Starting phenix.real_space_refine
on Thu Jul  2 06:04:01 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8iaz_35323/07_2026/8iaz_35323.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8iaz_35323/07_2026/8iaz_35323.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8iaz_35323/07_2026/8iaz_35323.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8iaz_35323/07_2026/8iaz_35323.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8iaz_35323/07_2026/8iaz_35323.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8iaz_35323/07_2026/8iaz_35323.cif"
  }
  resolution = 3.0
  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=   0.000 sd=   0.012
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     P     203      5.49       5
     S      16      5.16       5
     C    3919      2.51       5
     N    1333      2.21       5
     O    1924      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s

  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: 7396
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 3110
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 384, 3110
          Classifications: {'peptide': 384}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 9, 'TRANS': 374}
          Unresolved non-hydrogen bonds: 16
          Unresolved non-hydrogen angles: 20
          Unresolved non-hydrogen dihedrals: 12
          Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 16
    Chain: "E"
      Number of atoms: 3464
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 163, 3464
          Classifications: {'RNA': 163}
          Modifications used: {'rna2p_pur': 12, 'rna2p_pyr': 10, 'rna3p_pur': 74, 'rna3p_pyr': 61}
          Link IDs: {'rna2p': 22, 'rna3p': 140}
          Chain breaks: 3
          Unresolved chain link angles: 12
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 18
          Unresolved non-hydrogen dihedrals: 8
          Unresolved non-hydrogen chiralities: 6
    Chain: "B"
      Number of atoms: 490
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 24, 490
          Classifications: {'DNA': 24}
          Link IDs: {'rna3p': 23}
    Chain: "C"
      Number of atoms: 331
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 16, 331
          Classifications: {'DNA': 16}
          Link IDs: {'rna3p': 15}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   2769  SG  CYS A 343      12.251  39.929  54.366  0.35 19.85           S
  ATOM   2791  SG  CYS A 346       9.833  37.189  55.351  0.14 23.35           S
  ATOM   2917  SG  CYS A 362      11.328  37.075  51.877  0.33 19.10           S
  ATOM   2929  SG  CYS A 364       8.759  39.462  52.559  0.16 24.39           S

  Time building chain proxies: 1.51, per 1000 atoms: 0.20
  Number of scatterers: 7396
  At special positions: 0
  Unit cell: (98.04, 123.84, 98.9, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      1     29.99
     S      16     16.00
     P     203     15.00
     O    1924      8.00
     N    1333      7.00
     C    3919      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: 0.47
  Conformation dependent library (CDL) restraints added in 176.1 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 401 "
        pdb="ZN    ZN A 401 " - pdb=" SG  CYS A 362 "
        pdb="ZN    ZN A 401 " - pdb=" SG  CYS A 346 "
        pdb="ZN    ZN A 401 " - pdb=" SG  CYS A 364 "
        pdb="ZN    ZN A 401 " - pdb=" SG  CYS A 343 "
      Number of angles added : 6


  764 Ramachandran restraints generated.
    382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  732

  Finding SS restraints...
    Secondary structure from input PDB file:
      11 helices and 3 sheets defined
      47.4% alpha, 12.0% beta
      52 base pairs and 111 stacking pairs defined.
    Time for finding SS restraints: 0.75
  Creating SS restraints...
    Processing helix  chain 'A' and resid 15 through 47
    Processing helix  chain 'A' and resid 53 through 63
      removed outlier: 3.657A  pdb=" N   VAL A  58 " --> pdb=" O   LYS A  54 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 72 through 77
      removed outlier: 3.670A  pdb=" N   VAL A  77 " --> pdb=" O   ILE A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 78 through 98
      removed outlier: 3.717A  pdb=" N   VAL A  82 " --> pdb=" O   SER A  78 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   LYS A  83 " --> pdb=" O   SER A  79 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   ALA A  92 " --> pdb=" O   ASN A  88 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   PHE A  93 " --> pdb=" O   GLY A  89 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   LYS A  98 " --> pdb=" O   THR A  94 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 212 through 214
      No H-bonds generated for 'chain 'A' and resid 212 through 214'
    Processing helix  chain 'A' and resid 215 through 242
      removed outlier: 3.751A  pdb=" N   ARG A 234 " --> pdb=" O   ARG A 230 " (cutoff:3.500A)
      removed outlier: 4.091A  pdb=" N   LYS A 235 " --> pdb=" O   SER A 231 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   TYR A 236 " --> pdb=" O   LEU A 232 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   GLU A 237 " --> pdb=" O   SER A 233 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   LYS A 241 " --> pdb=" O   GLU A 237 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   GLY A 242 " --> pdb=" O   ASN A 238 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 248 through 282
    Processing helix  chain 'A' and resid 293 through 300
      removed outlier: 3.614A  pdb=" N   MET A 297 " --> pdb=" O   ASN A 293 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   ASN A 300 " --> pdb=" O   GLY A 296 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 303 through 311
      removed outlier: 3.710A  pdb=" N   LYS A 311 " --> pdb=" O   VAL A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 311 through 327
    Processing helix  chain 'A' and resid 370 through 380
    Processing sheet with id=AA1, first strand: chain 'A' and resid 116 through 119
      removed outlier: 4.309A  pdb=" N   SER A 160 " --> pdb=" O   LEU A 175 " (cutoff:3.500A)
      removed outlier: 5.005A  pdb=" N   TYR A 170 " --> pdb=" O   ILE A  12 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   VAL A 174 " --> pdb=" O   PHE A   8 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   ARG A 142 " --> pdb=" O   ASN A  13 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 208 through 210
      removed outlier: 6.155A  pdb=" N   ILE A 287 " --> pdb=" O   ARG A 331 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   VAL A 332 " --> pdb=" O   GLU A 385 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 359 through 361

    154 hydrogen bonds defined for protein.
    435 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      124 hydrogen bonds
      218 hydrogen bond angles
      0 basepair planarities
      52 basepair parallelities
      111 stacking parallelities
  Total time for adding SS restraints: 0.93

