal weight:    0.7980
   chunk 58 optimal weight:    0.4980
   chunk 19 optimal weight:    2.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
P  35 ASN
P 378 ASN
P 396 ASN
P 482 GLN
P 517 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4410 r_free = 0.4410 target = 0.190128 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4165 r_free = 0.4165 target = 0.166596 restraints weight = 11253.791|
|-----------------------------------------------------------------------------|
r_work (start): 0.4153 rms_B_bonded: 1.26
r_work: 0.4064 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.3956 rms_B_bonded: 3.82 restraints_weight: 0.2500
r_work (final): 0.3956
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7069
moved from start:          0.2516

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   7995  Z= 0.173
  Angle     :  0.615   8.086  11376  Z= 0.331
  Chirality :  0.039   0.227   1307
  Planarity :  0.004   0.036   1000
  Dihedral  : 24.955 165.848   2411
  Min Nonbonded Distance : 1.840

Molprobity Statistics.
  All-atom Clashscore : 7.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.67 %
    Favored  : 99.33 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 11.79 %
    Favored  : 85.45 %
  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 aren not related in a simple way.
  whole:  1.77 (0.34), residues: 596
  helix:  1.83 (0.28), residues: 337
  sheet:  0.25 (0.80), residues: 41
  loop :  0.46 (0.42), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG P 374 
 TYR   0.018   0.002   TYR P 283 
 PHE   0.018   0.002   PHE P  62 
 TRP   0.011   0.001   TRP P 570 
 HIS   0.006   0.001   HIS P 566 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 ( 7991)
  covalent geometry    : angle       0.61159 (11370)
  hydrogen bonds       : bond        0.04751 (  403)
  hydrogen bonds       : angle       4.15814 ( 1034)
  metal coordination   : bond        0.00695 (    4)
  metal coordination   : angle       3.01228 (    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
  137 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 122
  time to evaluate  : 0.215 
Fit side-chains
REVERT: P   62 PHE cc_start: 0.5693 (t80) cc_final: 0.3954 (t80)
REVERT: P  238 ASP cc_start: 0.7473 (t0) cc_final: 0.7252 (t0)
REVERT: P  362 LYS cc_start: 0.7467 (OUTLIER) cc_final: 0.7237 (mtmt)
REVERT: P  388 ASP cc_start: 0.7721 (m-30) cc_final: 0.7515 (m-30)
REVERT: P  445 MET cc_start: 0.4445 (OUTLIER) cc_final: 0.4016 (tmm)
REVERT: P  483 LYS cc_start: 0.8165 (tppt) cc_final: 0.7517 (tppt)
REVERT: P  487 ASP cc_start: 0.7390 (m-30) cc_final: 0.7152 (m-30)
REVERT: P  574 GLU cc_start: 0.7157 (tp30) cc_final: 0.6801 (tp30)
REVERT: P  602 TYR cc_start: 0.8156 (m-80) cc_final: 0.7874 (m-80)
  outliers start: 15
  outliers final: 5
  residues processed: 124
  average time/residue: 0.5813
  time to fit residues: 75.5663
Evaluate side-chains
  124 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 117
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
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  382 ILE
Chi-restraints excluded: chain P residue  445 MET
Chi-restraints excluded: chain P residue  545 SER
Chi-restraints excluded: chain P residue  577 ILE
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:    0.5980
   chunk 59 optimal weight:    0.9980
   chunk 19 optimal weight:    0.5980
   chunk 5 optimal weight:    0.9990
   chunk 28 optimal weight:    1.9990
   chunk 30 optimal weight:    0.6980
   chunk 53 optimal weight:    0.9990
   chunk 27 optimal weight:    0.7980
   chunk 8 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
P  35 ASN
P  58 HIS
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: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4387 r_free = 0.4387 target = 0.188102 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4141 r_free = 0.4141 target = 0.164615 restraints weight = 11340.121|
|-----------------------------------------------------------------------------|
r_work (start): 0.4128 rms_B_bonded: 1.27
r_work: 0.4037 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.3928 rms_B_bonded: 3.83 restraints_weight: 0.2500
r_work (final): 0.3928
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7110
moved from start:          0.2933