  Time building geometry restraints manager: 0.61 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 817
        1.32 -     1.44: 3287
        1.44 -     1.56: 3440
        1.56 -     1.69: 396
        1.69 -     1.81: 22
  Bond restraints: 7962
  Sorted by residual:
  bond pdb=" O3'   C E 196 "
       pdb=" P     C E 197 "
    ideal  model  delta    sigma   weight residual
    1.607  1.432  0.175 1.50e-02 4.44e+03 1.36e+02
  bond pdb=" P     C E 196 "
       pdb=" OP2   C E 196 "
    ideal  model  delta    sigma   weight residual
    1.485  1.363  0.122 2.00e-02 2.50e+03 3.70e+01
  bond pdb=" P     C E 197 "
       pdb=" OP2   C E 197 "
    ideal  model  delta    sigma   weight residual
    1.485  1.392  0.093 2.00e-02 2.50e+03 2.17e+01
  bond pdb=" C3'   C E 196 "
       pdb=" O3'   C E 196 "
    ideal  model  delta    sigma   weight residual
    1.417  1.350  0.067 1.50e-02 4.44e+03 1.97e+01
  bond pdb=" P     C E 196 "
       pdb=" OP1   C E 196 "
    ideal  model  delta    sigma   weight residual
    1.485  1.398  0.087 2.00e-02 2.50e+03 1.88e+01
  ... (remaining 7957 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.86: 11598
        3.86 -     7.73: 67
        7.73 -    11.59: 8
       11.59 -    15.45: 0
       15.45 -    19.32: 1
  Bond angle restraints: 11674
  Sorted by residual:
  angle pdb=" O2'   C E 197 "
        pdb=" C2'   C E 197 "
        pdb=" C1'   C E 197 "
      ideal   model   delta    sigma   weight residual
     108.40   89.08   19.32 1.50e+00 4.44e-01 1.66e+02
  angle pdb=" O2'   A E 198 "
        pdb=" C2'   A E 198 "
        pdb=" C1'   A E 198 "
      ideal   model   delta    sigma   weight residual
     108.40   97.97   10.43 1.50e+00 4.44e-01 4.84e+01
  angle pdb=" C3'   A E 198 "
        pdb=" C2'   A E 198 "
        pdb=" O2'   A E 198 "
      ideal   model   delta    sigma   weight residual
     110.70  100.37   10.33 1.50e+00 4.44e-01 4.74e+01
  angle pdb=" C4'  DG C   4 "
        pdb=" O4'  DG C   4 "
        pdb=" C1'  DG C   4 "
      ideal   model   delta    sigma   weight residual
     110.10  103.27    6.83 1.00e+00 1.00e+00 4.67e+01
  angle pdb=" C2'   C E 197 "
        pdb=" C1'   C E 197 "
        pdb=" N1    C E 197 "
      ideal   model   delta    sigma   weight residual
     112.00  120.95   -8.95 1.50e+00 4.44e-01 3.56e+01
  ... (remaining 11669 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.58: 4227
       35.58 -    71.16: 592
       71.16 -   106.74: 32
      106.74 -   142.32: 6
      142.32 -   177.89: 15
  Dihedral angle restraints: 4872
    sinusoidal: 3740
      harmonic: 1132
  Sorted by residual:
  dihedral pdb=" O4'   U E 189 "
           pdb=" C1'   U E 189 "
           pdb=" N1    U E 189 "
           pdb=" C2    U E 189 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -160.00   17.31 -177.31     1      1.50e+01 4.44e-03 8.53e+01
  dihedral pdb=" O4'   U E  82 "
           pdb=" C1'   U E  82 "
           pdb=" N1    U E  82 "
           pdb=" C2    U E  82 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -160.00   16.45 -176.45     1      1.50e+01 4.44e-03 8.53e+01
  dihedral pdb=" O4'   U E 134 "
           pdb=" C1'   U E 134 "
           pdb=" N1    U E 134 "
           pdb=" C2    U E 134 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -160.00    7.65 -167.65     1      1.50e+01 4.44e-03 8.43e+01
  ... (remaining 4869 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.070: 1256
       0.070 -    0.140: 138
       0.140 -    0.210: 26
       0.210 -    0.279: 5
       0.279 -    0.349: 3
  Chirality restraints: 1428
  Sorted by residual:
  chirality pdb=" P     C E 196 "
            pdb=" OP1   C E 196 "
            pdb=" OP2   C E 196 "
            pdb=" O5'   C E 196 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.06    0.35 2.00e-01 2.50e+01 3.05e+00
  chirality pdb=" P     C E 197 "
            pdb=" OP1   C E 197 "
            pdb=" OP2   C E 197 "
            pdb=" O5'   C E 197 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.06    0.35 2.00e-01 2.50e+01 3.01e+00
  chirality pdb=" C1'   C E 197 "
            pdb=" O4'   C E 197 "
            pdb=" C2'   C E 197 "
            pdb=" N1    C E 197 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.47    2.14    0.32 2.00e-01 2.50e+01 2.58e+00
  ... (remaining 1425 not shown)

  Planarity restraints: 736
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   C E 196 "    0.066 2.00e-02 2.50e+03   3.51e-02 2.78e+01
        pdb=" N1    C E 196 "   -0.047 2.00e-02 2.50e+03
        pdb=" C2    C E 196 "   -0.036 2.00e-02 2.50e+03
        pdb=" O2    C E 196 "    0.007 2.00e-02 2.50e+03
        pdb=" N3    C E 196 "    0.004 2.00e-02 2.50e+03
        pdb=" C4    C E 196 "   -0.022 2.00e-02 2.50e+03
        pdb=" N4    C E 196 "    0.040 2.00e-02 2.50e+03
        pdb=" C5    C E 196 "    0.017 2.00e-02 2.50e+03
        pdb=" C6    C E 196 "   -0.029 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   C E 197 "    0.037 2.00e-02 2.50e+03   2.72e-02 1.66e+01
        pdb=" N1    C E 197 "   -0.032 2.00e-02 2.50e+03
        pdb=" C2    C E 197 "   -0.001 2.00e-02 2.50e+03
        pdb=" O2    C E 197 "    0.015 2.00e-02 2.50e+03
        pdb=" N3    C E 197 "   -0.050 2.00e-02 2.50e+03
        pdb=" C4    C E 197 "    0.018 2.00e-02 2.50e+03
        pdb=" N4    C E 197 "    0.032 2.00e-02 2.50e+03
        pdb=" C5    C E 197 "   -0.007 2.00e-02 2.50e+03
        pdb=" C6    C E 197 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DG C   4 "   -0.021 2.00e-02 2.50e+03   1.78e-02 9.53e+00
        pdb=" N9   DG C   4 "    0.038 2.00e-02 2.50e+03
        pdb=" C8   DG C   4 "    0.023 2.00e-02 2.50e+03
        pdb=" N7   DG C   4 "   -0.013 2.00e-02 2.50e+03
        pdb=" C5   DG C   4 "   -0.021 2.00e-02 2.50e+03
        pdb=" C6   DG C   4 "   -0.011 2.00e-02 2.50e+03
        pdb=" O6   DG C   4 "    0.008 2.00e-02 2.50e+03
        pdb=" N1   DG C   4 "    0.004 2.00e-02 2.50e+03
        pdb=" C2   DG C   4 "    0.011 2.00e-02 2.50e+03
        pdb=" N2   DG C   4 "    0.008 2.00e-02 2.50e+03
        pdb=" N3   DG C   4 "   -0.017 2.00e-02 2.50e+03
        pdb=" C4   DG C   4 "   -0.009 2.00e-02 2.50e+03
  ... (remaining 733 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1414
        2.77 -     3.30: 5910
        3.30 -     3.84: 14132
        3.84 -     4.37: 16748
        4.37 -     4.90: 23310
  Nonbonded interactions: 61514
  Sorted by model distance:
  nonbonded pdb=" O2'   C E 152 "
            pdb=" OP1   G E 153 "
     model   vdw
     2.239 3.040
  nonbonded pdb=" O   SER A  52 "
            pdb=" OG  SER A  52 "
     model   vdw
     2.244 3.040
  nonbonded pdb=" O   MET A 298 "
            pdb=" OG  SER A 304 "
     model   vdw
     2.284 3.040
  nonbonded pdb=" O2'   A E  48 "
            pdb=" OP1   C E  49 "
     model   vdw
     2.284 3.040
  nonbonded pdb=" OE1 GLU A  11 "
            pdb=" O2'   G E  30 "
     model   vdw
     2.288 3.040
  ... (remaining 61509 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=0.00 max=1.00 mean=0.96
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:             1.220
  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:             0.020
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     7.520
  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:8.110
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.040
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8304
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.175   7966  Z= 0.507
  Angle     :  0.835  19.318  11680  Z= 0.660
  Chirality :  0.049   0.349   1428
  Planarity :  0.005   0.048    736
  Dihedral  : 26.191 177.894   4140
  Min Nonbonded Distance : 2.239

Molprobity Statistics.
  All-atom Clashscore : 8.08
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  7.07 %
    Favored  : 92.67 %
  Rotamer:
    Outliers :  4.37 %
    Allowed  : 34.69 %
    Favored  : 60.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.24 (0.43), residues: 382
  helix:  2.50 (0.40), residues: 167
  sheet: -0.18 (0.89), residues: 41
  loop : -2.29 (0.40), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 130 
 TYR   0.014   0.002   TYR A  44 
 PHE   0.014   0.002   PHE A 360 
 TRP   0.004   0.001   TRP A 140 
 HIS   0.005   0.001   HIS A  99 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00631 /  0.51 ( 7962)
  covalent geometry    : angle       0.82777 /  0.66 (11674)
  hydrogen bonds       : bond        0.15517 /  9.73 (  278)
  hydrogen bonds       : angle       4.60152 /  3.49 (  653)
  metal coordination   : bond        0.00755 /  0.38 (    4)
  metal coordination   : angle       4.95686 /  2.47 (    6)

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

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

  764 Ramachandran restraints generated.
    382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  764 Ramachandran restraints generated.
    382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 48
  time to evaluate  : 0.129 
Fit side-chains
   revert: symmetry clash
REVERT: A   51 MET cc_start: 0.8216 (ttm) cc_final: 0.7928 (ttm)
REVERT: A  188 ASN cc_start: 0.6485 (m-40) cc_final: 0.6041 (m110)
REVERT: A  210 LYS cc_start: 0.8479 (mtpm) cc_final: 0.8094 (mmtm)
REVERT: A  228 GLU cc_start: 0.8464 (mm-30) cc_final: 0.7980 (mm-30)
REVERT: A  254 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.7887 (mtm180)
REVERT: A  301 ARG cc_start: 0.8431 (tpp-160) cc_final: 0.8196 (tpp-160)
REVERT: A  336 TRP cc_start: 0.8144 (m-90) cc_final: 0.7833 (m100)
  outliers start: 15
  outliers final: 10
  residues processed: 63
  average time/residue: 0.4676
  time to fit residues: 31.1628
Evaluate side-chains
  50 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 39
  time to evaluate  : 0.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 ILE
Chi-restraints excluded: chain A residue   77 VAL
Chi-restraints excluded: chain A residue  101 SER
Chi-restraints excluded: chain A residue  137 SER
Chi-restraints excluded: chain A residue  152 THR
Chi-restraints excluded: chain A residue  164 SER
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  254 ARG
Chi-restraints excluded: chain A residue  280 VAL
Chi-restraints excluded: chain A residue  287 ILE
Chi-restraints excluded: chain A residue  362 CYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 54 optimal weight:   10.0000
   chunk 24 optimal weight:    3.9990
   chunk 48 optimal weight:    9.9990
   chunk 56 optimal weight:   10.0000
   chunk 26 optimal weight:    2.9990
   chunk 2 optimal weight:    0.6980
   chunk 16 optimal weight:    0.7980
   chunk 32 optimal weight:    0.3980
   chunk 31 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9990
   chunk 50 optimal weight:   10.0000
   overall best weight:    0.7784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  62 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.185578 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.150776 restraints weight = 7082.500|
|-----------------------------------------------------------------------------|
r_work (start): 0.3573 rms_B_bonded: 0.49
r_work: 0.3245 rms_B_bonded: 4.10 restraints_weight: 0.5000
r_work (final): 0.3245
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3176
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3176 r_free = 0.3176    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      200 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3162 r_free = 0.3162    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      205 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 7 (12 function evaluations)
r_final: 0.3162
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8447
moved from start:          0.0795

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   7966  Z= 0.144
  Angle     :  0.595  11.768  11680  Z= 0.353
  Chirality :  0.041   0.294   1428
  Planarity :  0.004   0.040    736
  Dihedral  : 26.754 178.792   3352
  Min Nonbonded Distance : 2.365

Molprobity Statistics.
  All-atom Clashscore : 6.33
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  6.54 %
    Favored  : 93.19 %
  Rotamer:
    Outliers :  6.12 %
    Allowed  : 30.32 %
    Favored  : 63.56 %
  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:  0.49 (0.43), residues: 382
  helix:  2.81 (0.39), residues: 169
  sheet: -0.16 (0.83), residues: 41
  loop : -2.31 (0.40), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  95 
 TYR   0.010   0.001   TYR A  33 
 PHE   0.011   0.001   PHE A 200 
 TRP   0.002   0.000   TRP A 336 
 HIS   0.004   0.001   HIS A  99 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00239 /  0.14 ( 7962)
  covalent geometry    : angle       0.58450 /  0.35 (11674)
  hydrogen bonds       : bond        0.06860 /  4.55 (  278)
  hydrogen bonds       : angle       3.64898 /  2.83 (  653)
  metal coordination   : bond        0.01070 /  0.54 (    4)
  metal coordination   : angle       4.87602 /  2.42 (    6)