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   7995  Z= 0.186
  Angle     :  0.624   7.668  11376  Z= 0.335
  Chirality :  0.039   0.250   1307
  Planarity :  0.004   0.041   1000
  Dihedral  : 24.854 167.605   2411
  Min Nonbonded Distance : 1.832

Molprobity Statistics.
  All-atom Clashscore : 7.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.67 %
    Favored  : 99.33 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 12.89 %
    Favored  : 84.71 %
  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 aren not related in a simple way.
  whole:  1.50 (0.34), residues: 596
  helix:  1.62 (0.28), residues: 338
  sheet:  0.29 (0.81), residues: 41
  loop :  0.29 (0.42), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG P 374 
 TYR   0.018   0.002   TYR P 283 
 PHE   0.022   0.002   PHE P 630 
 TRP   0.011   0.001   TRP P 570 
 HIS   0.006   0.001   HIS P 566 

Details of bonding type rmsd
  covalent geometry    : bond        0.00399 ( 7991)
  covalent geometry    : angle       0.61909 (11370)
  hydrogen bonds       : bond        0.04878 (  403)
  hydrogen bonds       : angle       4.23586 ( 1034)
  metal coordination   : bond        0.00762 (    4)
  metal coordination   : angle       3.40350 (    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
  125 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 112
  time to evaluate  : 0.137 
Fit side-chains
REVERT: P  238 ASP cc_start: 0.7483 (t0) cc_final: 0.7246 (t0)
REVERT: P  388 ASP cc_start: 0.7725 (m-30) cc_final: 0.7515 (m-30)
REVERT: P  442 MET cc_start: 0.4951 (OUTLIER) cc_final: 0.0372 (mpt)
REVERT: P  483 LYS cc_start: 0.8215 (tppt) cc_final: 0.7539 (tppt)
REVERT: P  487 ASP cc_start: 0.7392 (m-30) cc_final: 0.7143 (m-30)
REVERT: P  580 VAL cc_start: 0.8178 (t) cc_final: 0.7934 (t)
REVERT: P  602 TYR cc_start: 0.8152 (m-80) cc_final: 0.7892 (m-80)
  outliers start: 13
  outliers final: 6
  residues processed: 115
  average time/residue: 0.6098
  time to fit residues: 73.5284
Evaluate side-chains
  115 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 108
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
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  395 SER
Chi-restraints excluded: chain P residue  442 MET
Chi-restraints excluded: chain P residue  450 TYR
Chi-restraints excluded: chain P residue  545 SER
Chi-restraints excluded: chain P residue  577 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 10 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9990
   chunk 47 optimal weight:    0.5980
   chunk 22 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 58 optimal weight:    0.8980
   chunk 26 optimal weight:    2.9990
   chunk 1 optimal weight:    1.9990
   chunk 21 optimal weight:    0.8980
   chunk 69 optimal weight:    3.9990
   chunk 25 optimal weight:    0.9980
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
P  35 ASN
P  55 HIS
P 378 ASN
P 396 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4366 r_free = 0.4366 target = 0.186017 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4115 r_free = 0.4115 target = 0.162283 restraints weight = 11224.868|
|-----------------------------------------------------------------------------|
r_work (start): 0.4103 rms_B_bonded: 1.27
r_work: 0.4011 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.3899 rms_B_bonded: 3.85 restraints_weight: 0.2500
r_work (final): 0.3899
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7163
moved from start:          0.3343

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.032   7995  Z= 0.218
  Angle     :  0.670  10.735  11376  Z= 0.352
  Chirality :  0.041   0.291   1307
  Planarity :  0.005   0.047   1000
  Dihedral  : 24.754 164.403   2411
  Min Nonbonded Distance : 1.810

Molprobity Statistics.
  All-atom Clashscore : 8.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 13.63 %
    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 aren not related in a simple way.
  whole:  1.02 (0.33), residues: 596
  helix:  1.26 (0.27), residues: 339
  sheet:  0.19 (0.80), residues: 41
  loop : -0.02 (0.41), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG P 374 
 TYR   0.020   0.002   TYR P 450 
 PHE   0.021   0.002   PHE P 630 
 TRP   0.014   0.001   TRP P 570 
 HIS   0.006   0.001   HIS P 566 

Details of bonding type rmsd
  covalent geometry    : bond        0.00472 ( 7991)
  covalent geometry    : angle       0.66470 (11370)
  hydrogen bonds       : bond        0.05232 (  403)
  hydrogen bonds       : angle       4.41953 ( 1034)
  metal coordination   : bond        0.00904 (    4)
  metal coordination   : angle       3.66380 (    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
  125 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 110
  time to evaluate  : 0.162 
Fit side-chains
REVERT: P  238 ASP cc_start: 0.7513 (t0) cc_final: 0.7295 (t0)
REVERT: P  388 ASP cc_start: 0.7722 (m-30) cc_final: 0.7497 (m-30)
REVERT: P  419 ARG cc_start: 0.7959 (OUTLIER) cc_final: 0.7074 (ttp-170)
REVERT: P  442 MET cc_start: 0.4949 (OUTLIER) cc_final: 0.0441 (mpt)
REVERT: P  483 LYS cc_start: 0.8225 (tppt) cc_final: 0.7596 (tppt)
REVERT: P  487 ASP cc_start: 0.7420 (m-30) cc_final: 0.7165 (m-30)
  outliers start: 15
  outliers final: 7
  residues processed: 117
  average time/residue: 0.6060
  time to fit residues: 74.3404
Evaluate side-chains
  111 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 102
  time to evaluate  : 0.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue  141 THR
Chi-restraints excluded: chain P residue  327 THR
Chi-restraints excluded: chain P residue  382 ILE
Chi-restraints excluded: chain P residue  395 SER
Chi-restraints excluded: chain P residue  419 ARG
Chi-restraints excluded: chain P residue  442 MET
Chi-restraints excluded: chain P residue  450 TYR
Chi-restraints excluded: chain P residue  545 SER
Chi-restraints excluded: chain P residue  577 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 8 optimal weight:    0.5980
   chunk 51 optimal weight:    0.0980
   chunk 1 optimal weight:    1.9990
   chunk 12 optimal weight:    0.7980
   chunk 47 optimal weight:    0.9980
   chunk 56 optimal weight:    1.9990
   chunk 22 optimal weight:    0.7980
   chunk 26 optimal weight:    2.9990
   chunk 61 optimal weight:    1.9990
   chunk 3 optimal weight:    0.5980
   chunk 33 optimal weight:    0.8980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.4383 r_free = 0.4383 target = 0.187845 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4135 r_free = 0.4135 target = 0.164073 restraints weight = 11246.928|
|-----------------------------------------------------------------------------|
r_work (start): 0.4120 rms_B_bonded: 1.27
r_work: 0.4028 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.3918 rms_B_bonded: 3.85 restraints_weight: 0.2500
r_work (final): 0.3918
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7123
moved from start:          0.3363

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   7995  Z= 0.171
  Angle     :  0.622  12.108  11376  Z= 0.329
  Chirality :  0.038   0.243   1307
  Planarity :  0.005   0.046   1000
  Dihedral  : 24.530 166.365   2411
  Min Nonbonded Distance : 1.849