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

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

  764 Ramachandran restraints generated.
    382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  764 Ramachandran restraints generated.
    382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 36
  time to evaluate  : 0.119 
Fit side-chains
REVERT: A   41 LYS cc_start: 0.6975 (OUTLIER) cc_final: 0.6437 (ttpt)
REVERT: A   51 MET cc_start: 0.8115 (ttm) cc_final: 0.7761 (ttm)
REVERT: A   62 ASN cc_start: 0.8608 (m-40) cc_final: 0.8378 (m110)
REVERT: A   75 LYS cc_start: 0.7989 (OUTLIER) cc_final: 0.7581 (ptpt)
REVERT: A  152 THR cc_start: 0.9136 (OUTLIER) cc_final: 0.8890 (p)
REVERT: A  188 ASN cc_start: 0.6898 (m-40) cc_final: 0.6513 (m110)
REVERT: A  210 LYS cc_start: 0.8332 (mtpm) cc_final: 0.7966 (mmtm)
REVERT: A  256 LYS cc_start: 0.8331 (ttmm) cc_final: 0.8081 (mtmm)
REVERT: A  301 ARG cc_start: 0.8445 (tpp-160) cc_final: 0.8206 (tpp-160)
  outliers start: 21
  outliers final: 9
  residues processed: 56
  average time/residue: 0.4601
  time to fit residues: 27.2564
Evaluate side-chains
  45 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 33
  time to evaluate  : 0.112 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 ILE
Chi-restraints excluded: chain A residue   41 LYS
Chi-restraints excluded: chain A residue   52 SER
Chi-restraints excluded: chain A residue   75 LYS
Chi-restraints excluded: chain A residue   91 ILE
Chi-restraints excluded: chain A residue  101 SER
Chi-restraints excluded: chain A residue  152 THR
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  237 GLU
Chi-restraints excluded: chain A residue  287 ILE
Chi-restraints excluded: chain A residue  359 ILE
Chi-restraints excluded: chain A residue  362 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 28 optimal weight:    2.9990
   chunk 41 optimal weight:   10.0000
   chunk 26 optimal weight:    5.9990
   chunk 34 optimal weight:   10.0000
   chunk 2 optimal weight:    0.8980
   chunk 25 optimal weight:    2.9990
   chunk 22 optimal weight:    1.9990
   chunk 40 optimal weight:   10.0000
   chunk 0 optimal weight:    5.9990
   chunk 49 optimal weight:   10.0000
   chunk 1 optimal weight:    4.9990
   overall best weight:    2.7788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 373 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.178536 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.142604 restraints weight = 6967.361|
|-----------------------------------------------------------------------------|
r_work (start): 0.3516 rms_B_bonded: 0.87
r_work: 0.3228 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.3228
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3106
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3106 r_free = 0.3106    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      205 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3105 r_free = 0.3105    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      207 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (9 function evaluations)
r_final: 0.3105
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8533
moved from start:          0.1279

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.061   7966  Z= 0.226
  Angle     :  0.671  11.136  11680  Z= 0.393
  Chirality :  0.047   0.293   1428
  Planarity :  0.005   0.043    736
  Dihedral  : 26.722 178.281   3344
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 4.33
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  7.33 %
    Favored  : 92.41 %
  Rotamer:
    Outliers :  7.00 %
    Allowed  : 28.57 %
    Favored  : 64.43 %
  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:  0.25 (0.43), residues: 382
  helix:  2.37 (0.39), residues: 175
  sheet: -0.19 (0.84), residues: 41
  loop : -2.35 (0.40), residues: 166

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 130 
 TYR   0.011   0.002   TYR A 156 
 PHE   0.016   0.002   PHE A  35 
 TRP   0.004   0.001   TRP A 140 
 HIS   0.004   0.002   HIS A  39 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00456 /  0.23 ( 7962)
  covalent geometry    : angle       0.66309 /  0.39 (11674)
  hydrogen bonds       : bond        0.08921 /  6.12 (  278)
  hydrogen bonds       : angle       3.59626 /  2.74 (  653)
  metal coordination   : bond        0.01155 /  0.57 (    4)
  metal coordination   : angle       4.59181 /  1.97 (    6)

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

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

  764 Ramachandran restraints generated.
    382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  764 Ramachandran restraints generated.
    382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 33
  time to evaluate  : 0.098 
Fit side-chains
REVERT: A   41 LYS cc_start: 0.7127 (OUTLIER) cc_final: 0.6691 (ttpt)
REVERT: A   51 MET cc_start: 0.8188 (ttm) cc_final: 0.7867 (ttm)
REVERT: A   62 ASN cc_start: 0.8587 (m-40) cc_final: 0.8350 (m110)
REVERT: A   75 LYS cc_start: 0.7968 (OUTLIER) cc_final: 0.7337 (ptpt)
REVERT: A  127 ARG cc_start: 0.8500 (ptt180) cc_final: 0.8135 (ptt-90)
REVERT: A  202 ILE cc_start: 0.8072 (OUTLIER) cc_final: 0.7847 (tp)
REVERT: A  210 LYS cc_start: 0.8295 (mtpm) cc_final: 0.7851 (mmtm)
REVERT: A  385 GLU cc_start: 0.6673 (pt0) cc_final: 0.6374 (pm20)
  outliers start: 24
  outliers final: 11
  residues processed: 53
  average time/residue: 0.4563
  time to fit residues: 25.4911
Evaluate side-chains
  45 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 31
  time to evaluate  : 0.180 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 ILE
Chi-restraints excluded: chain A residue   41 LYS
Chi-restraints excluded: chain A residue   52 SER
Chi-restraints excluded: chain A residue   75 LYS
Chi-restraints excluded: chain A residue   82 VAL
Chi-restraints excluded: chain A residue   95 ARG
Chi-restraints excluded: chain A residue  162 THR
Chi-restraints excluded: chain A residue  202 ILE
Chi-restraints excluded: chain A residue  237 GLU
Chi-restraints excluded: chain A residue  254 ARG
Chi-restraints excluded: chain A residue  280 VAL
Chi-restraints excluded: chain A residue  287 ILE
Chi-restraints excluded: chain A residue  362 CYS
Chi-restraints excluded: chain A residue  383 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 10 optimal weight:    0.7980
   chunk 0 optimal weight:    5.9990
   chunk 7 optimal weight:    1.9990
   chunk 36 optimal weight:    0.7980
   chunk 23 optimal weight:    0.9990
   chunk 53 optimal weight:   10.0000
   chunk 35 optimal weight:    5.9990
   chunk 51 optimal weight:   20.0000
   chunk 8 optimal weight:    1.9990
   chunk 40 optimal weight:   10.0000
   chunk 33 optimal weight:    0.9980
   overall best weight:    1.1184

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.182968 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.147353 restraints weight = 7152.938|
|-----------------------------------------------------------------------------|
r_work (start): 0.3573 rms_B_bonded: 0.48
r_work: 0.3304 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.3304
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3180
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3180 r_free = 0.3180    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      207 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3179 r_free = 0.3179    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      208 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3179
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8440
moved from start:          0.1376

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   7966  Z= 0.138
  Angle     :  0.570  11.285  11680  Z= 0.338
  Chirality :  0.041   0.285   1428
  Planarity :  0.004   0.038    736
  Dihedral  : 26.612 178.924   3340
  Min Nonbonded Distance : 2.381

Molprobity Statistics.
  All-atom Clashscore : 5.13
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  6.81 %
    Favored  : 92.93 %
  Rotamer:
    Outliers :  4.96 %
    Allowed  : 30.90 %
    Favored  : 64.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.51 (0.43), residues: 382
  helix:  2.74 (0.39), residues: 174
  sheet: -0.01 (0.82), residues: 41
  loop : -2.40 (0.40), residues: 167

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  95 
 TYR   0.011   0.001   TYR A  33 
 PHE   0.009   0.001   PHE A 118 
 TRP   0.003   0.000   TRP A 336 
 HIS   0.004   0.001   HIS A  99 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00234 /  0.14 ( 7962)
  covalent geometry    : angle       0.55956 /  0.34 (11674)
  hydrogen bonds       : bond        0.06656 /  4.50 (  278)
  hydrogen bonds       : angle       3.41478 /  2.63 (  653)
  metal coordination   : bond        0.00694 /  0.35 (    4)
  metal coordination   : angle       4.90611 /  2.36 (    6)

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

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

  764 Ramachandran restraints generated.
    382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  764 Ramachandran restraints generated.
    382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 33
  time to evaluate  : 0.119 
Fit side-chains
REVERT: A   41 LYS cc_start: 0.6937 (tptm) cc_final: 0.6503 (ttpt)
REVERT: A   62 ASN cc_start: 0.8535 (m-40) cc_final: 0.8334 (m110)
REVERT: A   75 LYS cc_start: 0.7914 (OUTLIER) cc_final: 0.7166 (ptpt)
REVERT: A  127 ARG cc_start: 0.8459 (ptt180) cc_final: 0.8095 (ptt-90)
REVERT: A  210 LYS cc_start: 0.8166 (mtpm) cc_final: 0.7720 (mmtm)
REVERT: A  254 ARG cc_start: 0.8563 (OUTLIER) cc_final: 0.8031 (mtm180)
REVERT: A  256 LYS cc_start: 0.8280 (ttmm) cc_final: 0.8056 (mtmm)
REVERT: A  329 GLU cc_start: 0.8266 (pm20) cc_final: 0.7764 (pm20)
REVERT: A  357 ASP cc_start: 0.7352 (p0) cc_final: 0.6995 (p0)
REVERT: A  385 GLU cc_start: 0.6551 (pt0) cc_final: 0.6304 (pm20)
  outliers start: 17
  outliers final: 7
  residues processed: 47
  average time/residue: 0.5563
  time to fit residues: 27.4599
Evaluate side-chains
  41 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 32
  time to evaluate  : 0.116 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 ILE
Chi-restraints excluded: chain A residue   52 SER
Chi-restraints excluded: chain A residue   75 LYS
Chi-restraints excluded: chain A residue  237 GLU
Chi-restraints excluded: chain A residue  254 ARG
Chi-restraints excluded: chain A residue  280 VAL
Chi-restraints excluded: chain A residue  287 ILE
Chi-restraints excluded: chain A residue  359 ILE
Chi-restraints excluded: chain A residue  362 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 47 optimal weight:   10.0000
   chunk 42 optimal weight:   10.0000
   chunk 20 optimal weight:    6.9990
   chunk 25 optimal weight:    2.9990
   chunk 31 optimal weight:    0.6980
   chunk 56 optimal weight:   10.0000
   chunk 18 optimal weight:    9.9990
   chunk 54 optimal weight:    9.9990
   chunk 49 optimal weight:   10.0000
   chunk 46 optimal weight:   10.0000
   chunk 35 optimal weight:    5.9990
   overall best weight:    5.3388

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  68 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.178866 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.145001 restraints weight = 6932.962|
|-----------------------------------------------------------------------------|
r_work (start): 0.3469 rms_B_bonded: 0.88
r_work: 0.3148 rms_B_bonded: 3.74 restraints_weight: 0.5000
r_work (final): 0.3148
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3064
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3064 r_free = 0.3064    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      208 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3064 r_free = 0.3064    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      206 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (10 function evaluations)
r_final: 0.3064
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8609
moved from start:          0.1778

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.078   7966  Z= 0.362
  Angle     :  0.852  10.798  11680  Z= 0.483
  Chirality :  0.057   0.381   1428
  Planarity :  0.006   0.043    736
  Dihedral  : 26.817 178.444   3340
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 3.77
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  8.38 %
    Favored  : 91.36 %
  Rotamer:
    Outliers :  7.29 %
    Allowed  : 26.82 %
    Favored  : 65.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.36 (0.42), residues: 382
  helix:  1.73 (0.38), residues: 175
  sheet: -0.24 (0.80), residues: 41
  loop : -2.56 (0.40), residues: 166

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A 130 
 TYR   0.015   0.003   TYR A 171 
 PHE   0.027   0.003   PHE A  35 
 TRP   0.010   0.003   TRP A 140 
 HIS   0.006   0.002   HIS A  39 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00775 /  0.36 ( 7962)
  covalent geometry    : angle       0.84318 /  0.48 (11674)
  hydrogen bonds       : bond        0.11774 /  8.23 (  278)
  hydrogen bonds       : angle       3.77666 /  2.83 (  653)
  metal coordination   : bond        0.01306 /  0.64 (    4)
  metal coordination   : angle       5.30706 /  1.96 (    6)