Molprobity Statistics.
  All-atom Clashscore : 8.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.84 %
    Favored  : 99.16 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 14.55 %
    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 aren not related in a simple way.
  whole:  1.24 (0.33), residues: 596
  helix:  1.50 (0.28), residues: 338
  sheet:  0.10 (0.81), residues: 41
  loop :  0.02 (0.41), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG P 292 
 TYR   0.018   0.002   TYR P 283 
 PHE   0.023   0.002   PHE P 630 
 TRP   0.012   0.001   TRP P 570 
 HIS   0.005   0.001   HIS P 566 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 ( 7991)
  covalent geometry    : angle       0.61880 (11370)
  hydrogen bonds       : bond        0.04761 (  403)
  hydrogen bonds       : angle       4.25221 ( 1034)
  metal coordination   : bond        0.00566 (    4)
  metal coordination   : angle       2.65495 (    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
  129 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 115
  time to evaluate  : 0.169 
Fit side-chains
REVERT: P  238 ASP cc_start: 0.7488 (t0) cc_final: 0.7249 (t0)
REVERT: P  388 ASP cc_start: 0.7737 (m-30) cc_final: 0.7511 (m-30)
REVERT: P  419 ARG cc_start: 0.7974 (OUTLIER) cc_final: 0.7080 (ttp-170)
REVERT: P  442 MET cc_start: 0.4961 (OUTLIER) cc_final: 0.0467 (mpt)
REVERT: P  483 LYS cc_start: 0.8296 (tppt) cc_final: 0.7622 (tppt)
REVERT: P  487 ASP cc_start: 0.7392 (m-30) cc_final: 0.7131 (m-30)
REVERT: P  602 TYR cc_start: 0.8157 (m-80) cc_final: 0.7927 (m-80)
  outliers start: 14
  outliers final: 8
  residues processed: 120
  average time/residue: 0.5935
  time to fit residues: 74.8171
Evaluate side-chains
  117 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 107
  time to evaluate  : 0.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue  141 THR
Chi-restraints excluded: chain P residue  327 THR
Chi-restraints excluded: chain P residue  382 ILE
Chi-restraints excluded: chain P residue  395 SER
Chi-restraints excluded: chain P residue  419 ARG
Chi-restraints excluded: chain P residue  442 MET
Chi-restraints excluded: chain P residue  450 TYR
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 37 optimal weight:    1.9990
   chunk 34 optimal weight:    0.5980
   chunk 61 optimal weight:    1.9990
   chunk 56 optimal weight:    2.9990
   chunk 20 optimal weight:    2.9990
   chunk 48 optimal weight:    0.3980
   chunk 70 optimal weight:    2.9990
   chunk 66 optimal weight:    2.9990
   chunk 16 optimal weight:    5.9990
   chunk 5 optimal weight:    1.9990
   chunk 38 optimal weight:    0.7980
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
P  35 ASN
P 378 ASN
P 393 GLN
P 396 ASN
** P 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4345 r_free = 0.4345 target = 0.184238 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4092 r_free = 0.4092 target = 0.160401 restraints weight = 11042.674|
|-----------------------------------------------------------------------------|
r_work (start): 0.4080 rms_B_bonded: 1.26
r_work: 0.3988 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.3877 rms_B_bonded: 3.80 restraints_weight: 0.2500
r_work (final): 0.3877
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7203
moved from start:          0.3704

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.039   7995  Z= 0.267
  Angle     :  0.703   9.497  11376  Z= 0.373
  Chirality :  0.044   0.328   1307
  Planarity :  0.006   0.059   1000
  Dihedral  : 24.656 164.688   2411
  Min Nonbonded Distance : 1.813

Molprobity Statistics.
  All-atom Clashscore : 8.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 15.10 %
    Favored  : 83.24 %
  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 aren not related in a simple way.
  whole:  0.58 (0.33), residues: 596
  helix:  0.86 (0.27), residues: 339
  sheet: -0.41 (0.77), residues: 46
  loop : -0.02 (0.41), residues: 211

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG P 374 
 TYR   0.026   0.003   TYR P 450 
 PHE   0.023   0.003   PHE P 630 
 TRP   0.016   0.002   TRP P 570 
 HIS   0.006   0.001   HIS P 566 

Details of bonding type rmsd
  covalent geometry    : bond        0.00581 ( 7991)
  covalent geometry    : angle       0.69762 (11370)
  hydrogen bonds       : bond        0.05619 (  403)
  hydrogen bonds       : angle       4.54212 ( 1034)
  metal coordination   : bond        0.00982 (    4)
  metal coordination   : angle       3.72845 (    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
  124 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 115
  time to evaluate  : 0.225 
Fit side-chains
REVERT: P  238 ASP cc_start: 0.7505 (t0) cc_final: 0.7302 (t0)
REVERT: P  388 ASP cc_start: 0.7763 (m-30) cc_final: 0.7540 (m-30)
REVERT: P  419 ARG cc_start: 0.7946 (OUTLIER) cc_final: 0.7082 (ttp-170)
REVERT: P  483 LYS cc_start: 0.8267 (tppt) cc_final: 0.7554 (tppt)
REVERT: P  487 ASP cc_start: 0.7387 (m-30) cc_final: 0.7136 (m-30)
  outliers start: 9
  outliers final: 9
  residues processed: 120
  average time/residue: 0.5748
  time to fit residues: 72.2910
Evaluate side-chains
  123 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 113
  time to evaluate  : 0.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue  141 THR
Chi-restraints excluded: chain P residue  304 MET
Chi-restraints excluded: chain P residue  327 THR
Chi-restraints excluded: chain P residue  382 ILE
Chi-restraints excluded: chain P residue  395 SER
Chi-restraints excluded: chain P residue  419 ARG
Chi-restraints excluded: chain P residue  450 TYR
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 30 optimal weight:    0.7980
   chunk 36 optimal weight:    1.9990
   chunk 23 optimal weight:    2.9990
   chunk 40 optimal weight:    0.5980
   chunk 4 optimal weight:    0.8980
   chunk 59 optimal weight:    0.7980
   chunk 69 optimal weight:    3.9990
   chunk 45 optimal weight:    0.9990
   chunk 41 optimal weight:    0.6980
   chunk 67 optimal weight:    1.9990
   chunk 55 optimal weight:    3.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
P  35 ASN
P 378 ASN
P 393 GLN
P 396 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4367 r_free = 0.4367 target = 0.186119 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4118 r_free = 0.4118 target = 0.162391 restraints weight = 11146.286|
|-----------------------------------------------------------------------------|
r_work (start): 0.4104 rms_B_bonded: 1.26
r_work: 0.4014 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.3904 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.3904
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7159
moved from start:          0.3712