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

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

  764 Ramachandran restraints generated.
    382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  764 Ramachandran restraints generated.
    382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 39
  time to evaluate  : 0.107 
Fit side-chains
REVERT: A   41 LYS cc_start: 0.7329 (OUTLIER) cc_final: 0.6930 (ttpt)
REVERT: A   62 ASN cc_start: 0.8529 (m-40) cc_final: 0.8325 (m110)
REVERT: A  106 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8284 (mp)
REVERT: A  210 LYS cc_start: 0.8372 (mtpm) cc_final: 0.7886 (mttm)
REVERT: A  385 GLU cc_start: 0.6658 (pt0) cc_final: 0.6357 (pm20)
  outliers start: 25
  outliers final: 12
  residues processed: 60
  average time/residue: 0.5267
  time to fit residues: 33.1413
Evaluate side-chains
  46 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 32
  time to evaluate  : 0.138 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 ILE
Chi-restraints excluded: chain A residue   41 LYS
Chi-restraints excluded: chain A residue   52 SER
Chi-restraints excluded: chain A residue   95 ARG
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  137 SER
Chi-restraints excluded: chain A residue  162 THR
Chi-restraints excluded: chain A residue  237 GLU
Chi-restraints excluded: chain A residue  245 THR
Chi-restraints excluded: chain A residue  254 ARG
Chi-restraints excluded: chain A residue  280 VAL
Chi-restraints excluded: chain A residue  287 ILE
Chi-restraints excluded: chain A residue  362 CYS
Chi-restraints excluded: chain A residue  383 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 11 optimal weight:    1.9990
   chunk 29 optimal weight:    4.9990
   chunk 25 optimal weight:    0.9980
   chunk 50 optimal weight:   10.0000
   chunk 54 optimal weight:    9.9990
   chunk 41 optimal weight:   10.0000
   chunk 45 optimal weight:   20.0000
   chunk 47 optimal weight:   10.0000
   chunk 38 optimal weight:    8.9990
   chunk 24 optimal weight:    2.9990
   chunk 20 optimal weight:    1.9990
   overall best weight:    2.5988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  68 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.176754 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.140942 restraints weight = 7078.765|
|-----------------------------------------------------------------------------|
r_work (start): 0.3404 rms_B_bonded: 0.80
r_work: 0.3119 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.3119
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3071
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3071 r_free = 0.3071    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      206 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3071 r_free = 0.3071    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      206 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (10 function evaluations)
r_final: 0.3071
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8543
moved from start:          0.1780

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   7966  Z= 0.209
  Angle     :  0.671  11.037  11680  Z= 0.392
  Chirality :  0.047   0.293   1428
  Planarity :  0.004   0.038    736
  Dihedral  : 26.734 178.638   3340
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 4.81
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  6.81 %
    Favored  : 92.93 %
  Rotamer:
    Outliers :  5.25 %
    Allowed  : 30.03 %
    Favored  : 64.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.12 (0.43), residues: 382
  helix:  2.11 (0.39), residues: 174
  sheet: -0.15 (0.81), residues: 41
  loop : -2.64 (0.40), residues: 167

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A  95 
 TYR   0.013   0.002   TYR A  33 
 PHE   0.016   0.002   PHE A  35 
 TRP   0.005   0.001   TRP A 336 
 HIS   0.005   0.001   HIS A  99 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00418 /  0.21 ( 7962)
  covalent geometry    : angle       0.66165 /  0.39 (11674)
  hydrogen bonds       : bond        0.08943 /  6.18 (  278)
  hydrogen bonds       : angle       3.59163 /  2.73 (  653)
  metal coordination   : bond        0.00846 /  0.42 (    4)
  metal coordination   : angle       5.04676 /  2.15 (    6)

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

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

  764 Ramachandran restraints generated.
    382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  764 Ramachandran restraints generated.
    382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 34
  time to evaluate  : 0.107 
Fit side-chains
REVERT: A   41 LYS cc_start: 0.7170 (OUTLIER) cc_final: 0.6708 (ttpt)
REVERT: A  124 LYS cc_start: 0.7687 (OUTLIER) cc_final: 0.7368 (ttpt)
REVERT: A  210 LYS cc_start: 0.8297 (mtpm) cc_final: 0.7805 (mttm)
REVERT: A  385 GLU cc_start: 0.6604 (pt0) cc_final: 0.6300 (pm20)
  outliers start: 18
  outliers final: 9
  residues processed: 48
  average time/residue: 0.5862
  time to fit residues: 29.3810
Evaluate side-chains
  43 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 32
  time to evaluate  : 0.106 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 ILE
Chi-restraints excluded: chain A residue   41 LYS
Chi-restraints excluded: chain A residue   52 SER
Chi-restraints excluded: chain A residue   94 THR
Chi-restraints excluded: chain A residue   95 ARG
Chi-restraints excluded: chain A residue  124 LYS
Chi-restraints excluded: chain A residue  162 THR
Chi-restraints excluded: chain A residue  237 GLU
Chi-restraints excluded: chain A residue  254 ARG
Chi-restraints excluded: chain A residue  280 VAL
Chi-restraints excluded: chain A residue  287 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 33 optimal weight:    0.0060
   chunk 31 optimal weight:    1.9990
   chunk 49 optimal weight:   10.0000
   chunk 7 optimal weight:    3.9990
   chunk 43 optimal weight:   20.0000
   chunk 32 optimal weight:    0.0370
   chunk 39 optimal weight:   10.0000
   chunk 47 optimal weight:   10.0000
   chunk 41 optimal weight:   10.0000
   chunk 2 optimal weight:    0.9990
   chunk 34 optimal weight:    0.9990
   overall best weight:    0.8080

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  68 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.182370 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.146780 restraints weight = 7140.905|
|-----------------------------------------------------------------------------|
r_work (start): 0.3570 rms_B_bonded: 0.51
r_work: 0.3315 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work (final): 0.3315
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3207
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3207 r_free = 0.3207    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      206 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3206 r_free = 0.3206    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      208 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (10 function evaluations)
r_final: 0.3206
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8429
moved from start:          0.1809

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   7966  Z= 0.132
  Angle     :  0.568  11.223  11680  Z= 0.339
  Chirality :  0.040   0.289   1428
  Planarity :  0.004   0.037    736
  Dihedral  : 26.552 179.769   3339
  Min Nonbonded Distance : 2.382

Molprobity Statistics.
  All-atom Clashscore : 5.21
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  6.54 %
    Favored  : 93.19 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 30.90 %
    Favored  : 65.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.43 (0.44), residues: 382
  helix:  2.71 (0.40), residues: 171
  sheet:  0.30 (0.84), residues: 41
  loop : -2.48 (0.41), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  95 
 TYR   0.012   0.001   TYR A  33 
 PHE   0.006   0.001   PHE A 118 
 TRP   0.003   0.000   TRP A 336 
 HIS   0.004   0.001   HIS A  99 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00207 /  0.13 ( 7962)
  covalent geometry    : angle       0.55803 /  0.34 (11674)
  hydrogen bonds       : bond        0.06552 /  4.47 (  278)
  hydrogen bonds       : angle       3.43201 /  2.65 (  653)
  metal coordination   : bond        0.00466 /  0.23 (    4)
  metal coordination   : angle       4.76330 /  2.30 (    6)