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   7995  Z= 0.199
  Angle     :  0.649   9.054  11376  Z= 0.345
  Chirality :  0.040   0.270   1307
  Planarity :  0.005   0.055   1000
  Dihedral  : 24.559 164.797   2411
  Min Nonbonded Distance : 1.831

Molprobity Statistics.
  All-atom Clashscore : 8.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.17 %
    Favored  : 98.83 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  : 15.65 %
    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 aren not related in a simple way.
  whole:  0.72 (0.33), residues: 596
  helix:  1.01 (0.27), residues: 339
  sheet:  0.15 (0.83), residues: 41
  loop : -0.16 (0.41), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG P 374 
 TYR   0.020   0.002   TYR P 450 
 PHE   0.023   0.002   PHE P 630 
 TRP   0.013   0.001   TRP P 570 
 HIS   0.005   0.001   HIS P 566 

Details of bonding type rmsd
  covalent geometry    : bond        0.00432 ( 7991)
  covalent geometry    : angle       0.64594 (11370)
  hydrogen bonds       : bond        0.05057 (  403)
  hydrogen bonds       : angle       4.40696 ( 1034)
  metal coordination   : bond        0.00707 (    4)
  metal coordination   : angle       2.91529 (    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
  125 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 117
  time to evaluate  : 0.186 
Fit side-chains
REVERT: P  238 ASP cc_start: 0.7508 (t0) cc_final: 0.7303 (t0)
REVERT: P  388 ASP cc_start: 0.7763 (m-30) cc_final: 0.7544 (m-30)
REVERT: P  419 ARG cc_start: 0.7949 (OUTLIER) cc_final: 0.7059 (ttp-170)
REVERT: P  483 LYS cc_start: 0.8267 (tppt) cc_final: 0.7571 (tppt)
REVERT: P  487 ASP cc_start: 0.7383 (m-30) cc_final: 0.7129 (m-30)
  outliers start: 8
  outliers final: 7
  residues processed: 121
  average time/residue: 0.5409
  time to fit residues: 68.8473
Evaluate side-chains
  117 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 109
  time to evaluate  : 0.152 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue  141 THR
Chi-restraints excluded: chain P residue  382 ILE
Chi-restraints excluded: chain P residue  395 SER
Chi-restraints excluded: chain P residue  419 ARG
Chi-restraints excluded: chain P residue  450 TYR
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 17 optimal weight:    2.9990
   chunk 9 optimal weight:    0.7980
   chunk 10 optimal weight:    0.9980
   chunk 64 optimal weight:    1.9990
   chunk 50 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9990
   chunk 57 optimal weight:    0.6980
   chunk 30 optimal weight:    0.5980
   chunk 25 optimal weight:    6.9990
   chunk 43 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
P  35 ASN
P 378 ASN
P 393 GLN
P 396 ASN
P 517 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4363 r_free = 0.4363 target = 0.185714 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4112 r_free = 0.4112 target = 0.161922 restraints weight = 11051.805|
|-----------------------------------------------------------------------------|
r_work (start): 0.4100 rms_B_bonded: 1.26
r_work: 0.4010 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.3901 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.3901
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7165
moved from start:          0.3807