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

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

  764 Ramachandran restraints generated.
    382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  764 Ramachandran restraints generated.
    382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 33
  time to evaluate  : 0.112 
Fit side-chains
REVERT: A   41 LYS cc_start: 0.6914 (OUTLIER) cc_final: 0.6487 (ttpt)
REVERT: A  124 LYS cc_start: 0.7570 (OUTLIER) cc_final: 0.7313 (tppt)
REVERT: A  210 LYS cc_start: 0.8148 (mtpm) cc_final: 0.7671 (mttm)
REVERT: A  254 ARG cc_start: 0.8538 (OUTLIER) cc_final: 0.8032 (mtm180)
REVERT: A  385 GLU cc_start: 0.6441 (pt0) cc_final: 0.6186 (pm20)
  outliers start: 14
  outliers final: 4
  residues processed: 44
  average time/residue: 0.5407
  time to fit residues: 24.9767
Evaluate side-chains
  37 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 30
  time to evaluate  : 0.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 ILE
Chi-restraints excluded: chain A residue   41 LYS
Chi-restraints excluded: chain A residue   52 SER
Chi-restraints excluded: chain A residue  124 LYS
Chi-restraints excluded: chain A residue  237 GLU
Chi-restraints excluded: chain A residue  254 ARG
Chi-restraints excluded: chain A residue  287 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 54 optimal weight:    9.9990
   chunk 38 optimal weight:   10.0000
   chunk 29 optimal weight:    6.9990
   chunk 17 optimal weight:    1.9990
   chunk 56 optimal weight:   20.0000
   chunk 43 optimal weight:   20.0000
   chunk 51 optimal weight:   20.0000
   chunk 21 optimal weight:    3.9990
   chunk 37 optimal weight:    2.9990
   chunk 41 optimal weight:   10.0000
   chunk 45 optimal weight:   20.0000
   overall best weight:    5.1990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  68 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.173866 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.138126 restraints weight = 7117.641|
|-----------------------------------------------------------------------------|
r_work (start): 0.3431 rms_B_bonded: 0.93
r_work: 0.3104 rms_B_bonded: 3.94 restraints_weight: 0.5000
r_work (final): 0.3104
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3015
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3015 r_free = 0.3015    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      208 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3014 r_free = 0.3014    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      207 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (10 function evaluations)
r_final: 0.3014
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8610
moved from start:          0.1995

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.066   7966  Z= 0.353
  Angle     :  0.820  10.837  11680  Z= 0.465
  Chirality :  0.056   0.368   1428
  Planarity :  0.006   0.042    736
  Dihedral  : 26.713 179.800   3339
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 3.93
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  8.38 %
    Favored  : 91.36 %
  Rotamer:
    Outliers :  4.37 %
    Allowed  : 31.20 %
    Favored  : 64.43 %
  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: -0.34 (0.42), residues: 382
  helix:  1.83 (0.39), residues: 174
  sheet: -0.10 (0.81), residues: 41
  loop : -2.69 (0.40), residues: 167

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A  95 
 TYR   0.014   0.003   TYR A 171 
 PHE   0.023   0.003   PHE A  35 
 TRP   0.009   0.003   TRP A 140 
 HIS   0.005   0.001   HIS A  39 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00754 /  0.35 ( 7962)
  covalent geometry    : angle       0.81188 /  0.47 (11674)
  hydrogen bonds       : bond        0.11131 /  7.78 (  278)
  hydrogen bonds       : angle       3.71150 /  2.81 (  653)
  metal coordination   : bond        0.01097 /  0.54 (    4)
  metal coordination   : angle       5.08249 /  1.91 (    6)

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

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

  764 Ramachandran restraints generated.
    382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  764 Ramachandran restraints generated.
    382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 33
  time to evaluate  : 0.133 
Fit side-chains
REVERT: A   41 LYS cc_start: 0.7352 (OUTLIER) cc_final: 0.6920 (ttpt)
REVERT: A  210 LYS cc_start: 0.8349 (mtpm) cc_final: 0.7848 (mttm)
REVERT: A  385 GLU cc_start: 0.6639 (pt0) cc_final: 0.6431 (pm20)
  outliers start: 15
  outliers final: 11
  residues processed: 45
  average time/residue: 0.5682
  time to fit residues: 26.8846
Evaluate side-chains
  44 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 32
  time to evaluate  : 0.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 SER
Chi-restraints excluded: chain A residue   32 ILE
Chi-restraints excluded: chain A residue   41 LYS
Chi-restraints excluded: chain A residue   52 SER
Chi-restraints excluded: chain A residue   95 ARG
Chi-restraints excluded: chain A residue  162 THR
Chi-restraints excluded: chain A residue  237 GLU
Chi-restraints excluded: chain A residue  245 THR
Chi-restraints excluded: chain A residue  254 ARG
Chi-restraints excluded: chain A residue  280 VAL
Chi-restraints excluded: chain A residue  287 ILE
Chi-restraints excluded: chain A residue  383 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 2 optimal weight:    0.8980
   chunk 36 optimal weight:    0.9980
   chunk 17 optimal weight:    7.9990
   chunk 39 optimal weight:   10.0000
   chunk 18 optimal weight:    5.9990
   chunk 23 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9980
   chunk 14 optimal weight:    0.7980
   chunk 54 optimal weight:    9.9990
   chunk 13 optimal weight:    0.6980
   chunk 38 optimal weight:    8.9990
   overall best weight:    0.8780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  23 HIS
A  68 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.181746 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.146326 restraints weight = 7079.578|
|-----------------------------------------------------------------------------|
r_work (start): 0.3466 rms_B_bonded: 0.47
r_work: 0.3201 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.3201
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3172
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3172 r_free = 0.3172    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      207 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3172 r_free = 0.3172    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      208 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3172
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8460
moved from start:          0.1946

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   7966  Z= 0.141
  Angle     :  0.590  11.207  11680  Z= 0.349
  Chirality :  0.041   0.297   1428
  Planarity :  0.004   0.036    736
  Dihedral  : 26.537 179.765   3339
  Min Nonbonded Distance : 2.378

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  7.07 %
    Favored  : 92.67 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 31.78 %
    Favored  : 65.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.15 (0.44), residues: 382
  helix:  2.60 (0.40), residues: 168
  sheet:  0.24 (0.83), residues: 41
  loop : -2.71 (0.39), residues: 173

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  95 
 TYR   0.012   0.001   TYR A  33 
 PHE   0.011   0.001   PHE A 312 
 TRP   0.006   0.001   TRP A 336 
 HIS   0.003   0.001   HIS A  84 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00236 /  0.14 ( 7962)
  covalent geometry    : angle       0.58089 /  0.35 (11674)
  hydrogen bonds       : bond        0.06892 /  4.69 (  278)
  hydrogen bonds       : angle       3.43873 /  2.65 (  653)
  metal coordination   : bond        0.00511 /  0.25 (    4)
  metal coordination   : angle       4.71591 /  2.28 (    6)

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

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

  764 Ramachandran restraints generated.
    382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  764 Ramachandran restraints generated.
    382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 31
  time to evaluate  : 0.104 
Fit side-chains
REVERT: A   41 LYS cc_start: 0.7049 (tptm) cc_final: 0.6571 (ttpt)
REVERT: A  210 LYS cc_start: 0.8177 (mtpm) cc_final: 0.7709 (mttm)
  outliers start: 11
  outliers final: 8
  residues processed: 42
  average time/residue: 0.4901
  time to fit residues: 21.6856
Evaluate side-chains
  38 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 30
  time to evaluate  : 0.094 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 SER
Chi-restraints excluded: chain A residue   32 ILE
Chi-restraints excluded: chain A residue   52 SER
Chi-restraints excluded: chain A residue   82 VAL
Chi-restraints excluded: chain A residue  162 THR
Chi-restraints excluded: chain A residue  237 GLU
Chi-restraints excluded: chain A residue  280 VAL
Chi-restraints excluded: chain A residue  287 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 6 optimal weight:    0.6980
   chunk 31 optimal weight:    1.9990
   chunk 40 optimal weight:   10.0000
   chunk 8 optimal weight:    3.9990
   chunk 29 optimal weight:    6.9990
   chunk 53 optimal weight:   10.0000
   chunk 37 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   chunk 49 optimal weight:   10.0000
   chunk 45 optimal weight:   20.0000
   chunk 32 optimal weight:    0.9990
   overall best weight:    1.5388

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  23 HIS
A  68 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.180740 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.145506 restraints weight = 7041.890|
|-----------------------------------------------------------------------------|
r_work (start): 0.3453 rms_B_bonded: 0.44
r_work: 0.3185 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.3185
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3163
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3163 r_free = 0.3163    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      208 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3163 r_free = 0.3163    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      208 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3163
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8486
moved from start:          0.1935

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7966  Z= 0.157
  Angle     :  0.601  11.048  11680  Z= 0.354
  Chirality :  0.042   0.279   1428
  Planarity :  0.004   0.036    736
  Dihedral  : 26.469 179.075   3339
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 4.65
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  6.81 %
    Favored  : 92.93 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 32.07 %
    Favored  : 65.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.41 (0.44), residues: 382
  helix:  2.66 (0.40), residues: 171
  sheet:  0.31 (0.82), residues: 41
  loop : -2.47 (0.41), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  95 
 TYR   0.011   0.001   TYR A  33 
 PHE   0.010   0.001   PHE A 118 
 TRP   0.004   0.001   TRP A 336 
 HIS   0.004   0.001   HIS A  99 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00292 /  0.16 ( 7962)
  covalent geometry    : angle       0.59240 /  0.35 (11674)
  hydrogen bonds       : bond        0.07189 /  4.94 (  278)
  hydrogen bonds       : angle       3.39804 /  2.62 (  653)
  metal coordination   : bond        0.00621 /  0.31 (    4)
  metal coordination   : angle       4.51525 /  2.04 (    6)

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

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

  764 Ramachandran restraints generated.
    382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  764 Ramachandran restraints generated.
    382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 33
  time to evaluate  : 0.099 
Fit side-chains
REVERT: A   41 LYS cc_start: 0.7063 (tptm) cc_final: 0.6596 (ttpt)
REVERT: A  210 LYS cc_start: 0.8201 (mtpm) cc_final: 0.7713 (mttm)
REVERT: A  256 LYS cc_start: 0.8287 (ttmm) cc_final: 0.7926 (mttp)
REVERT: A  329 GLU cc_start: 0.8321 (pm20) cc_final: 0.7794 (pm20)
  outliers start: 10
  outliers final: 7
  residues processed: 42
  average time/residue: 0.4938
  time to fit residues: 21.8260
Evaluate side-chains
  38 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 31
  time to evaluate  : 0.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 SER
Chi-restraints excluded: chain A residue   32 ILE
Chi-restraints excluded: chain A residue   52 SER
Chi-restraints excluded: chain A residue  162 THR
Chi-restraints excluded: chain A residue  237 GLU
Chi-restraints excluded: chain A residue  280 VAL
Chi-restraints excluded: chain A residue  287 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 12 optimal weight:    4.9990
   chunk 6 optimal weight:    2.9990
   chunk 38 optimal weight:   10.0000
   chunk 20 optimal weight:    0.9990
   chunk 45 optimal weight:   20.0000
   chunk 40 optimal weight:   10.0000
   chunk 30 optimal weight:    0.8980
   chunk 52 optimal weight:   10.0000
   chunk 46 optimal weight:   10.0000
   chunk 22 optimal weight:    0.8980
   chunk 37 optimal weight:    3.9990
   overall best weight:    1.9586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  23 HIS
A  68 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.179521 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.143538 restraints weight = 7044.981|
|-----------------------------------------------------------------------------|
r_work (start): 0.3545 rms_B_bonded: 0.47
r_work: 0.3229 rms_B_bonded: 3.80 restraints_weight: 0.5000
r_work (final): 0.3229
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3107
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3107 r_free = 0.3107    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      208 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3107 r_free = 0.3107    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      210 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3107
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8522
moved from start:          0.1985

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7966  Z= 0.173
  Angle     :  0.609  10.920  11680  Z= 0.358
  Chirality :  0.043   0.277   1428
  Planarity :  0.004   0.038    736
  Dihedral  : 26.452 179.039   3339
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 4.81
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  6.54 %
    Favored  : 93.19 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 32.36 %
    Favored  : 65.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.24 (0.44), residues: 382
  helix:  2.48 (0.40), residues: 174
  sheet:  0.33 (0.82), residues: 41
  loop : -2.64 (0.40), residues: 167

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A  95 
 TYR   0.012   0.002   TYR A  33 
 PHE   0.011   0.002   PHE A 118 
 TRP   0.005   0.001   TRP A 336 
 HIS   0.005   0.001   HIS A  99 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00332 /  0.17 ( 7962)
  covalent geometry    : angle       0.60096 /  0.36 (11674)
  hydrogen bonds       : bond        0.07558 /  5.20 (  278)
  hydrogen bonds       : angle       3.42059 /  2.63 (  653)
  metal coordination   : bond        0.00672 /  0.33 (    4)
  metal coordination   : angle       4.38943 /  1.93 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1663.96 seconds
wall clock time: 29 minutes 11.20 seconds (1751.20 seconds total)