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   7995  Z= 0.210
  Angle     :  0.662   8.899  11376  Z= 0.352
  Chirality :  0.041   0.276   1307
  Planarity :  0.005   0.055   1000
  Dihedral  : 24.589 165.570   2411
  Min Nonbonded Distance : 1.877

Molprobity Statistics.
  All-atom Clashscore : 8.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.34 %
    Favored  : 98.66 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 16.21 %
    Favored  : 81.77 %
  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 aren not related in a simple way.
  whole:  0.54 (0.33), residues: 596
  helix:  0.88 (0.27), residues: 339
  sheet:  0.16 (0.83), residues: 41
  loop : -0.29 (0.41), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG P 374 
 TYR   0.022   0.002   TYR P 450 
 PHE   0.023   0.002   PHE P 630 
 TRP   0.015   0.001   TRP P 570 
 HIS   0.006   0.001   HIS P 566 

Details of bonding type rmsd
  covalent geometry    : bond        0.00457 ( 7991)
  covalent geometry    : angle       0.65785 (11370)
  hydrogen bonds       : bond        0.05192 (  403)
  hydrogen bonds       : angle       4.44146 ( 1034)
  metal coordination   : bond        0.00709 (    4)
  metal coordination   : angle       3.26420 (    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: 11
    poor density    : 111
  time to evaluate  : 0.188 
Fit side-chains
REVERT: P  238 ASP cc_start: 0.7524 (t0) cc_final: 0.7303 (t0)
REVERT: P  388 ASP cc_start: 0.7783 (m-30) cc_final: 0.7555 (m-30)
REVERT: P  419 ARG cc_start: 0.7957 (OUTLIER) cc_final: 0.7097 (ttp-170)
REVERT: P  483 LYS cc_start: 0.8276 (tppt) cc_final: 0.7583 (tppt)
REVERT: P  487 ASP cc_start: 0.7383 (m-30) cc_final: 0.7124 (m-30)
  outliers start: 11
  outliers final: 8
  residues processed: 116
  average time/residue: 0.5855
  time to fit residues: 71.2752
Evaluate side-chains
  114 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 105
  time to evaluate  : 0.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue  141 THR
Chi-restraints excluded: chain P residue  327 THR
Chi-restraints excluded: chain P residue  382 ILE
Chi-restraints excluded: chain P residue  395 SER
Chi-restraints excluded: chain P residue  419 ARG
Chi-restraints excluded: chain P residue  450 TYR
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 49 optimal weight:    0.6980
   chunk 65 optimal weight:    1.9990
   chunk 2 optimal weight:    0.0870
   chunk 54 optimal weight:    0.6980
   chunk 28 optimal weight:    0.5980
   chunk 56 optimal weight:    0.5980
   chunk 42 optimal weight:    0.6980
   chunk 48 optimal weight:    0.5980
   chunk 22 optimal weight:    0.9990
   chunk 70 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9980
   overall best weight:    0.5158

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

Flipped N/Q/H residues before XYZ refinement:
P  35 ASN
P 378 ASN
P 393 GLN
P 396 ASN
P 517 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4386 r_free = 0.4386 target = 0.187872 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4139 r_free = 0.4139 target = 0.164199 restraints weight = 11229.030|
|-----------------------------------------------------------------------------|
r_work (start): 0.4126 rms_B_bonded: 1.27
r_work: 0.4037 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.3927 rms_B_bonded: 3.82 restraints_weight: 0.2500
r_work (final): 0.3927
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7117
moved from start:          0.3785

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= 0.164
  Angle     :  0.624   8.482  11376  Z= 0.333
  Chirality :  0.038   0.232   1307
  Planarity :  0.005   0.051   1000
  Dihedral  : 24.512 166.877   2411
  Min Nonbonded Distance : 1.885

Molprobity Statistics.
  All-atom Clashscore : 8.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.34 %
    Favored  : 98.66 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 16.39 %
    Favored  : 81.77 %
  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 aren not related in a simple way.
  whole:  0.81 (0.33), residues: 596
  helix:  1.18 (0.27), residues: 338
  sheet:  0.01 (0.82), residues: 41
  loop : -0.26 (0.41), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG P 374 
 TYR   0.017   0.002   TYR P 283 
 PHE   0.023   0.002   PHE P 630 
 TRP   0.013   0.001   TRP P 570 
 HIS   0.005   0.001   HIS P 566 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 ( 7991)
  covalent geometry    : angle       0.62191 (11370)
  hydrogen bonds       : bond        0.04758 (  403)
  hydrogen bonds       : angle       4.27858 ( 1034)
  metal coordination   : bond        0.00507 (    4)
  metal coordination   : angle       2.45136 (    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
  127 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 117
  time to evaluate  : 0.167 
Fit side-chains
REVERT: P  238 ASP cc_start: 0.7474 (t0) cc_final: 0.7252 (t0)
REVERT: P  388 ASP cc_start: 0.7795 (m-30) cc_final: 0.7568 (m-30)
REVERT: P  419 ARG cc_start: 0.7939 (OUTLIER) cc_final: 0.7056 (ttp-170)
REVERT: P  483 LYS cc_start: 0.8289 (tppt) cc_final: 0.7663 (tppt)
REVERT: P  487 ASP cc_start: 0.7407 (m-30) cc_final: 0.7180 (m-30)
REVERT: P  602 TYR cc_start: 0.8155 (m-80) cc_final: 0.7926 (m-80)
  outliers start: 10
  outliers final: 8
  residues processed: 119
  average time/residue: 0.5514
  time to fit residues: 68.9071
Evaluate side-chains
  122 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 113
  time to evaluate  : 0.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue  141 THR
Chi-restraints excluded: chain P residue  304 MET
Chi-restraints excluded: chain P residue  327 THR
Chi-restraints excluded: chain P residue  382 ILE
Chi-restraints excluded: chain P residue  419 ARG
Chi-restraints excluded: chain P residue  450 TYR
Chi-restraints excluded: chain P residue  541 GLU
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:    0.6980
   chunk 35 optimal weight:    0.5980
   chunk 53 optimal weight:    0.5980
   chunk 6 optimal weight:    0.9990
   chunk 1 optimal weight:    1.9990
   chunk 36 optimal weight:    0.9990
   chunk 40 optimal weight:    0.8980
   chunk 2 optimal weight:    0.0270
   chunk 68 optimal weight:   10.0000
   chunk 16 optimal weight:    0.9990
   chunk 17 optimal weight:    0.7980
   overall best weight:    0.5438

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

Flipped N/Q/H residues before XYZ refinement:
P  35 ASN
P 378 ASN
P 393 GLN
P 396 ASN
P 517 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4386 r_free = 0.4386 target = 0.187875 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4138 r_free = 0.4138 target = 0.164098 restraints weight = 11209.760|
|-----------------------------------------------------------------------------|
r_work (start): 0.4126 rms_B_bonded: 1.28
r_work: 0.4036 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.3926 rms_B_bonded: 3.84 restraints_weight: 0.2500
r_work (final): 0.3926
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7114
moved from start:          0.3826

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   7995  Z= 0.168
  Angle     :  0.622   8.394  11376  Z= 0.332
  Chirality :  0.038   0.236   1307
  Planarity :  0.005   0.051   1000
  Dihedral  : 24.520 167.072   2411
  Min Nonbonded Distance : 1.894

Molprobity Statistics.
  All-atom Clashscore : 8.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.01 %
    Favored  : 98.99 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  : 16.21 %
    Favored  : 82.32 %
  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 aren not related in a simple way.
  whole:  0.77 (0.33), residues: 596
  helix:  1.14 (0.27), residues: 339
  sheet:  0.08 (0.84), residues: 41
  loop : -0.30 (0.41), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG P 374 
 TYR   0.018   0.002   TYR P 283 
 PHE   0.022   0.002   PHE P 630 
 TRP   0.014   0.001   TRP P 570 
 HIS   0.005   0.001   HIS P 566 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 ( 7991)
  covalent geometry    : angle       0.61858 (11370)
  hydrogen bonds       : bond        0.04795 (  403)
  hydrogen bonds       : angle       4.31712 ( 1034)
  metal coordination   : bond        0.00552 (    4)
  metal coordination   : angle       2.70907 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2943.83 seconds
wall clock time: 50 minutes 43.62 seconds (3043.62 seconds total)